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A

A - Variable in class meshi.optimizers.BFGS
 
A - Variable in class meshi.symmetryComplex.utils.LoopUtils.Line
 
A - Variable in class meshi.util.mathTools.Jama.Matrix
Array for internal storage of elements.
a0x - Variable in class meshi.geometry.Torsion
 
a0y - Variable in class meshi.geometry.Torsion
 
a0z - Variable in class meshi.geometry.Torsion
 
a1 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
a1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a1toAtomList - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a1x - Variable in class meshi.geometry.Torsion
 
a1y - Variable in class meshi.geometry.Torsion
 
a1z - Variable in class meshi.geometry.Torsion
 
a2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
a2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a2toAtomList - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a2x - Variable in class meshi.geometry.Torsion
 
a2y - Variable in class meshi.geometry.Torsion
 
a2z - Variable in class meshi.geometry.Torsion
 
a3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a3toAtomList - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
a4toAtomList - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
aa - Variable in class meshi.geometry.Torsion
 
aa - Variable in class meshi.util.dssp.DSSP
 
AA_SEQUENCE - Static variable in interface meshi.util.KeyWords
 
aac - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
aaLetter - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
aaLetter - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
AAofRes(int) - Method in class meshi.util.dssp.DSSP
 
ab - Variable in class meshi.geometry.Torsion
 
AbInitio - Class in <Unnamed>
Created by IntelliJ IDEA.
AbInitio() - Constructor for class AbInitio
 
AbInitio.AbInitioLogger - Class in <Unnamed>
 
AbInitio.AbInitioLogger(Protein, CommandList, String, String) - Constructor for class AbInitio.AbInitioLogger
 
AbitSmarterLoopBuilder - Class in meshi.applications.prediction
 
AbitSmarterLoopBuilder() - Constructor for class meshi.applications.prediction.AbitSmarterLoopBuilder
 
AbitSmarterLoopBuilder.Loop - Class in meshi.applications.prediction
 
AbitSmarterLoopBuilder.Loop(double, int, int) - Constructor for class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
AbitSmarterLoopBuilder.Loop.End - Enum in meshi.applications.prediction
 
AbitSmarterLoopBuilder.Loop.End() - Constructor for enum meshi.applications.prediction.AbitSmarterLoopBuilder.Loop.End
 
AbitSmarterLoopBuilder.LoopComperator - Class in meshi.applications.prediction
 
AbitSmarterLoopBuilder.LoopComperator() - Constructor for class meshi.applications.prediction.AbitSmarterLoopBuilder.LoopComperator
 
about() - Static method in class meshi.util.MeshiProgram
What you always wanted to know.
aboveHigh - Variable in class meshi.util.histogram.Histogram
 
abs(double) - Static method in class meshi.optimizers.BFGS
 
absentMap - Static variable in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
absentMap() - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
absentMap(int) - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
absentMap() - Method in class meshi.symmetryComplex.topologyMap.Topology
 
absentResiduesFilter - Static variable in class meshi.symmetryComplex.utils.GJFilters
 
AbstractEnergy - Class in meshi.energy
A super class for all meshi energy terms.
AbstractEnergy() - Constructor for class meshi.energy.AbstractEnergy
Construct a dummy object that cannot be evaluated.
AbstractEnergy(Updateable[], double) - Constructor for class meshi.energy.AbstractEnergy
construct An energy term.
AbstractEnergy.IsEnergy - Class in meshi.energy
 
AbstractEnergy.IsEnergy() - Constructor for class meshi.energy.AbstractEnergy.IsEnergy
 
AbstractEnergy.UpdateableList - Class in meshi.energy
A list of updateable elements (implementing the meshi.util.Updateable interface).
AbstractEnergy.UpdateableList(Updateable[]) - Constructor for class meshi.energy.AbstractEnergy.UpdateableList
 
AbstractEnergy.UpdateableList() - Constructor for class meshi.energy.AbstractEnergy.UpdateableList
 
AbstractHydrogenBond - Class in meshi.energy.solvate.hydrogenBonds
A super class with the most general treatment of hydrogen bond.
AbstractHydrogenBond() - Constructor for class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
AbstractHydrogenBond(DistanceMatrix, AtomList) - Constructor for class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
AbstractHydrogenBondList - Class in meshi.energy.solvate.hydrogenBonds
A super class with the most general treatment of a list of hydrogen bonds in an atom list.
AbstractHydrogenBondList() - Constructor for class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
AbstractHydrogenBondList(DistanceMatrix, AtomList, int) - Constructor for class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
AbstractPunishAngleEnergy - Class in meshi.energy.hydrogenBondsAngle
Created by IntelliJ IDEA.
AbstractPunishAngleEnergy() - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergy(DistanceMatrix, HBondList, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergy(DistanceMatrix, HBondList, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergy(DistanceMatrix, HBondList, double, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergy(DistanceMatrix, HBondList, double, DistanceList) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergy(DistanceMatrix, HBondList, double, DistanceList, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergy(DistanceMatrix, HBondList, double, DistanceList, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
AbstractPunishAngleEnergyElement - Class in meshi.energy.hydrogenBondsAngle
Created by IntelliJ IDEA.
AbstractPunishAngleEnergyElement(DistanceMatrix, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
AbstractPunishAngleEnergyElement(DistanceMatrix, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
AbstractPunishAngleEnergyElement(DistanceMatrix, double, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
ac - Variable in class meshi.geometry.Torsion
 
accept(Object) - Method in class HydrogenTest.ResWithSSFilter
 
accept(Object) - Method in class meshi.applications.prediction.homology.CaAtomFilter
 
accept(File) - Method in class meshi.applications.prediction.homology.gui.HomologyFileFilter
 
accept(Object) - Method in class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
accept(Object) - Method in class meshi.applications.prediction.OriginalAtom.OriginalAtomFilter
 
accept(Object) - Method in class meshi.energy.AbstractEnergy.IsEnergy
 
accept(Object) - Method in class meshi.energy.hydrogenBond.GoodResiduesForHB
 
accept(Object) - Method in class meshi.energy.hydrogenBond.GoodResiduesForHB.GoodSS
 
accept(Object) - Method in class meshi.energy.hydrogenBond.GoodResiduesForHB.IsNot13
 
accept(Object) - Method in class meshi.energy.hydrogenBond.HBondList.IsAlive
 
accept(Object) - Method in class meshi.energy.hydrogenBond.HBondList.IsWithInRmax
 
accept(Object) - Method in class meshi.energy.hydrogenBond.IsHO
 
accept(Object) - Method in class meshi.energy.hydrogenBond.LennardJonesParameters.isA
 
accept(Object) - Method in class meshi.energy.hydrogenBondsPairs.BetaParametersList.IsHydrogenBondsPairsParameters
 
accept(Object) - Method in class meshi.energy.hydrogenBondsPairs.HelixParametersList.IsHydrogenBondsPairsParameters
 
accept(Object) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList.NoElements
 
accept(Object) - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.IsWithInRmax
 
accept(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters.isA
 
accept(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters.isA
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParameters.isA
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.bond.BondParameters.isA
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.CompleteResidueFilter
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.IncompleteResidueFilter
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.PhiPsiResidueFilter
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.GoodBonds
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate.TargetFilter
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters.isA
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters.isA
 
accept(Object) - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator.HaveParametersFilter
 
accept(Object) - Method in class meshi.energy.TotalEnergy.FreeAtom
 
accept(Object) - Method in class meshi.energy.TotalEnergy.IsEnergy
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterChi1
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterChi2
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterChi3
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterChi4
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterOOP
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterPhi
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterPsi
 
accept(Object) - Method in class meshi.geometry.TorsionList.FilterSideChain
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.AcceptChainFilter
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.BackboneFilter
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.IsAtom
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.IsDefrostedFilter
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.IsFrozenFilter
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.NonHydrogen
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomList.RejectChainFilter
 
accept(Object) - Method in class meshi.molecularElements.atoms.AtomPairList.IsAtomPair
 
accept(Object) - Method in class meshi.molecularElements.Chain.IsResidue
 
accept(Object) - Method in class meshi.molecularElements.ChainList.IsChain
 
accept(Object) - Method in class meshi.molecularElements.Protein.BackboneFilter
 
accept(Object) - Method in class meshi.molecularElements.ResidueList.NonDummyFilter
 
accept(Object) - Method in class meshi.PDB.isAPdbFile
 
accept(Object) - Method in class meshi.PDB.OneOfTwenty
 
accept(Object) - Method in class meshi.PDB.PdbLineFilter
 
accept(Object) - Method in class meshi.sequences.AccesibilitySequence.AccesibilitySequenceCharFilter
 
accept(Object) - Method in class meshi.sequences.AtomAlignment.IsAlignmentColumn
 
accept(Object) - Method in class meshi.sequences.ResidueSequence.ResidueSequenceCharFilter
 
accept(Object) - Method in class meshi.sequences.SecondaryStructureSequence.SecondaryStructureSequenceCharFilter
 
accept(Object) - Method in class meshi.sequences.Sequence.kolDichfin
 
accept(Object) - Method in class meshi.sequences.SequenceList.AcceptAll
 
accept(Object) - Method in class meshi.sequences.SequenceList.IsSequenceFilter
 
accept(Object) - Method in class meshi.symmetryComplex.molecularImageElements.ImageChain.IsImageChain
 
accept(Object) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesFilter
 
accept(Object) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller.SpecialHBPairs
 
accept(Object) - Method in class meshi.symmetryComplex.utils.GJFilters.AcceptChainFilter
 
accept(Object) - Method in class meshi.symmetryComplex.utils.GJFilters.AndFilter
 
accept(Object) - Method in class meshi.symmetryComplex.utils.GJFilters.RejectChainFilter
 
accept(Object) - Method in class meshi.symmetryComplex.utils.GJFilters.ResidueRangeFilter
 
accept(Object) - Method in class meshi.util.filters.AcceptAll
 
accept(Object) - Method in class meshi.util.filters.BackboneFilter
 
accept(Object) - Method in class meshi.util.filters.CaFilter
 
accept(Object) - Method in class meshi.util.filters.Differs
 
accept(Object) - Method in class meshi.util.filters.Equals
 
accept(Object) - Method in interface meshi.util.filters.Filter
 
accept(Object) - Method in class meshi.util.filters.HeavyAtomsFilter
 
accept(Object) - Method in class meshi.util.filters.IsClass
 
accept(Object) - Method in class meshi.util.filters.KolDichfin
 
accept(Object) - Method in class meshi.util.filters.OriginalAtoms
 
accept(Object) - Method in class meshi.util.histogram.Histogram.IsBin
 
accept(Object) - Method in class meshi.util.histogram.Histogram.RepresentativesIterator.ThresholdFilter
 
accept(Object) - Method in class meshi.util.string.StringFilter
 
accept(String, String) - Method in class meshi.util.string.StringFilter
 
accept(String, String) - Method in class meshi.util.string.StringFilterEndsWith
 
accept(String, String) - Method in class meshi.util.string.StringFilterEquals
 
accept(String, String) - Method in class meshi.util.string.StringFilterGrep
 
accept(String, String) - Method in class meshi.util.string.StringFilterStartsWith
 
accept(Object) - Method in class meshi.util.string.StringList.IsString
 
accept(Object) - Method in class Pdb2Fasta.MyFilter
 
AcceptAll - Class in meshi.util.filters
 
AcceptAll() - Constructor for class meshi.util.filters.AcceptAll
 
acceptAllChars - Static variable in class meshi.sequences.SequenceList
 
acceptPdbLine(PdbLine) - Method in class meshi.PDB.PdbLineATOM
 
acceptPdbLine(PdbLine) - Method in class meshi.PDB.PdbLineATOMorHETATOM
 
acceptPdbLine(PdbLine) - Method in class meshi.PDB.PdbLineFilter
 
acceptPdbLine(PdbLine) - Method in class meshi.PDB.PdbLineSEQRES
 
ACCESIBILITY_SEQUENCE - Static variable in interface meshi.util.KeyWords
 
AccesibilityCharFilter - Static variable in class meshi.sequences.AccesibilitySequence
 
AccesibilitySequence - Class in meshi.sequences
 
AccesibilitySequence(String, String) - Constructor for class meshi.sequences.AccesibilitySequence
 
AccesibilitySequence.AccesibilitySequenceCharFilter - Class in meshi.sequences
 
AccesibilitySequence.AccesibilitySequenceCharFilter() - Constructor for class meshi.sequences.AccesibilitySequence.AccesibilitySequenceCharFilter
 
accessibility - Variable in class meshi.molecularElements.Residue
 
accessibility() - Method in class meshi.molecularElements.Residue
 
ACCESSIBLE - Static variable in interface meshi.parameters.MeshiPotential
 
ACCofRes(int) - Method in class meshi.util.dssp.DSSP
 
acos(double) - Method in class meshi.geometry.Angle
Calculate the arc-cosine function.
acos(double) - Static method in class meshi.geometry.ArcCos
 
acos(double) - Method in class meshi.geometry.QuickAndDirtyAngle
An approximated fast arc-cos function that uses the ArcCos class.
acos(double) - Method in class meshi.geometry.QuickAndDirtyTorsion
An approximated fast arc-cos function that uses the ArcCos class.
acos(double) - Method in class meshi.geometry.Torsion
Calculate the arc-cosine function.
acos_chebychev(double) - Static method in class meshi.geometry.ArcCos
 
ACOS_LOOKUP - Static variable in class meshi.geometry.ArcCos
 
active() - Method in class meshi.molecularElements.atoms.Atom
 
active() - Method in enum meshi.molecularElements.atoms.AtomStatus
 
activeOrImage() - Method in enum meshi.molecularElements.atoms.AtomStatus
 
add(ResidueAlignmentColumn) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
add(ResidueAlignment) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
add(Parameters) - Method in class meshi.energy.simpleEnergyTerms.ParametersList
Adds an element (must be an instance of Parameters) to the list.
add(ResidueAlignmentColumn) - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
add(ResidueAlignment) - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
add(TotalEnergy) - Method in class meshi.energy.TotalEnergy
 
add(Distance) - Method in class meshi.geometry.DistanceList
 
add(Atom) - Method in class meshi.molecularElements.atoms.AtomList
 
add(AtomPairList) - Method in class meshi.molecularElements.atoms.AtomPairList
 
add(int, AlignmentCell) - Method in class meshi.sequences.AlignmentColumn
 
add(ResidueAlignmentColumn) - Method in class meshi.sequences.ResidueAlignment
 
add(SequenceAlignmentColumn) - Method in class meshi.sequences.Sequence
 
add(SequenceAlignmentCell) - Method in class meshi.sequences.Sequence
 
add(int, char, int) - Method in class meshi.sequences.SequenceAlignmentColumn
 
add(String, Object) - Method in class meshi.util.MeshiProgram.GlobalElementList
 
add(Residue, Residue, MeshiLog) - Method in class Pdb2Fasta.MyChain
 
addAtomAttributes(Protein) - Static method in class CalculateEnergyFromStructuresListAverages
 
addAtomAttributes(Protein) - Static method in class ColorByEnergy
 
addAtoms(Protein, CommandList) - Static method in class meshi.util.Utils
 
addAtoms(Protein, CommandList, int) - Static method in class meshi.util.Utils
 
addAtomsAndBonds() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
AddAtomsFlag - Enum in meshi.parameters
 
AddAtomsFlag() - Constructor for enum meshi.parameters.AddAtomsFlag
 
addAttribute(MeshiAttribute) - Method in class meshi.energy.AbstractEnergy
 
addAttribute(MeshiAttribute) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
addAttribute(MeshiAttribute) - Method in class meshi.geometry.Distance
 
addAttribute(MeshiAttribute) - Method in class meshi.molecularElements.atoms.Atom
 
addAttribute(MeshiAttribute) - Method in class meshi.molecularElements.Residue
 
addAttribute(MeshiAttribute) - Method in class meshi.sequences.AlignmentCell
 
addAttribute(MeshiAttribute) - Method in interface meshi.util.Attributable
 
addAttribute(MeshiAttribute) - Method in class meshi.util.AttributesRack
 
addCell(GridCell, DistanceList, ArrayList<DistanceList>) - Method in class meshi.geometry.MatrixRow
 
addCell(GridCell, DistanceList, ArrayList<DistanceList>) - Method in class meshi.symmetryComplex.geometryImage.MatrixRowNoImageAtoms
 
addChain(Chain) - Method in class meshi.molecularElements.Protein
 
addEnergy(double) - Method in class meshi.molecularElements.atoms.Atom
 
addForce(double, double, double) - Method in class meshi.molecularElements.atoms.AtomCore
 
addHydrogens(BondParametersList, AngleParametersList) - Method in class meshi.molecularElements.extendedAtoms.Arg
 
addHydrogens(BondParametersList, AngleParametersList) - Method in class meshi.molecularElements.extendedAtoms.Asn
 
addHydrogens(BondParametersList, AngleParametersList) - Method in class meshi.molecularElements.extendedAtoms.Gln
 
addHydrogens(BondParametersList, AngleParametersList) - Method in class meshi.molecularElements.extendedAtoms.His
 
addHydrogens(BondParametersList, AngleParametersList) - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
addHydrogens(BondParametersList, AngleParametersList) - Method in class meshi.molecularElements.extendedAtoms.Trp
 
addHydrogens(Protein, CommandList) - Static method in class meshi.util.Utils
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.HomologyFrame11Layout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.InflateParametersLayout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.OptionDialog3Layout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout
 
addLayoutComponent(String, Component) - Method in class meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout
 
addLoopQD(Protein, HomologyModeling.Loop, CommandList, double, int) - Static method in class HomologyModeling
 
addLoops(ResidueSequence, Protein, Beautify.BeautifyLogger) - Static method in class Beautify
 
addLoops(Protein, double, int, int) - Static method in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
addLoopsQuickAndDirty(Protein, List<HomologyModeling.Loop>, CommandList, double, int) - Static method in class HomologyModeling
 
addNewBondsToList() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
This methods add new h-bonds to the bondList vector.
addTerm(AbstractEnergy) - Method in class meshi.energy.TotalEnergy
 
addTermToAtoms(Protein, AbstractEnergy) - Static method in class CalculateEnergyFromStructuresListAverages
 
addTo(Protein) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
addToFx(double) - Method in class meshi.geometry.Coordinates
 
addToFx(double) - Method in class meshi.molecularElements.atoms.Atom
Adds the parameter to the force operating on the atom in the X direction.
addToFy(double) - Method in class meshi.geometry.Coordinates
 
addToFy(double) - Method in class meshi.molecularElements.atoms.Atom
Adds the parameter to the force operating on the atom in the Y direction.
addToFz(double) - Method in class meshi.geometry.Coordinates
 
addToFz(double) - Method in class meshi.molecularElements.atoms.Atom
Adds the parameter to the force operating on the atom in the Z direction.
addToLUTvec(AbstractHydrogenBond[][], Atom, AbstractHydrogenBond) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
Auxilarry method: Updating a vector, 'vec' similar to the lutHB field, with the new HB The reason we do not access lutHB directly, is that this method is also called from the 'removeBrokenHB' method, and there a different vector need updating.
addToValue(double) - Method in class meshi.util.Pair
 
addToX(double) - Method in class meshi.geometry.Coordinates
 
addToX(double) - Method in class meshi.molecularElements.atoms.Atom
Adds the parameter to the X coordinate of the atom.
addToY(double) - Method in class meshi.geometry.Coordinates
 
addToY(double) - Method in class meshi.molecularElements.atoms.Atom
Adds the parameter to the Y coordinate of the atom.
addToZ(double) - Method in class meshi.geometry.Coordinates
 
addToZ(double) - Method in class meshi.molecularElements.atoms.Atom
Adds the parameter to the Y coordinate of the atom.
afterBBcorrection(Protein, String) - Method in class HomologyModeling.HomologyLogger
 
afterRelax(Protein, TotalEnergy, String) - Method in class AbInitio.AbInitioLogger
 
afterRelax(Protein, TotalEnergy, String) - Method in class Optimize.OptimizeLogger
 
afterRelax(Protein, TotalEnergy, String) - Method in class Refine.RefineLogger
 
afterRelaxation(Protein, TotalEnergy, String) - Method in class HomologyModeling.HomologyLogger
 
afterRelaxation2(Protein, TotalEnergy) - Method in class HomologyModeling.HomologyLogger
 
afterRelaxation3(Protein, TotalEnergy) - Method in class HomologyModeling.HomologyLogger
 
Ala - Class in meshi.molecularElements.extendedAtoms
Alanin from Levitt, JMB 168:592 (1983) table 2.
Ala(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Ala
 
aligner - package aligner
 
alignment - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
AlignmentCell - Class in meshi.sequences
A container for a protein element and its number.
AlignmentCell(Object, int) - Constructor for class meshi.sequences.AlignmentCell
 
AlignmentCell(Object, int, String) - Constructor for class meshi.sequences.AlignmentCell
 
AlignmentColumn - Class in meshi.sequences
A container for an ordered set of coresponding protein elements.
AlignmentColumn(int) - Constructor for class meshi.sequences.AlignmentColumn
Utility constructor for the sub-classes.
AlignmentColumn(AlignmentCell, AlignmentCell) - Constructor for class meshi.sequences.AlignmentColumn
 
AlignmentTools - Class in meshi.util.alignmentTools
 
AlignmentTools() - Constructor for class meshi.util.alignmentTools.AlignmentTools
 
alignProteinsByAlignmentFile(CommandList, Key, Chain, Chain) - Static method in class meshi.util.Utils
 
ALINMENT_FILE_PATH - Static variable in interface meshi.util.KeyWords
 
alive - Variable in class meshi.util.Rms
 
ALL - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
ALL_CA - Static variable in interface meshi.util.KeyWords
 
allGaps() - Method in class meshi.sequences.AlignmentColumn
 
allHasNext(Iterator[]) - Method in class meshi.sequences.ResidueAlignmentOfModels
 
allowedMaxH - Variable in class meshi.optimizers.BFGS
 
allowedMaxR - Variable in class meshi.optimizers.LBFGS
 
allYouWantToKnow() - Method in class meshi.molecularElements.Protein
 
alnFileButton - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
alnFiltPathText - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
ALPHA - Static variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
ALPHA - Static variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
ALPHA - Static variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
ALPHA - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
ALPHA is the transition zone (in Ang) where the energy change in the forth power 0.0 to 1.0.
ALPHA - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
ALPHA is the transition zone (in Ang) where the energy change in the forth power 0.0 to 1.0.
ALPHA - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
ALPHA is the transition zone (in Ang) where the energy change in the forth power 0.0 to 1.0.
ALPHA - Static variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
ALPHA - Static variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
alpha - Variable in class meshi.optimizers.LBFGS
 
ALPHA1 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
ALPHA is the transition zone (in Ang) where the energy change in the forth power 0.0 to 1.0.
ALPHA2 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
ALPHA_ANGLE_ENERGY - Static variable in interface meshi.util.KeyWords
 
ALPHA_ANGLE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
ALPHA_TORSION_ENERGY - Static variable in interface meshi.util.KeyWords
 
ALPHA_TORSION_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
alphaAngleCreator - Static variable in class Beautify
 
AlphaAngleCreator - Class in meshi.energy.simpleEnergyTerms.alphaAngle
 
AlphaAngleCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleCreator
 
AlphaAngleCreator() - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleCreator
 
AlphaAngleEnergy - Class in meshi.energy.simpleEnergyTerms.alphaAngle
This class limits the alpha angle (3 consecutive CAs) to be in a specific range.
AlphaAngleEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
AlphaAngleEnergy(AngleList, DistanceMatrix, AlphaAngleParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
AlphaAngleEnergyElement - Class in meshi.energy.simpleEnergyTerms.alphaAngle
 
AlphaAngleEnergyElement(Angle, AlphaAngleParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
The constructor needs a CA3 angle.
AlphaAngleParameters - Class in meshi.energy.simpleEnergyTerms.alphaAngle
Parsing a line in the parameter file of the alpha angle energy.
AlphaAngleParameters(String) - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
AlphaAngleParametersList - Class in meshi.energy.simpleEnergyTerms.alphaAngle
 
AlphaAngleParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParametersList
 
alphaFinal - Variable in class meshi.optimizers.WolfConditionLineSearch
 
alphaI - Variable in class meshi.optimizers.WolfConditionLineSearch
 
alphaI1 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
alphaTorsionCreator - Static variable in class Beautify
 
AlphaTorsionCreator - Class in meshi.energy.simpleEnergyTerms.alphaTorsion
 
AlphaTorsionCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionCreator
 
AlphaTorsionCreator() - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionCreator
 
AlphaTorsionEnergy - Class in meshi.energy.simpleEnergyTerms.alphaTorsion
This energy limits the alpha torsion (4 consecutive CAs) to be in a specific range.
AlphaTorsionEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
AlphaTorsionEnergy(TorsionList, DistanceMatrix, AlphaTorsionParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
AlphaTorsionEnergyElement - Class in meshi.energy.simpleEnergyTerms.alphaTorsion
 
AlphaTorsionEnergyElement(Torsion, AlphaTorsionParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
An energy element handling one alpha torsion.
AlphaTorsionParameters - Class in meshi.energy.simpleEnergyTerms.alphaTorsion
Parsing a line in the parameter file of the alpha torsion energy.
AlphaTorsionParameters(String) - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
AlphaTorsionParametersList - Class in meshi.energy.simpleEnergyTerms.alphaTorsion
 
AlphaTorsionParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParametersList
 
alternateLocation() - Method in class meshi.molecularElements.atoms.Atom
 
alternateLocation - Variable in class meshi.PDB.PdbLine
 
alternateLocation() - Method in class meshi.PDB.PdbLine
 
alternateLocation - Variable in class Pdb2Fasta.MyAtom
 
alternateLocation() - Method in class Pdb2Fasta.MyAtom
 
amideH() - Method in class meshi.molecularElements.Residue
 
amideN() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
amideN() - Method in class meshi.molecularElements.Residue
 
amino_a - Variable in class aligner.AminoAcidSubstitutionMatrix
 
AminoAcidSubstitutionMatrix - Class in aligner
Created by IntelliJ IDEA.
AminoAcidSubstitutionMatrix(String) - Constructor for class aligner.AminoAcidSubstitutionMatrix
 
angle - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
angle - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
angle - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
Angle - Class in meshi.geometry
--------------------------- Angle -----------------------------------
Angle(Atom, Atom, Atom, DistanceMatrix) - Constructor for class meshi.geometry.Angle
 
Angle(AtomPair, AtomPair, DistanceMatrix) - Constructor for class meshi.geometry.Angle
 
angle - Variable in class meshi.geometry.Angle
 
angle() - Method in class meshi.geometry.Angle
 
ANGLE1 - Variable in class meshi.geometry.Torsion
 
ANGLE2 - Variable in class meshi.geometry.Torsion
 
ANGLE_ENERGY - Static variable in interface meshi.util.KeyWords
 
ANGLE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
ANGLE_X - Static variable in interface meshi.util.KeyWords
 
ANGLE_Z - Static variable in interface meshi.util.KeyWords
 
angleAt(int) - Method in class meshi.geometry.AngleList
 
angleCode - Variable in class meshi.geometry.Angle
 
angleCreator - Static variable in class Beautify
 
AngleCreator - Class in meshi.energy.simpleEnergyTerms.angle
 
AngleCreator() - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleCreator
 
AngleCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleCreator
 
angleEnergy - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
AngleEnergy - Class in meshi.energy.simpleEnergyTerms.angle
Angle energy term.
AngleEnergy(AngleList, DistanceMatrix, AngleParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleEnergy
 
AngleEnergyElement - Class in meshi.energy.simpleEnergyTerms.angle
 
AngleEnergyElement(Angle, Parameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
angleList - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
angleList - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergy
The list of angles that needs to be evaluated.
AngleList - Class in meshi.geometry
 
AngleList() - Constructor for class meshi.geometry.AngleList
 
AngleList(AtomPairList, DistanceMatrix) - Constructor for class meshi.geometry.AngleList
 
angleName - Variable in class meshi.geometry.Angle
 
AngleParameters - Class in meshi.energy.simpleEnergyTerms.angle
 
AngleParameters() - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
AngleParameters(AtomType, AtomType, AtomType) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
AngleParameters(String) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
AngleParameters(StringTokenizer) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
AngleParameters(AtomType, AtomType, AtomType, double, double) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
AngleParameters.isA - Class in meshi.energy.simpleEnergyTerms.angle
 
AngleParameters.isA() - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParameters.isA
 
AngleParametersList - Class in meshi.energy.simpleEnergyTerms.angle
 
AngleParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.angle.AngleParametersList
 
angleResName - Variable in class meshi.geometry.Angle
 
angleResNum - Variable in class meshi.geometry.Angle
 
angles - Variable in class meshi.molecularElements.Protein
 
angleValue - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
angleValue2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
angleXfrom - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
angleXfrom - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
angleXfrom() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
angleXto - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
angleXto - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
angleXto() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
angleZfrom - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
angleZfrom - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
angleZfrom() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
angleZto - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
angleZto - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
angleZto() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
angSigmoidBegins - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
angSigmoidEnds - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
antiParalel - Variable in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
antiParallel - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
antiParallel(HydrogenBondsPairsParameters) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
antiParallelshift(int, int) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
antyparallelPrecentage - Variable in class meshi.util.dssp.DSSP
 
applyForce(int, double) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
Applies force to torsion angles.
applyForcesToAtoms(double) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
FOLLOWING the activation of "update" this method can be activated, where it will apply the forces to the atoms participating in the HB.
ArcCos - Class in meshi.geometry
Class ArcCos.
ArcCos() - Constructor for class meshi.geometry.ArcCos
 
Arg - Class in meshi.molecularElements.extendedAtoms
ARGININ O | N - CA - C...n | | H CB | CG - CD - NE - CZ - NH1 | NH2
Arg(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Arg
 
array - Variable in class meshi.geometry.DistanceList.DistanceIterator
 
arrayLeftDivide(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Element-by-element multiplication in place, A = A.*B
Asn - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - ND2 - HD21 | | OD1 HD22
Asn(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Asn
 
Asp - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - OD2 | (-) OD1
Asp(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Asp
 
assertChain() - Method in class meshi.molecularElements.Chain
Asserts that this chain is comprised of residues with the same chain string.
assertSingleResidue() - Method in class meshi.molecularElements.atoms.AtomList
Asserts that this AtomList is comprised of atoms belonging to a single residue.
assignBackboneCoordinates(AtomList, AtomList) - Static method in class meshi.util.Utils
 
assignCoordinates(Protein, int, int, int) - Method in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
assignCoordinates(CommandList, Topology) - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter
 
AssignDSSP(Protein, CommandList, Key) - Static method in class meshi.util.Utils
 
AssignDSSP(Protein, String) - Static method in class meshi.util.Utils
 
assignForcesToAtoms() - Method in class meshi.energy.solvate.SolvateEnergy
 
assignMissingAndHotSidechains(Protein, CommandList) - Static method in class HomologyModeling
 
assignName() - Method in class meshi.geometry.Angle
Assigns a meaningful name to an angle.
assignName() - Method in class meshi.geometry.Torsion
Assigns a meaningful name to a torsion.
assignRandomCaCoordinates(Chain) - Static method in class meshi.util.Utils
 
assignRandomCoordinates(Residue, CommandList, int) - Static method in class meshi.util.Utils
 
assignSecondaryStructure(Protein, CommandList, Key) - Static method in class meshi.util.Utils
 
assignSecondaryStructure(Chain, CommandList, Key) - Static method in class meshi.util.Utils
 
assignSecondaryStructure(Protein, SequenceAlignment) - Static method in class meshi.util.Utils
 
atm1 - Variable in class meshi.geometry.Torsion
 
atm2 - Variable in class meshi.geometry.Torsion
 
atm3 - Variable in class meshi.geometry.Torsion
 
atm4 - Variable in class meshi.geometry.Torsion
 
atom - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
atom - Static variable in class meshi.energy.solvate.SolvateEnergy
 
atom - Variable in class meshi.geometry.MatrixRow
 
Atom - Class in meshi.molecularElements.atoms
A generic atom.
Atom(String, Residue, AtomType, Coordinates, Double) - Constructor for class meshi.molecularElements.atoms.Atom
A generic atom with unspecified coordinates.
Atom(PdbLine) - Constructor for class meshi.molecularElements.atoms.Atom
 
atom - Variable in class meshi.molecularElements.atoms.AtomCore
 
atom() - Method in class meshi.sequences.AtomAlignmentCell
 
atom - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The atom which is kept in the cylinder.
atom - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
 
atom1 - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
atom1 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
atom1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atom1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
atom1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
atom1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
atom1 - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
atom1 - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
atom1 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
atom1 - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
atom1 - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
atom1 - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
atom1() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom1() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
atom1() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
atom1 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
atom1 - Variable in class meshi.geometry.Angle
 
atom1() - Method in class meshi.geometry.Angle
 
atom1 - Variable in class meshi.geometry.Distance
This object represent the distance between atom1 and atom2.
atom1() - Method in class meshi.geometry.Distance
Get atom1.
atom1 - Variable in class meshi.geometry.Torsion
 
atom1 - Variable in class meshi.molecularElements.atoms.AtomPair
 
atom1() - Method in class meshi.molecularElements.atoms.AtomPair
 
atom1Copy - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
atom1Number - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
atom1Number - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
atom1number - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
atom1Number - Variable in class meshi.geometry.Distance
 
atom1Number - Variable in class meshi.molecularElements.atoms.AtomPair
 
atom1Number() - Method in class meshi.molecularElements.atoms.AtomPair
 
atom1TypeOrdinal - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atom2 - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
atom2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
atom2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atom2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
atom2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
atom2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
atom2 - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
atom2 - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
atom2 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
atom2 - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
atom2 - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
atom2 - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
atom2() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom2() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
atom2() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
atom2 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
atom2 - Variable in class meshi.geometry.Angle
 
atom2() - Method in class meshi.geometry.Angle
 
atom2 - Variable in class meshi.geometry.Distance
This object represent the distance between atom1 and atom2.
atom2() - Method in class meshi.geometry.Distance
Get atom2.
atom2 - Static variable in class meshi.geometry.MatrixRow
 
atom2 - Variable in class meshi.geometry.Torsion
 
atom2 - Variable in class meshi.molecularElements.atoms.AtomPair
 
atom2() - Method in class meshi.molecularElements.atoms.AtomPair
 
atom2Copy - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
atom2Number - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
atom2Number - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
atom2number - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
atom2Number - Variable in class meshi.geometry.Distance
 
atom2Number() - Method in class meshi.geometry.Distance
 
atom2number - Static variable in class meshi.geometry.MatrixRow
 
atom2Number - Variable in class meshi.molecularElements.atoms.AtomPair
 
atom2Number() - Method in class meshi.molecularElements.atoms.AtomPair
 
atom2TypeOrdinal - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atom3 - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
atom3() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
atom3 - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom3() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom3 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
atom3 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
atom3 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
atom3 - Variable in class meshi.geometry.Angle
 
atom3() - Method in class meshi.geometry.Angle
 
atom3 - Variable in class meshi.geometry.Torsion
 
atom4 - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom4() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
atom4 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
atom4 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
atom4 - Variable in class meshi.geometry.Torsion
 
ATOM_BONDED_CAPACITY - Variable in class meshi.molecularElements.atoms.Atom
Atoms bonded to this atom.
ATOM_PAIR_CAPACITY - Static variable in class meshi.molecularElements.atoms.AtomPair
 
AtomAlignment - Class in meshi.sequences
 
AtomAlignment() - Constructor for class meshi.sequences.AtomAlignment
 
AtomAlignment(AtomList, AtomList) - Constructor for class meshi.sequences.AtomAlignment
 
AtomAlignment(ResidueAlignment) - Constructor for class meshi.sequences.AtomAlignment
 
AtomAlignment(ResidueAlignment, Filter) - Constructor for class meshi.sequences.AtomAlignment
 
AtomAlignment.IsAlignmentColumn - Class in meshi.sequences
 
AtomAlignment.IsAlignmentColumn() - Constructor for class meshi.sequences.AtomAlignment.IsAlignmentColumn
 
AtomAlignmentCell - Class in meshi.sequences
 
AtomAlignmentCell(Atom, String) - Constructor for class meshi.sequences.AtomAlignmentCell
 
AtomAlignmentColumn - Class in meshi.sequences
 
AtomAlignmentColumn(Atom, String, Atom, String) - Constructor for class meshi.sequences.AtomAlignmentColumn
 
AtomAlignmentColumn(Atom, Atom) - Constructor for class meshi.sequences.AtomAlignmentColumn
 
atomArray - Variable in class meshi.geometry.OldDistanceMatrix
An array of all atoms in the molecular system.
atomAt(int) - Method in class meshi.molecularElements.atoms.AtomList
Returns the atom in position i of the list.
atomAt(int, int) - Method in class meshi.sequences.AtomAlignment
 
atomAt(int) - Method in class meshi.sequences.AtomAlignmentColumn
 
AtomComparator - Class in meshi.molecularElements.atoms
 
AtomComparator() - Constructor for class meshi.molecularElements.atoms.AtomComparator
 
AtomCore - Class in meshi.molecularElements.atoms
A shortcut into the atom's guts.
AtomCore(Atom, AtomType, AtomStatus, int, double, double, double) - Constructor for class meshi.molecularElements.atoms.AtomCore
 
atomEnergies - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atomHeight - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The atom's cylindrical coordinates.
ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY - Static variable in interface meshi.util.KeyWords
 
ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
AtomicPairwisePMFSumma - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Atomic pairwise potential of mean force, original energy term by Chris Summa.
AtomicPairwisePMFSumma(DistanceMatrix, double, AtomicPairwisePMFSummaParameters) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atomicPairwisePMFSumma - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
atomicPairwisePMFSumma - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
atomicPairwisePMFSumma - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
AtomicPairwisePMFSummaCreator - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
 
AtomicPairwisePMFSummaCreator() - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaCreator
 
AtomicPairwisePMFSummaCreator(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaCreator
 
atomicPairwisePMFSummaCreator - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaCreator
 
atomicPairwisePMFSummaCreator - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaCreator
 
atomicPairwisePMFSummaCreator - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSummaCreator
 
AtomicPairwisePMFSummaParameters - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Parameters for the atomic pairwise PMF.
AtomicPairwisePMFSummaParameters(CommandList) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
Load parameters list from file.
atomicTypeConverter - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
atomicTypeConverter - Variable in class meshi.energy.solvate.SolvateParametersList
 
atomicTypeConverter - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
atomList - Static variable in class HeliumClusterMinimization
List of atoms to optimize.
atomList - Variable in class meshi.energy.CooperativeEnergyTerm
The atoms relevent to this energy.
atomList - Static variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
atomList - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
atomList() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
atomList - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
atomList - Variable in class meshi.energy.TotalEnergy
 
atomList() - Method in class meshi.energy.TotalEnergy
 
atomList() - Method in class meshi.geometry.AngleList
 
atomList - Variable in class meshi.geometry.OldDistanceMatrix
The list of all atoms in the molecular system.
atomList() - Method in class meshi.geometry.OldDistanceMatrix
 
atomList() - Method in class meshi.geometry.TorsionList
 
AtomList - Class in meshi.molecularElements.atoms
A list of Atoms
AtomList() - Constructor for class meshi.molecularElements.atoms.AtomList
 
AtomList(Atom) - Constructor for class meshi.molecularElements.atoms.AtomList
 
AtomList(int) - Constructor for class meshi.molecularElements.atoms.AtomList
 
AtomList(MeshiLineReader, Filter) - Constructor for class meshi.molecularElements.atoms.AtomList
An atom list based on a PDB file In a multiple model file (such as NMR's) only model 1 is read.
AtomList(PdbReader) - Constructor for class meshi.molecularElements.atoms.AtomList
An atom list based on a PDB file
AtomList(String, String) - Constructor for class meshi.molecularElements.atoms.AtomList
 
AtomList(String, Filter) - Constructor for class meshi.molecularElements.atoms.AtomList
 
AtomList(String) - Constructor for class meshi.molecularElements.atoms.AtomList
 
AtomList(ResidueList) - Constructor for class meshi.molecularElements.atoms.AtomList
An atom list based on a residue list
atomList() - Method in class meshi.molecularElements.atoms.AtomPairList
 
atomList(int) - Method in class meshi.sequences.AtomAlignment
 
atomList - Variable in class meshi.util.RgCalculator
 
AtomList.AcceptChainFilter - Class in meshi.molecularElements.atoms
 
AtomList.AcceptChainFilter(String) - Constructor for class meshi.molecularElements.atoms.AtomList.AcceptChainFilter
 
AtomList.BackboneFilter - Class in meshi.molecularElements.atoms
 
AtomList.BackboneFilter() - Constructor for class meshi.molecularElements.atoms.AtomList.BackboneFilter
 
AtomList.IsAtom - Class in meshi.molecularElements.atoms
 
AtomList.IsAtom() - Constructor for class meshi.molecularElements.atoms.AtomList.IsAtom
 
AtomList.IsDefrostedFilter - Class in meshi.molecularElements.atoms
 
AtomList.IsDefrostedFilter() - Constructor for class meshi.molecularElements.atoms.AtomList.IsDefrostedFilter
 
AtomList.IsFrozenFilter - Class in meshi.molecularElements.atoms
 
AtomList.IsFrozenFilter() - Constructor for class meshi.molecularElements.atoms.AtomList.IsFrozenFilter
 
AtomList.NonHydrogen - Class in meshi.molecularElements.atoms
 
AtomList.NonHydrogen() - Constructor for class meshi.molecularElements.atoms.AtomList.NonHydrogen
 
AtomList.RejectChainFilter - Class in meshi.molecularElements.atoms
 
AtomList.RejectChainFilter(String) - Constructor for class meshi.molecularElements.atoms.AtomList.RejectChainFilter
 
atomListCopy - Static variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
atomListSize - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
atomListSize - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
atomListSize - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
atomListSize - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
atomListTo1_4numbering() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
atomNames - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
atomNamesTranslationsMESHI - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
atomNamesTranslationsSumma - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
atomNumber - Variable in class meshi.geometry.MatrixRowCaOnly
 
AtomPair - Class in meshi.molecularElements.atoms
 
AtomPair(Atom, Atom) - Constructor for class meshi.molecularElements.atoms.AtomPair
 
atomPair1 - Variable in class meshi.geometry.Angle
 
atomPair1() - Method in class meshi.geometry.Angle
 
atomPair2 - Variable in class meshi.geometry.Angle
 
atomPair2() - Method in class meshi.geometry.Angle
 
AtomPairList - Class in meshi.molecularElements.atoms
 
AtomPairList() - Constructor for class meshi.molecularElements.atoms.AtomPairList
An empty AtomPair list
AtomPairList(ChainList) - Constructor for class meshi.molecularElements.atoms.AtomPairList
 
AtomPairList.IsAtomPair - Class in meshi.molecularElements.atoms
 
AtomPairList.IsAtomPair() - Constructor for class meshi.molecularElements.atoms.AtomPairList.IsAtomPair
 
atomR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The atom's cylindrical coordinates.
atoms - Variable in class meshi.energy.EnergyElement
 
atoms() - Method in class meshi.energy.EnergyElement
 
atoms - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
atoms() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
atoms - Variable in class meshi.energy.TotalEnergy.SortedAtoms
 
atoms - Variable in class meshi.geometry.Grid
 
atoms - Variable in class meshi.geometry.OldGrid
 
atoms() - Method in class meshi.geometry.Torsion
 
atoms - Variable in class meshi.molecularElements.atoms.AtomPair
 
atoms() - Method in class meshi.molecularElements.atoms.AtomPair
 
atoms() - Method in class meshi.molecularElements.Chain
 
atoms - Variable in class meshi.molecularElements.Protein
A list of the protein's atoms.
atoms() - Method in class meshi.molecularElements.Protein
A list of the protein's atoms.
atoms - Variable in class meshi.molecularElements.Residue
Atoms of this residue;
atoms() - Method in class meshi.molecularElements.Residue
Returns a list of the residue atoms.
atoms() - Method in class meshi.molecularElements.ResidueList
 
atomsArray - Variable in class meshi.util.filters.OriginalAtoms
 
atomsCAOfLoopNumber(AtomList, int) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
atomsCAOfLoops(AtomList) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
atomsOfLoopNumber(AtomList, int) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
atomsOfLoops(AtomList) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
AtomStatus - Enum in meshi.molecularElements.atoms
 
AtomStatus() - Constructor for enum meshi.molecularElements.atoms.AtomStatus
 
AtomSumSigmC - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
AtomSumSigmC - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
These are fields for temporary array results that are needed in the evaluation stage.
AtomSumSigmC - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
AtomSumSigmHB - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
atomTheta - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The atom's cylindrical coordinates.
atomType - Static variable in class meshi.energy.solvate.SolvateEnergy
 
AtomType - Enum in meshi.parameters
 
AtomType(BBatom, Element) - Constructor for enum meshi.parameters.AtomType
 
AtomType(Element) - Constructor for enum meshi.parameters.AtomType
 
AtomType(BBatom) - Constructor for enum meshi.parameters.AtomType
 
AtomType() - Constructor for enum meshi.parameters.AtomType
 
atomTypeNumber - Static variable in class meshi.energy.solvate.SolvateEnergy
 
atomTypeOrdinal - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
atomTypeSplines - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
atomTypeSplines - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
attach(ResidueAlignment) - Static method in class Beautify
 
Attributable - Interface in meshi.util
 
attribute - Static variable in class HomologyModeling.LoopAttribute
 
attribute - Static variable in class meshi.applications.prediction.OriginalAtom
 
attributes - Variable in class meshi.energy.AbstractEnergy
 
attributes - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
attributes - Variable in class meshi.geometry.Distance
 
attributes - Variable in class meshi.molecularElements.atoms.Atom
 
attributes - Variable in class meshi.molecularElements.Residue
 
attributes - Variable in class meshi.sequences.AlignmentCell
 
AttributesRack - Class in meshi.util
 
AttributesRack() - Constructor for class meshi.util.AttributesRack
 
aux1 - Variable in class meshi.geometry.Torsion
 
aux2 - Variable in class meshi.geometry.Torsion
 
aux3 - Variable in class meshi.geometry.Torsion
 
aux4 - Variable in class meshi.geometry.Torsion
 
averages0001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
averages001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
averages01 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
averages1 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
averages10 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
avg - Variable in class meshi.energy.TotalEnergy.SortedAtoms
 
avg() - Method in class meshi.energy.TotalEnergy.SortedAtoms
 
avg0001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
avg001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
avg01 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
avg1 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
avg10 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
AVG_ENERGY_INDEX - Static variable in class meshi.applications.prediction.ModelData
 
avgEnergy() - Method in class meshi.energy.TotalEnergy
 
avgFilteredEnergy(double) - Method in class meshi.energy.TotalEnergy
 
avgModel(List<ModelData>, ModelData) - Static method in class meshi.applications.prediction.ModelData
 
ax - Variable in class meshi.geometry.Torsion
 
ay - Variable in class meshi.geometry.Torsion
 
az - Variable in class meshi.geometry.Torsion
 

B

B - Variable in class meshi.symmetryComplex.utils.LoopUtils.Line
 
b0x - Variable in class meshi.geometry.Torsion
 
b0y - Variable in class meshi.geometry.Torsion
 
b0z - Variable in class meshi.geometry.Torsion
 
b1 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
b1x - Variable in class meshi.geometry.Torsion
 
b1y - Variable in class meshi.geometry.Torsion
 
b1z - Variable in class meshi.geometry.Torsion
 
b2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
b2x - Variable in class meshi.geometry.Torsion
 
b2y - Variable in class meshi.geometry.Torsion
 
b2z - Variable in class meshi.geometry.Torsion
 
back - Variable in class meshi.sequences.aligner.Cell
 
backbone() - Method in class meshi.molecularElements.atoms.AtomList
 
backbone() - Method in enum meshi.parameters.AtomType
 
backboneC() - Method in class meshi.molecularElements.atoms.Atom
 
backboneC() - Method in enum meshi.parameters.AtomType
 
backboneCA() - Method in class meshi.molecularElements.atoms.Atom
 
backboneCA() - Method in enum meshi.parameters.AtomType
 
BackboneCompleterAndMinimizer - Class in meshi.symmetryComplex.proteinsGJ
 
BackboneCompleterAndMinimizer(String, CommandList, String) - Constructor for class meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer
 
BackboneCompleterAndMinimizer(String, String, CommandList, String, Boolean) - Constructor for class meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer
 
BackboneFilter - Class in meshi.util.filters
 
BackboneFilter() - Constructor for class meshi.util.filters.BackboneFilter
 
backboneH() - Method in class meshi.molecularElements.atoms.Atom
 
backboneH() - Method in enum meshi.parameters.AtomType
 
BackboneMCM - Class in meshi.symmetryComplex.proteinsGJ
Created by IntelliJ IDEA.
BackboneMCM(String, String, CommandList, String) - Constructor for class meshi.symmetryComplex.proteinsGJ.BackboneMCM
 
backboneMCM() - Method in class meshi.symmetryComplex.proteinsGJ.BackboneMCM
 
backboneMinimization() - Method in class meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer
 
backboneMinimization(String) - Method in class meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer
 
backboneN() - Method in class meshi.molecularElements.atoms.Atom
 
backboneN() - Method in enum meshi.parameters.AtomType
 
backboneO() - Method in class meshi.molecularElements.atoms.Atom
 
backboneO() - Method in enum meshi.parameters.AtomType
 
backboneRelax() - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
BackboneResidue - Class in meshi.molecularElements.extendedAtoms
Alanin from Levitt, JMB 168:592 (1983) table 2.
BackboneResidue(String) - Constructor for class meshi.molecularElements.extendedAtoms.BackboneResidue
 
BackboneResidue(ResidueType, AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.BackboneResidue
 
backTrack() - Method in class meshi.sequences.aligner.DpMatrix
 
base() - Static method in class meshi.geometry.OldDistanceMatrix
 
BASE_ATOM_NUMBER - Static variable in class meshi.geometry.OldDistanceMatrix
 
BASE_INDEX - Static variable in class meshi.applications.prediction.ModelData
 
baseAtom - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
baseAtom - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
This array stores pointers to the base atoms of every non-hydrogen polar atom in the protein.
BasicLoopResult - Class in meshi.applications.corpus
 
BasicLoopResult() - Constructor for class meshi.applications.corpus.BasicLoopResult
 
BasicLoopResult(double, double, int[], double[][], double[][]) - Constructor for class meshi.applications.corpus.BasicLoopResult
 
bb - Variable in class meshi.geometry.Torsion
 
bbAtom() - Method in class meshi.molecularElements.atoms.Atom
 
bbAtom - Variable in enum meshi.parameters.AtomType
 
bbAtom() - Method in enum meshi.parameters.AtomType
 
BBatom - Enum in meshi.parameters
 
BBatom() - Constructor for enum meshi.parameters.BBatom
 
bbCoors - Variable in class meshi.applications.corpus.LoopResults
 
bbSplines - Variable in class meshi.energy.solvate.SolvateParametersList
 
bc - Variable in class meshi.geometry.Torsion
 
Beautify - Class in <Unnamed>
 
Beautify() - Constructor for class Beautify
 
Beautify.BeautifyLogger - Class in <Unnamed>
 
Beautify.BeautifyLogger(MeshiWriter, Protein, CommandList) - Constructor for class Beautify.BeautifyLogger
 
BEAUTIFY_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
BEAUTIFY_PROBLEMATIC_RANGE - Static variable in interface meshi.util.KeyWords
 
BeautifyAttribute - Class in meshi.applications.prediction.beautify
 
BeautifyAttribute() - Constructor for class meshi.applications.prediction.beautify.BeautifyAttribute
 
belowLow - Variable in class meshi.util.histogram.Histogram
 
BETA - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
BETA - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
BETA - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
BETA - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
beta - Variable in class meshi.optimizers.ConjugateGradient
 
beta - Variable in class meshi.optimizers.LBFGS
 
betaPair - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
BetaParametersList - Class in meshi.energy.hydrogenBondsPairs
Created by IntelliJ IDEA.
BetaParametersList() - Constructor for class meshi.energy.hydrogenBondsPairs.BetaParametersList
 
BetaParametersList(String) - Constructor for class meshi.energy.hydrogenBondsPairs.BetaParametersList
 
betaParametersList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
 
betaParametersList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
betaParametersList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
BetaParametersList.IsHydrogenBondsPairsParameters - Class in meshi.energy.hydrogenBondsPairs
 
BetaParametersList.IsHydrogenBondsPairsParameters() - Constructor for class meshi.energy.hydrogenBondsPairs.BetaParametersList.IsHydrogenBondsPairsParameters
 
BFGS - Class in meshi.optimizers
This class implements a BFGS minimizer according to the scheme in: Numerical Optimization by J.
BFGS(TotalEnergy, double, int, int) - Constructor for class meshi.optimizers.BFGS
 
BFGS(TotalEnergy, double, int, int, double, int, double, double, double, int, int, double, double, double) - Constructor for class meshi.optimizers.BFGS
 
BFGS - Static variable in interface meshi.util.KeyWords
 
bfgsError - Variable in class meshi.optimizers.BFGS
 
bfgsError - Variable in class meshi.optimizers.LBFGS
 
bfgsErrorString - Variable in class meshi.optimizers.BFGS
 
bfgsErrorString - Variable in class meshi.optimizers.LBFGS
 
bin - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
bins - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
bins - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
 
blosum62 - Static variable in class meshi.applications.corpus.Corpus
 
bond(Atom) - Method in class meshi.molecularElements.atoms.Atom
Bonds the other atom to this one.
BOND_ELEMENT_CLASS - Static variable in interface meshi.util.Classes
 
BOND_ENERGY - Static variable in interface meshi.util.KeyWords
 
BOND_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
BOND_PARAMETERS_CLASS - Static variable in interface meshi.util.Classes
 
bondCreator - Static variable in class Beautify
 
BondCreator - Class in meshi.energy.simpleEnergyTerms.bond
A factory for BondEnergy objects.
BondCreator() - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondCreator
 
BondCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondCreator
 
bondDepth - Variable in class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
bonded - Variable in enum meshi.geometry.DistanceMode
 
bonded - Variable in class meshi.molecularElements.atoms.Atom
 
bonded() - Method in class meshi.molecularElements.atoms.Atom
Returns the list of atoms bonded to this one.
BondedDistance - Class in meshi.geometry
 
BondedDistance(Atom, Atom, double, double, double, double) - Constructor for class meshi.geometry.BondedDistance
 
BondedFrozenDistance - Class in meshi.geometry
 
BondedFrozenDistance(Atom, Atom, double, double, double, double) - Constructor for class meshi.geometry.BondedFrozenDistance
 
bondedList - Variable in class meshi.geometry.DistanceMatrix
Atom pairs with inter-atomic distances that are always relatively small.
bondedList() - Method in class meshi.geometry.DistanceMatrix
 
bondedList - Variable in class meshi.geometry.OldDistanceMatrix
Atom pairs with inter-atomic distances that are always relatively small.
bondedList() - Method in class meshi.geometry.OldDistanceMatrix
 
bondedListDepth - Variable in class meshi.geometry.DistanceMatrix
 
bondedListDepth - Variable in class meshi.geometry.OldDistanceMatrix
 
BondEnergy - Class in meshi.energy.simpleEnergyTerms.bond
Bond energy term.
BondEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondEnergy
 
BondEnergy(AtomPairList, DistanceMatrix, BondParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondEnergy
 
BondEnergyElement - Class in meshi.energy.simpleEnergyTerms.bond
 
BondEnergyElement() - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
BondEnergyElement(AtomPair, Parameters, DistanceMatrix, double) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
bondList - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
BondParameters - Class in meshi.energy.simpleEnergyTerms.bond
The energy parameters associated with a bond between two atoms.
BondParameters() - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParameters
Auxiliary constructor.
BondParameters(String) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParameters
Constructs BondParmeters from a string (typically a line in the bondParameters file).
BondParameters(StringTokenizer) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParameters
A helper constructor for ( BondParameters(String line) ).
BondParameters(AtomType, AtomType, double, double) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParameters
A helper constructor for ( BondParameters(String line) ).
BondParameters(AtomType, AtomType) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParameters
For search keys in parameterList
BondParameters.isA - Class in meshi.energy.simpleEnergyTerms.bond
 
BondParameters.isA() - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParameters.isA
 
BondParametersList - Class in meshi.energy.simpleEnergyTerms.bond
ParametersList for BondEnergy.
BondParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.bond.BondParametersList
 
bonds - Variable in class meshi.molecularElements.Protein
A list of the protein's bonds.
bonds() - Method in class meshi.molecularElements.Protein
 
bonds - Variable in class meshi.molecularElements.Residue
Co-valiant bonds in the residue.
bonds() - Method in class meshi.molecularElements.Residue
Returns a list of the residue bonds.
BoundariesMap - Class in meshi.symmetryComplex.topologyMap
Created by IntelliJ IDEA.
BoundariesMap(CommandList) - Constructor for class meshi.symmetryComplex.topologyMap.BoundariesMap
 
BoundariesMap(String) - Constructor for class meshi.symmetryComplex.topologyMap.BoundariesMap
 
bounds - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
bounds() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
breakEnergy - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
breakEnergy4 - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
breakEnergySquare4 - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
breakFileName(String) - Static method in class meshi.util.string.StringParser
 
breakInterval - Variable in class meshi.util.mathTools.Spline1D
 
breakIntervalX - Variable in class meshi.util.mathTools.Spline2D
 
breakIntervalY - Variable in class meshi.util.mathTools.Spline2D
 
breakPath(String) - Static method in class meshi.util.string.StringParser
 
breaks - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
breaks - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
 
breaks - Variable in class meshi.util.mathTools.Spline1D
 
BREAKS_PADDING - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
 
breaksX - Variable in class meshi.util.mathTools.Spline2D
 
breaksY - Variable in class meshi.util.mathTools.Spline2D
 
BUFF - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
BUFF - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
BUFF - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
The variable BUFF allow a buffer zone around the target, where the energy is flat.
buffer - Variable in class meshi.geometry.DistanceMatrix
 
buffer() - Method in class meshi.geometry.DistanceMatrix
 
buffer - Variable in class meshi.geometry.OldDistanceMatrix
 
buffer() - Method in class meshi.geometry.OldDistanceMatrix
 
BUFFER_SIZE - Static variable in interface meshi.util.KeyWords
 
bufferCoordinates - Variable in class meshi.optimizers.BFGS
 
bufferCoordinates - Variable in class meshi.optimizers.ConjugateGradient
 
bufferCoordinates - Variable in class meshi.optimizers.LBFGS
 
bufferCoordinates - Variable in class meshi.optimizers.SteepestDecent
 
bufferOneThirdSqr - Static variable in class meshi.geometry.DistanceMatrix
(buffer/3)^2
bufferOneThirdSqr - Static variable in class meshi.geometry.OldDistanceMatrix
(buffer/3)^2
build(Protein) - Method in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
build(Protein, int, int, AbitSmarterLoopBuilder.Loop.End) - Method in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
build() - Method in class meshi.geometry.Grid
Builds the grid.
build() - Method in class meshi.geometry.OldGrid
Builds the grid.
build(Residue, int, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
build(Residue, ResidueType, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
build_best_distance(double[], HubbardPosition[]) - Static method in class meshi.util.GDTcalculator
 
buildALA(Residue) - Static method in class meshi.geometry.ResidueBuilder
 
buildARG(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildASN(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildASP(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildBackbone(Residue, double, double) - Static method in class meshi.geometry.ResidueBuilder
 
buildCYS(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
builder - Variable in class meshi.optimizers.MCM
 
buildGLN(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildGLU(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildGLY(Residue) - Static method in class meshi.geometry.ResidueBuilder
 
buildHIS(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildILE(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildLEU(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildLib(double[], int, boolean) - Method in class meshi.applications.corpus.LocalFragmentLib
 
buildLocation() - Method in class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
buildLYS(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildMET(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildPHE(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildPRO(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildSER(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildSpecificStructures() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
This method should build any implementation-specific data structures needed.
buildSpecificStructures() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
This method updates the pointers in the baseAtom array.
buildTHR(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildTRP(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildTYR(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
buildUngappedArray(int) - Method in class meshi.applications.corpus.Corpus
 
buildUngappedArray(int, String[]) - Method in class meshi.applications.corpus.Corpus
Building the ungapped array for fragments of length fragL.
buildUngappedArraynoPG(int) - Method in class meshi.applications.corpus.Corpus
 
buildVAL(Residue, double[]) - Static method in class meshi.geometry.ResidueBuilder
 
BURIED - Static variable in interface meshi.parameters.MeshiPotential
 
buttonDistanceConstrainParameters - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonDoneNonFrozenRange - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
buttonDoneOptionDialog - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonEnergyWeights - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonExitSave - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
buttonInflate - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonMinimizationParametersFull - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonMinimizationParametersShort - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonNonFrozenRange - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonParameters - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
buttonParametersForChainCompletion - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
buttonReset - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
buttonSecondaryStructure - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
bvector - Static variable in class meshi.util.overlap.Overlap
 
bx - Variable in class meshi.geometry.Torsion
 
by - Variable in class meshi.geometry.Torsion
 
byPosition(String, ArrayList<Integer>) - Static method in class meshi.util.string.StringParser
 
bySeparator(String, String) - Static method in class meshi.util.string.StringParser
 
bySeparators(String, StringList) - Static method in class meshi.util.string.StringParser
 
bz - Variable in class meshi.geometry.Torsion
 

C

C - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]
C - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]
C - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]
C - Variable in class meshi.geometry.fragments.DresserFullFrag
 
C - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
c() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
C - Variable in class meshi.symmetryComplex.utils.LoopUtils.Line
 
c0x - Variable in class meshi.geometry.Torsion
 
c0y - Variable in class meshi.geometry.Torsion
 
c0z - Variable in class meshi.geometry.Torsion
 
C1 - Variable in class meshi.applications.hubbard.HubbardPosition
 
c1 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
C1 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
C1 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]
c1 - Variable in class meshi.optimizers.BFGS
 
c1 - Variable in class meshi.optimizers.ConjugateGradient
 
c1 - Variable in class meshi.optimizers.LBFGS
 
c1 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
C1 - Static variable in class meshi.util.GDTcalculator
 
C2 - Variable in class meshi.applications.hubbard.HubbardPosition
 
c2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
C2 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
C2 - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
C is the parameter of EV = C*(d-sigma)^4 in the range [0,sigma]
c2 - Variable in class meshi.optimizers.BFGS
 
c2 - Variable in class meshi.optimizers.ConjugateGradient
 
c2 - Variable in class meshi.optimizers.LBFGS
 
c2 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
C2 - Static variable in class meshi.util.GDTcalculator
 
CA - Variable in class meshi.geometry.fragments.DresserFullFrag
 
CA - Variable in class meshi.molecularElements.ca.CaResidue
 
CA - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
ca() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
ca() - Method in class meshi.molecularElements.Residue
 
CA_CA_DISTANCE - Static variable in class HomologyModeling
 
CA_CA_DISTANCE - Static variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
CA_CA_DISTANCE - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
CA_CA_DISTANCE2 - Static variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
CA_CA_DISTANCE2 - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
CA_CLASH_DISTANCE - Static variable in interface meshi.util.KeyWords
 
CA_LONG_DISTANCE - Static variable in interface meshi.util.KeyWords
 
CA_MODEL - Static variable in interface meshi.util.KeyWords
 
CA_SHORT_DISTANCE - Static variable in interface meshi.util.KeyWords
 
CA_TETHER_ENERGY - Static variable in interface meshi.util.KeyWords
 
CaAtomFilter - Class in meshi.applications.prediction.homology
 
CaAtomFilter() - Constructor for class meshi.applications.prediction.homology.CaAtomFilter
 
caEnergyCreators - Static variable in class Beautify
 
caEnergyCreators1 - Static variable in class Beautify
 
CAFilter() - Method in class meshi.molecularElements.atoms.AtomList
 
CaFilter - Class in meshi.util.filters
 
CaFilter() - Constructor for class meshi.util.filters.CaFilter
 
caHelicesProtein - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
calc(double, double, double, double[]) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
calc(double) - Method in class meshi.util.mathTools.Spline1D
 
calc(double, double) - Method in class meshi.util.mathTools.Spline2D
 
calcBvectors() - Static method in class meshi.util.overlap.Overlap
Calculating the B vectors (equation 12 at Kabsch-1976)
calcCharPol(double[][]) - Static method in class meshi.util.overlap.Overlap
this function will calculate the characteristic polynom after caululating the determinant manually
calcEvenBreaks(double) - Method in class meshi.util.mathTools.Spline1D
 
calcEvenBreaks(double, double) - Method in class meshi.util.mathTools.Spline2D
 
CalcGDT - Class in <Unnamed>
 
CalcGDT() - Constructor for class CalcGDT
 
calcMeansAndStd(double[][]) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
calcMeansAndStd(double[][]) - Method in class meshi.energy.solvateRot1.SolvateRot1Energy
 
calcRMS(Protein, int, int, double[][]) - Method in class meshi.applications.corpus.CorrectRottenRamachandrans
 
calcRMS(LoopResults) - Method in class meshi.applications.corpus.LoopResults
 
calcRMS(AtomList, AtomList) - Static method in class meshi.util.rotamericTools.RotamericTools
 
calcRmsBetweenStruct(int, int, int, int, int) - Method in class meshi.applications.corpus.Corpus
This method gives the rms between two fragments in the corpus (starting in ind1 and ind2).
CalculateEnergyFromStructuresListAverages - Class in <Unnamed>
This program receives a list of structures, a list of energy terms, and a list of alpha values.
CalculateEnergyFromStructuresListAverages() - Constructor for class CalculateEnergyFromStructuresListAverages
 
CalculateEnergyFromStructuresListAverages.AveragesAndMaxs - Class in <Unnamed>
 
CalculateEnergyFromStructuresListAverages.AveragesAndMaxs(int, MeshiWriter) - Constructor for class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute - Class in <Unnamed>
 
CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute(double) - Constructor for class CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute
 
CalculateEnergyFromStructuresListAverages.GaussianAttribute - Class in <Unnamed>
 
CalculateEnergyFromStructuresListAverages.GaussianAttribute(double, double, double, double, double) - Constructor for class CalculateEnergyFromStructuresListAverages.GaussianAttribute
 
CalculateEnergyFromStructuresListAverages.GaussianAttributes - Class in <Unnamed>
 
CalculateEnergyFromStructuresListAverages.GaussianAttributes() - Constructor for class CalculateEnergyFromStructuresListAverages.GaussianAttributes
 
calculateRms() - Static method in class meshi.util.overlap.Overlap
 
calculateSolRot1(String, CommandList) - Method in class meshi.applications.corpus.Corpus
 
calculateThreadingEnergy() - Method in class meshi.applications.corpus.LocalFragmentLib
 
calculatingTheSolvationEnergiesOfEachAtom(boolean, double, double, double) - Method in class meshi.energy.solvate.SolvateEnergy
 
calcVariousEnergies(int, double, int, Protein, TotalEnergy, DistanceMatrix, SideChainSolvateEnergy, ExcludedVolParametersList) - Static method in class meshi.util.Scmod
 
CALPHA_HYDROGEN_BONDS - Static variable in interface meshi.util.KeyWords
 
CALPHA_HYDROGEN_BONDS_PLANE - Static variable in interface meshi.util.KeyWords
 
CAnoImageFilter() - Method in class meshi.molecularElements.atoms.AtomList
 
capacity - Variable in class meshi.geometry.DistanceList
 
CAPACITY - Static variable in class meshi.geometry.MatrixRow
 
carbonylC() - Method in class meshi.molecularElements.Residue
 
carbonylO() - Method in class meshi.molecularElements.Residue
 
caRelax() - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
CaResidue - Class in meshi.molecularElements.ca
 
CaResidue(String) - Constructor for class meshi.molecularElements.ca.CaResidue
Use this constructor to instantiate a creator object..
CaResidue(String, ResidueType, ResidueIdentifier, AtomList, ResidueMode) - Constructor for class meshi.molecularElements.ca.CaResidue
 
CASP_GROUP - Static variable in interface meshi.util.KeyWords
 
caType - Variable in enum meshi.parameters.ResidueType
 
caType() - Method in enum meshi.parameters.ResidueType
 
CB - Variable in class meshi.geometry.fragments.DresserFullFrag
 
CB - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
cb() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
cb() - Method in class meshi.molecularElements.Residue
 
cbType - Variable in enum meshi.parameters.ResidueType
 
cbType() - Method in enum meshi.parameters.ResidueType
 
cc - Variable in class meshi.applications.corpus.LoopResults
 
cc - Variable in class meshi.geometry.Torsion
 
CD - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
CD - Variable in class meshi.molecularElements.extendedAtoms.Gln
 
CD - Variable in class meshi.molecularElements.extendedAtoms.Glu
 
CD - Variable in class meshi.molecularElements.extendedAtoms.Lys
 
CD - Variable in class meshi.molecularElements.extendedAtoms.Pro
 
CD1 - Variable in class meshi.molecularElements.extendedAtoms.Ile
 
CD1 - Variable in class meshi.molecularElements.extendedAtoms.Leu
 
CD1 - Variable in class meshi.molecularElements.extendedAtoms.Phe
 
CD1 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
CD1 - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
CD2 - Variable in class meshi.molecularElements.extendedAtoms.His
 
CD2 - Variable in class meshi.molecularElements.extendedAtoms.Leu
 
CD2 - Variable in class meshi.molecularElements.extendedAtoms.Phe
 
CD2 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
CD2 - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
cdiv(double, double, double, double) - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
cdivi - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
cdivr - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
CE - Variable in class meshi.molecularElements.extendedAtoms.Lys
 
CE - Variable in class meshi.molecularElements.extendedAtoms.Met
 
CE1 - Variable in class meshi.molecularElements.extendedAtoms.His
 
CE1 - Variable in class meshi.molecularElements.extendedAtoms.Phe
 
CE1 - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
CE2 - Variable in class meshi.molecularElements.extendedAtoms.Phe
 
CE2 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
CE2 - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
CE3 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
Cell - Class in meshi.sequences.aligner
Created by IntelliJ IDEA.
Cell(int, int, DpMatrix) - Constructor for class meshi.sequences.aligner.Cell
 
cell(int) - Method in class meshi.sequences.AlignmentColumn
 
cell(int) - Method in class meshi.sequences.Sequence
 
cell0() - Method in class meshi.sequences.AlignmentColumn
 
cell1() - Method in class meshi.sequences.AlignmentColumn
 
cellCapacity - Variable in class meshi.geometry.Grid
 
cellCapacity - Variable in class meshi.geometry.OldGrid
 
cells - Variable in class meshi.geometry.Grid
 
cells - Variable in class meshi.geometry.OldGrid
 
cells - Variable in class meshi.sequences.AlignmentColumn
 
CellScorer - Interface in meshi.sequences.aligner
 
cellScorer - Variable in class meshi.sequences.aligner.DpMatrix
 
Cend - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
cEnd - Variable in class meshi.energy.solvate.SolvateParametersList
 
Cend - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
centerOfBin(int) - Method in class meshi.util.histogram.Histogram
 
centerOfMass0 - Variable in class meshi.util.Rms
 
centerOfMass0() - Method in class meshi.util.Rms
 
centerOfMass1 - Variable in class meshi.util.Rms
 
centerOfMass1() - Method in class meshi.util.Rms
 
centerValue - Variable in class meshi.util.histogram.HistogramBin
 
centerValue() - Method in class meshi.util.histogram.HistogramBin
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Asn
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Asp
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Gln
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Glu
 
CG - Variable in class meshi.molecularElements.extendedAtoms.His
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Leu
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Lys
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Met
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Phe
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Pro
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
CG - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
cg() - Method in class meshi.molecularElements.Residue
 
CG - Static variable in interface meshi.util.KeyWords
 
CG1 - Variable in class meshi.molecularElements.extendedAtoms.Ile
 
CG1 - Variable in class meshi.molecularElements.extendedAtoms.Val
 
CG2 - Variable in class meshi.molecularElements.extendedAtoms.Ile
 
CG2 - Variable in class meshi.molecularElements.extendedAtoms.Thr
 
CG2 - Variable in class meshi.molecularElements.extendedAtoms.Val
 
CH2 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
chain() - Method in class meshi.molecularElements.atoms.Atom
Returns the Atom's chain.
CHAIN - Variable in class meshi.molecularElements.atoms.AtomList.AcceptChainFilter
 
CHAIN - Variable in class meshi.molecularElements.atoms.AtomList.RejectChainFilter
 
Chain - Class in meshi.molecularElements
A list of residues of the same chain.
Chain(String, Protein) - Constructor for class meshi.molecularElements.Chain
Empty list.
Chain(Sequence, ResidueCreator, Protein) - Constructor for class meshi.molecularElements.Chain
Constructs a Chain from a sequence (a string of one letter codes).
Chain(Sequence, ResidueCreator, String, Protein) - Constructor for class meshi.molecularElements.Chain
Constructs a Chain from a sequence (a string of one letter codes).
Chain(AtomList, ResidueCreator, Protein) - Constructor for class meshi.molecularElements.Chain
Constructs a Chain from a list of atoms.
Chain(AtomList, ResidueCreator, String, Protein) - Constructor for class meshi.molecularElements.Chain
Constructs a Chain from a list of atoms.
Chain(AtomList, ResidueCreator, String, Protein, MolecularSystem, MolecularSystem) - Constructor for class meshi.molecularElements.Chain
 
chain() - Method in class meshi.molecularElements.Protein
 
chain() - Method in class meshi.molecularElements.Residue
 
chain - Variable in class meshi.molecularElements.ResidueIdentifier
 
chain() - Method in class meshi.molecularElements.ResidueIdentifier
 
chain - Variable in class meshi.PDB.PdbLine
 
chain() - Method in class meshi.PDB.PdbLine
 
chain - Variable in class meshi.symmetryComplex.utils.GJFilters.AcceptChainFilter
 
chain - Variable in class meshi.symmetryComplex.utils.GJFilters.RejectChainFilter
 
Chain.IsResidue - Class in meshi.molecularElements
 
Chain.IsResidue() - Constructor for class meshi.molecularElements.Chain.IsResidue
 
CHAIN_LETTERS - Static variable in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
chainA_Ca_loops_Atom_Filter - Static variable in class meshi.symmetryComplex.utils.GJFilters
 
chainLetters - Variable in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
chainLetters() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
ChainList - Class in meshi.molecularElements
A list of residues.
ChainList(Protein) - Constructor for class meshi.molecularElements.ChainList
Empty list.
ChainList(AtomList, ResidueCreator, Protein) - Constructor for class meshi.molecularElements.ChainList
 
ChainList.IsChain - Class in meshi.molecularElements
 
ChainList.IsChain() - Constructor for class meshi.molecularElements.ChainList.IsChain
 
chainName - Variable in class Pdb2Fasta.MyFilter
 
chainNames - Variable in class meshi.PDB.PdbLineATOM
 
chains - Variable in class meshi.molecularElements.Protein
 
chains() - Method in class meshi.molecularElements.Protein
 
charAt(int) - Method in class meshi.sequences.Sequence
 
charFilter - Variable in class meshi.sequences.Sequence
 
charges - Static variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticCreator
 
charges - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
CHECK_INTERLOOP_DISTANCE - Static variable in interface meshi.util.KeyWords
 
checkEigenval(double[]) - Static method in class meshi.util.overlap.Overlap
We now have to find the corresponding eigenvectors so we check if all eigenvalues are different or not.
checkEigenVec() - Static method in class meshi.util.overlap.Overlap
In order to get the proper rotation matrix (kabsch 1978) when a1,a2,a3 are out eigenvectors we make sure that a1*a2 = a3
checkMatrixDimensions(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Check if size(A) == size(B)
checkSimilarity(int, int[], int, boolean) - Method in class meshi.applications.corpus.LocalFragmentLib
This method checks if the fragment 'ind' (given in the ungapped indexing) is similar to a fragment already in the lib.
checkSingleResidue() - Method in class meshi.molecularElements.atoms.AtomList
Checks if this AtomList is comprised of atoms belonging to a single residue.
chi1Filter() - Method in class meshi.geometry.TorsionList
Returns a sub-list that is accepted by the parameter
CHI_1 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
chi_1_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
CHI_2 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
chi_2_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
CHI_3 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
chi_3_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
CHI_4 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
chi_4_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
chol() - Method in class meshi.util.mathTools.Jama.Matrix
Cholesky Decomposition
CholeskyDecomposition - Class in meshi.util.mathTools.Jama
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class meshi.util.mathTools.Jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
ChooseTemplate - Class in <Unnamed>
 
ChooseTemplate() - Constructor for class ChooseTemplate
 
chooseTemplatePair(CommandList, Protein, Protein, DunbrackLib, double[][], double[][]) - Static method in class ChooseTemplate
 
chooseTemplatePair(CommandList, Protein, Protein, DunbrackLib, double[][], double[][]) - Static method in class ModelRanker
 
CIS - Static variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
CIS_TRANS - Static variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
CLASH_DISTANCE - Static variable in interface meshi.util.KeyWords
 
clashDistance - Variable in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
clashDistance - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
clashDistanceLabel - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
clashDistanceText - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
clashesWithImages(Coordinates, double) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
Classes - Interface in meshi.util
 
cleanList() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
save only the live elements inthis list
cleanList_dm() - Method in class meshi.energy.hydrogenBond.HBondList
save only the live elements in this list
clear() - Method in class meshi.geometry.DistanceList
 
clone() - Method in class meshi.util.mathTools.Jama.Matrix
Clone the Matrix object.
close() - Method in class aligner.FWriter
 
cls - Variable in class meshi.util.filters.IsClass
 
cmx - Variable in class meshi.util.RgCalculator
 
cmx() - Method in class meshi.util.RgCalculator
 
cmy - Variable in class meshi.util.RgCalculator
 
cmy() - Method in class meshi.util.RgCalculator
 
cmz - Variable in class meshi.util.RgCalculator
 
cmz() - Method in class meshi.util.RgCalculator
 
CN_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
CNC - Variable in class meshi.energy.solvate.SolvateEnergy
These are fields for temporary array results that are needed in the evaluation stage.
co - Variable in class meshi.geometry.fragments.DresserFullFrag
 
co1 - Variable in class meshi.geometry.Torsion
 
co2 - Variable in class meshi.geometry.fragments.DresserFullFrag
 
code - Variable in exception meshi.optimizers.LineSearchException
 
CoefficientsMatrixForAtomPairSpline - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Coefficients matrix for a single atom pair spline.
CoefficientsMatrixForAtomPairSpline(double[], int, String) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
Creates new coefficients matrix.
coefs - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
coefs - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
coefs - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
 
coefs - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
coefs - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
 
coefs - Variable in class meshi.util.mathTools.Spline1D
 
coefs - Variable in class meshi.util.mathTools.Spline2D
 
COIL - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
COIL - Static variable in interface meshi.parameters.MeshiPotential
 
colNumber - Variable in class meshi.sequences.aligner.Cell
 
ColorByEnergy - Class in <Unnamed>
 
ColorByEnergy() - Constructor for class ColorByEnergy
 
colorByEnergy(AtomList) - Static method in class meshi.util.Utils
 
ColorByEnergy.DistanceFromCatalyticAttribute - Class in <Unnamed>
 
ColorByEnergy.DistanceFromCatalyticAttribute(double) - Constructor for class ColorByEnergy.DistanceFromCatalyticAttribute
 
ColorByEnergy.GaussianAttribute - Class in <Unnamed>
 
ColorByEnergy.GaussianAttribute(double, double, double, double, double) - Constructor for class ColorByEnergy.GaussianAttribute
 
ColorByEnergy.GaussianAttributes - Class in <Unnamed>
 
ColorByEnergy.GaussianAttributes() - Constructor for class ColorByEnergy.GaussianAttributes
 
column() - Method in class meshi.sequences.AlignmentCell
 
columnChar(int) - Method in class meshi.sequences.aligner.DpMatrix
 
columns - Variable in class meshi.symmetryComplex.transformations.Matrix1D
 
Command - Class in meshi.util
 
Command() - Constructor for class meshi.util.Command
 
Command(String, String) - Constructor for class meshi.util.Command
 
commandFileException(String, Exception) - Method in class meshi.util.CommandsException
 
commandLine - Static variable in class meshi.util.MeshiProgram
The command line with which the program was called.
CommandList - Class in meshi.util
Command File Parser.
CommandList(CommandsException) - Constructor for class meshi.util.CommandList
An empty commands List,
CommandList(String[], CommandsException) - Constructor for class meshi.util.CommandList
Constract a CommandList object from a file.
CommandList(String, CommandsException) - Constructor for class meshi.util.CommandList
 
CommandListComment() - Method in interface meshi.util.CommandListGenerator
 
CommandListGenerator - Interface in meshi.util
 
commands - Variable in class AbInitio.AbInitioLogger
 
commands - Static variable in class AbInitio
 
commands - Static variable in class HydrogenTest
 
commands - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
commands - Variable in class meshi.optimizers.Perturbation
 
commands - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
commands - Variable in class Optimize.OptimizeLogger
 
commands - Variable in class Refine.RefineLogger
 
commands - Static variable in class SimplestMinimizeProtein
 
commandsButton - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
commandsComment - Variable in class meshi.util.Command
 
commandsException - Variable in class meshi.util.CommandList
 
CommandsException - Class in meshi.util
 
CommandsException(String) - Constructor for class meshi.util.CommandsException
 
commandsFileName - Static variable in class ChooseTemplate
 
commandsFileName - Static variable in class ModelRanker
 
commandsFileName - Static variable in class SimplestMinimizeProtein
 
comment - Variable in class meshi.energy.AbstractEnergy
A short name for the energy term.
comment() - Method in class meshi.energy.AbstractEnergy
 
comment() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
comment() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
comment() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
comment - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherCreator
 
comment - Variable in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
comment() - Method in class meshi.molecularElements.atoms.Atom
Returns atom's comment.
comment - Variable in class meshi.molecularElements.atoms.AtomList
 
comment() - Method in class meshi.molecularElements.atoms.AtomList
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Ala
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Ala
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Arg
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Arg
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Asn
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Asn
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Asp
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Asp
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.BackboneResidue
 
comment() - Method in class meshi.molecularElements.extendedAtoms.BackboneResidue
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Cys
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Cys
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Gln
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Gln
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Glu
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Glu
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Gly
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Gly
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.His
 
comment() - Method in class meshi.molecularElements.extendedAtoms.His
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Ile
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Ile
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Leu
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Leu
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Lys
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Lys
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Met
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Met
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Phe
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Phe
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Pro
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Pro
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Ser
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Ser
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Thr
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Thr
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Trp
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Trp
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Tyr
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Tyr
 
COMMENT - Static variable in class meshi.molecularElements.extendedAtoms.Val
 
comment() - Method in class meshi.molecularElements.extendedAtoms.Val
 
comment() - Method in class meshi.molecularElements.Residue
 
comment - Variable in class meshi.sequences.AlignmentCell
 
comment() - Method in class meshi.sequences.Sequence
 
comment - Variable in class meshi.util.CommandList
The file from which the comands were read.
comment(String) - Method in class meshi.util.CommandList
 
comment() - Method in class meshi.util.CommandList
 
comment - Static variable in class meshi.util.overlap.Overlap
 
comment - Variable in class meshi.util.string.StringList
 
comment2 - Static variable in class meshi.util.overlap.Overlap
 
comments - Variable in class meshi.sequences.ResidueAlignment
 
comments - Variable in class meshi.sequences.SequenceAlignment
 
compare(Object, Object) - Method in class HomologyModeling.LoopComperator
 
compare(Object, Object) - Method in class meshi.applications.prediction.AbitSmarterLoopBuilder.LoopComperator
 
compare(ModelData, ModelData) - Method in class meshi.applications.prediction.ModelData.TermComparator
 
compare(Object, Object) - Method in class meshi.energy.TotalEnergy.EnergyComparator
 
compare(Object, Object) - Method in class meshi.geometry.DistanceMatrixBondedOnly.DistanceComparator
 
compare(Object, Object) - Method in class meshi.molecularElements.atoms.AtomComparator
 
compare(Object, Object) - Method in class SelectModels.ModelComparator
 
compareTo(Object) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
compareTo(Object) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
compareTo(Object) - Method in class meshi.energy.simpleEnergyTerms.bond.BondParameters
Defines order within objects and thus allows sorting for more efficient searches.
compareTo(Object) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
compareTo(Object) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
compareTo(Object) - Method in class meshi.molecularElements.atoms.Atom
 
compareTo(Object) - Method in class meshi.molecularElements.atoms.AtomPair
 
compareTo(Object) - Method in class meshi.molecularElements.Residue
Compares this residue with the given residue according to the order of their ResidueIdentifiers.
compareTo(Object) - Method in class meshi.molecularElements.ResidueIdentifier
Compares this ResidueIdentifier to another object.
compareTo(Object) - Method in class meshi.util.histogram.HistogramBin
 
completeResiduesWithRandomCoordinates(Protein, ResidueAlignment, CommandList) - Static method in class HomologyModeling
Adds random coordinates to residues that have some coordinates but miss a few (<3) other.
compose(Transformation) - Method in class meshi.symmetryComplex.transformations.Transformation
 
COMPOSITE_PROPENSITY_2D_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COMPOSITE_PROPENSITY_2D_WITH_PP_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COMPOSITE_PROPENSITY_ENERGY - Static variable in interface meshi.util.KeyWords
 
COMPOSITE_PROPENSITY_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COMPOSITE_TORSIONS_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
CompositePropensity2DCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP
The propensity 2D energy calculates the proensity of each amino acid to be in a specific position at the (phi,psi) torsion space.
CompositePropensity2DCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DCreator
 
CompositePropensity2DCreator() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DCreator
 
CompositePropensity2DEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP
 
CompositePropensity2DEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergy
 
CompositePropensity2DEnergy(ResidueTorsionsList, DistanceMatrix, CompositePropensity2DParametersList, double, String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergy
 
CompositePropensity2DEnergyElement - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP
 
CompositePropensity2DEnergyElement(ResidueTorsions, CompositePropensity2DParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement
 
CompositePropensity2DParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP
 
CompositePropensity2DParameters(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters
 
CompositePropensity2DParametersList - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP
 
CompositePropensity2DParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList
 
compositePropensityCreator - Static variable in class Beautify
 
CompositePropensityCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
The propensity energy identifies each amino acid's favorable positions on the (phi,psi,chi_1) torsion space.
CompositePropensityCreator() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityCreator
 
compositePropensityCreator - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityCreator
 
compositePropensityCreator - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityCreator
 
CompositePropensityEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
 
CompositePropensityEnergy(ResidueTorsionsList, DistanceMatrix, CompositePropensityParametersList, double, String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
CompositePropensityEnergyElement - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
 
CompositePropensityEnergyElement(ResidueTorsions, CompositePropensityParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
CompositePropensityParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
 
CompositePropensityParameters(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters
 
CompositePropensityParametersList - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
 
CompositePropensityParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList
 
CompositeTorsionsDefinitions - Interface in meshi.energy.simpleEnergyTerms.compositeTorsions
Definitions and constants used throughout the CompositeTorsionsEnergy term.
cond() - Method in class meshi.util.mathTools.Jama.Matrix
Matrix condition (2 norm)
cond() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Two norm condition number
ConjugateGradient - Class in meshi.optimizers
This class implements a nonlinear Conjugate Gradient minimizer PR+ algorithm is implemented.
ConjugateGradient(TotalEnergy, double, int, int, double, double, double, int, int) - Constructor for class meshi.optimizers.ConjugateGradient
 
ConjugateGradient(TotalEnergy, double, int, int) - Constructor for class meshi.optimizers.ConjugateGradient
 
ConjugateGradient(TotalEnergy, double, int, int, int) - Constructor for class meshi.optimizers.ConjugateGradient
 
ConjugateGradient(TotalEnergy) - Constructor for class meshi.optimizers.ConjugateGradient
 
CONSENSUS_ENERGY - Static variable in interface meshi.util.KeyWords
 
CONSTRICT - Static variable in interface meshi.util.KeyWords
 
constructWithCopy(double[][]) - Static method in class meshi.util.mathTools.Jama.Matrix
Construct a matrix from a copy of a 2-D array.
constSmooth - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
contact - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
contact - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
contact(double) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
contact() - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
contact - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
contact(double) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
contact() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
contactAtoms(double) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
contactAtoms(double) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
CONTACTS_ENVIRONMENT_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
CONTACTS_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COOPERATIVE_PERATOM_SUMMA_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_PERATOM_SUMMA_FILENAME - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_PROPENSITY_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_PROPENSITY_FILENAME - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_PROPENSITY_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COOPERATIVE_RAMACHANDRAN_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_RAMACHANDRAN_FILENAME - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_RAMACHANDRAN_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
COOPERATIVE_Z_PROPENSITY_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_Z_PROPENSITY_FILENAME - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_Z_RAMACHANDRAN_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_Z_RAMACHANDRAN_FILENAME - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_Z_SUMMA_ENERGY - Static variable in interface meshi.util.KeyWords
 
COOPERATIVE_Z_SUMMA_FILENAME - Static variable in interface meshi.util.KeyWords
 
CooperativeAtomicPairwisePMFSumma - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
 
CooperativeAtomicPairwisePMFSumma(DistanceMatrix, double, CooperativeAtomicPairwisePMFSummaParameters, AtomicPairwisePMFSumma) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
CooperativeAtomicPairwisePMFSummaCreator - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
 
CooperativeAtomicPairwisePMFSummaCreator(AtomicPairwisePMFSummaCreator) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaCreator
 
CooperativeAtomicPairwisePMFSummaParameters - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
 
CooperativeAtomicPairwisePMFSummaParameters(CommandList) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaParameters
 
CooperativeEnergyTerm - Class in meshi.energy
A super class for those energy terms that operate on the entire protein, or on a specific group of atoms that occur only once.
CooperativeEnergyTerm() - Constructor for class meshi.energy.CooperativeEnergyTerm
 
CooperativeEnergyTerm(Updateable[], AtomList, DistanceMatrix, Parameters, double) - Constructor for class meshi.energy.CooperativeEnergyTerm
 
CooperativePerAtomSumma - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Created by IntelliJ IDEA.
CooperativePerAtomSumma(DistanceMatrix, double, CooperativePerAtomSummaParameters, AtomicPairwisePMFSumma) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
CooperativePerAtomSummaCreator - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Created by IntelliJ IDEA.
CooperativePerAtomSummaCreator(AtomicPairwisePMFSummaCreator) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaCreator
 
CooperativePerAtomSummaParameters - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Created by IntelliJ IDEA.
CooperativePerAtomSummaParameters(CommandList) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaParameters
 
CooperativePropensityCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
Created by IntelliJ IDEA.
CooperativePropensityCreator(CompositePropensityCreator) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityCreator
 
CooperativePropensityEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
Created by IntelliJ IDEA.
CooperativePropensityEnergy(CompositePropensityEnergy, double, CooperativePropensityParameters) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
CooperativePropensityParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
Created by IntelliJ IDEA.
CooperativePropensityParameters(CommandList) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityParameters
 
CooperativeRamachandran - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
CooperativeRamachandran(RamachandranSidechainEnergy, double, CooperativeRamachandranParameters) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
CooperativeRamachandranCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
CooperativeRamachandranCreator(RamachandranSidechainEnergyCreator) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranCreator
 
CooperativeRamachandranParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
CooperativeRamachandranParameters(CommandList) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranParameters
 
CooperativeZParameters - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Created by IntelliJ IDEA.
CooperativeZParameters(CommandList) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZParameters
 
CooperativeZPropensityCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
Created by IntelliJ IDEA.
CooperativeZPropensityCreator(CompositePropensityCreator) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityCreator
 
CooperativeZPropensityEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
Created by IntelliJ IDEA.
CooperativeZPropensityEnergy(CompositePropensityEnergy, double, CooperativeZPropensityParameters) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
CooperativeZPropensityParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
Created by IntelliJ IDEA.
CooperativeZPropensityParameters(CommandList) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityParameters
 
CooperativeZRamachandran - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Created by IntelliJ IDEA.
CooperativeZRamachandran(RamachandranSidechainEnergy, double, CooperativeZRamachandranParameters) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
CooperativeZRamachandranCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Created by IntelliJ IDEA.
CooperativeZRamachandranCreator(RamachandranSidechainEnergyCreator) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranCreator
 
CooperativeZRamachandranParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Created by IntelliJ IDEA.
CooperativeZRamachandranParameters(CommandList) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranParameters
 
CooperativeZSumma - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Created by IntelliJ IDEA.
CooperativeZSumma(DistanceMatrix, double, CooperativeZParameters, AtomicPairwisePMFSumma) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
CooperativeZSummaCreator - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Created by IntelliJ IDEA.
CooperativeZSummaCreator(AtomicPairwisePMFSummaCreator) - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSummaCreator
 
coor - Static variable in class meshi.util.overlap.Overlap
 
coor2 - Static variable in class meshi.util.overlap.Overlap
 
coordinates - Variable in class meshi.energy.CooperativeEnergyTerm
 
coordinates - Static variable in class meshi.energy.TotalEnergy
 
coordinates() - Method in class meshi.energy.TotalEnergy
 
Coordinates - Class in meshi.geometry
 
Coordinates() - Constructor for class meshi.geometry.Coordinates
 
Coordinates(Atom) - Constructor for class meshi.geometry.Coordinates
 
Coordinates(double, double, double) - Constructor for class meshi.geometry.Coordinates
 
Coordinates(Coordinates) - Constructor for class meshi.geometry.Coordinates
 
Coordinates(Coordinates, double) - Constructor for class meshi.geometry.Coordinates
 
coordinates - Variable in class meshi.optimizers.BFGS
 
coordinates - Variable in class meshi.optimizers.ConjugateGradient
 
coordinates - Variable in class meshi.optimizers.LBFGS
 
coordinates - Variable in class meshi.optimizers.SimpleStepLength
 
coordinates - Variable in class meshi.optimizers.SteepestDecent
 
coordinates - Variable in class meshi.optimizers.WolfConditionLineSearch
 
CoordinatesAssigner - Class in meshi.symmetryComplex.proteinsGJ
Created by IntelliJ IDEA.
CoordinatesAssigner(SymmetricComplex, CommandList, ResidueList, double, int, int, Topology) - Constructor for class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
CoordinatesAssigner(ResidueList, double, int, int, Topology) - Constructor for class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
coors - Variable in class meshi.applications.corpus.BasicLoopResult
 
coors - Variable in class meshi.applications.corpus.Corpus
 
copy(Residue, Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
copy(ResidueAlignment) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
copy() - Method in class meshi.util.mathTools.Jama.Matrix
Make a deep copy of a matrix
copy(File, File) - Static method in class SelectModels
 
copyCoordinates(ResidueAlignment) - Static method in class Beautify
 
copyCoordinatesFromTemplate(Protein, ResidueAlignment, CommandList) - Static method in class HomologyModeling
When Done all the available information was extracted from the template.
copyMat(double[][]) - Static method in class meshi.util.overlap.Overlap
 
core - Variable in class meshi.molecularElements.atoms.Atom
 
Corpus - Class in meshi.applications.corpus
A class that hold the 20-type-mutation energy data of one or several proteins.
Corpus(String, CommandList, EnergyCreator[]) - Constructor for class meshi.applications.corpus.Corpus
 
Corpus(String) - Constructor for class meshi.applications.corpus.Corpus
Reading a corpus from file.
corpus - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
corpus - Variable in class meshi.applications.corpus.LocalFragmentLib
 
CORPUS_FILE_NAME - Static variable in interface meshi.util.KeyWords
 
corpusFileName - Static variable in class meshi.applications.corpus.RunThreadingExperiment
 
correctFrag(Protein, Vector<Integer>) - Method in class meshi.applications.corpus.CorrectRottenRamachandrans
 
correctRottenRamachandrans(Protein, CommandList) - Static method in class HomologyModeling
 
CorrectRottenRamachandrans - Class in meshi.applications.corpus
 
CorrectRottenRamachandrans(CommandList, Corpus) - Constructor for class meshi.applications.corpus.CorrectRottenRamachandrans
 
CorrectRottenRamachandrans(CommandList, Corpus, DunbrackLib) - Constructor for class meshi.applications.corpus.CorrectRottenRamachandrans
The Dunbrack lib is needed for Rot1 only.
cosAngle - Variable in class meshi.geometry.Angle
 
cosAngle() - Method in class meshi.geometry.Angle
 
cosTorsion - Variable in class meshi.geometry.Torsion
 
cosTorsion() - Method in class meshi.geometry.Torsion
 
CoulombElectrostaticCreator - Class in meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics
Creates a CoulombElectrostaticTerm for the protein with a given weight.
CoulombElectrostaticCreator(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticCreator
A CoulombElectrostaticCreator constructor that takes the weight given to this energy term as a parameter.
CoulombElectrostaticCreator() - Constructor for class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticCreator
default constructor
CoulombElectrostaticEnergyElement - Class in meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics
This object represents Electrostatic Energy between two Atoms.
CoulombElectrostaticEnergyElement() - Constructor for class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
default constructor
CoulombElectrostaticEnergyElement(DistanceMatrix, double, double, double[]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
constructor
CoulombElectrostatics - Class in meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics
An implementation of Coulomb's law.
CoulombElectrostatics() - Constructor for class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostatics
default Constructor
CoulombElectrostatics(DistanceMatrix, double, double, double[]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostatics
constructor
counter - Static variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
counter - Static variable in class meshi.geometry.DistanceMatrixCaOnly
 
countUpdates - Variable in class meshi.energy.hydrogenBond.HBondList
 
countUpdates() - Method in class meshi.energy.hydrogenBond.HBondList
 
Cp1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
cP1 - Variable in class meshi.energy.solvate.SolvateParametersList
 
Cp1 - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
Cp2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
cP2 - Variable in class meshi.energy.solvate.SolvateParametersList
 
Cp2 - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
cpp - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
cpp - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement
 
cpp - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement
 
create(StringTokenizer) - Method in class meshi.energy.hydrogenBond.LennardJonesParameters
 
create(StringTokenizer) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
create(StringTokenizer) - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
create(StringTokenizer) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
create(StringTokenizer) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
create(StringTokenizer) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
create(Distance, SolvateParametersList, AbstractHydrogenBondList) - Static method in class meshi.energy.solvate.SolvateDistanceAttributeCreator
 
create(AtomList, ResidueIdentifier, ResidueMode) - Method in class meshi.molecularElements.ca.CaResidue
 
create(AtomList, ResidueIdentifier, ResidueMode) - Method in class meshi.molecularElements.extendedAtoms.BackboneResidue
 
create(AtomList, ResidueIdentifier, ResidueMode) - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtomsCreator
 
create(AtomList, ResidueIdentifier, ResidueMode) - Method in class meshi.molecularElements.Residue
create a residue based on an atoms list.
create(AtomList, ResidueIdentifier, ResidueMode) - Method in interface meshi.molecularElements.ResidueCreator
 
create() - Method in class meshi.util.histogram.Histogram.BinCreator
 
createAndAddResidue(ResidueCreator, AtomList, ResidueMode) - Method in class meshi.molecularElements.Chain
 
createAtomCore(Atom, AtomType, AtomStatus, double, double, double) - Method in class meshi.molecularElements.atoms.MolecularSystem
 
createBackboneModel(Sequence, Protein, Protein, CommandList, Beautify.BeautifyLogger) - Static method in class Beautify
 
createCaModel(Protein, Protein, CommandList) - Static method in class Beautify
 
createCell(char, int) - Static method in class meshi.sequences.SequenceAlignmentColumn
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
 
createElement(Object) - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
createElement(Object, Parameters) - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
createElement(Object, Parameters) - Method in class meshi.symmetryComplex.energy.cylinder.CylinderEnergy
 
createElement(Object, Parameters) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergy
 
createElement(Object, Parameters) - Method in class meshi.symmetryComplex.energy.SymmetryEnergy
 
createElementsList(DistanceList) - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
createElementsList(ArrayList) - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
Creates the fixed list of energy elements in the initiation phase of a simulation.
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.EnergyCreator
Where each sub class gets the chance to show what it knows.
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.linearRG.LinearRgCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSummaCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticCreator
the creator: 1.
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.RG.RgCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.bond.BondCreator
hides all the hard work needed to generate a BondEnergy object.
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.simpleEnergyTerms.tether.TetherCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.solvate.SolvateCreatorLongHB
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.solvate.SolvateCreatorRegularHB
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.solvateRot1.SolvateRot1Creator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.energy.templateEnergy.TemplateEnergyCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator
 
createEnergyTerm(Protein, DistanceMatrix, CommandList) - Method in class meshi.symmetryComplex.energy.SymmetryCreator
 
createHBfromPolars(Atom, Atom) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
This method should build an implementaion specific HB from two polar atoms given as parameters.
createHBfromPolars(Atom, Atom) - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
Creating a Dahiyat-like hydrogen-bond.
createP() - Static method in class meshi.util.overlap.Overlap
Building a P matrix according to equation 10
which is R*Rt(1976)
createPairsList(DistanceList) - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
createParameters(String) - Method in class meshi.energy.hydrogenBond.HydrogenBondsParametersList
 
createParameters(String) - Method in class meshi.energy.hydrogenBond.LennardJonesParametersList
 
createParameters(String) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
createParameters(String) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameterList
 
createParameters(String) - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParametersList
 
createParameters(String) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.bond.BondParametersList
 
createParameters(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList
 
createParameters(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList
 
createParameters(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList
 
createParameters(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList
Creates a RamachandranSidechainParameters for residue type.
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList
Obsolete in RamachandranSidechainParametersList.
createParameters(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList
Creates a SmoothRotamerLibraryParameters for residue type.
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList
Obsolete in SmoothRotamerLibraryParametersList.
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.inflate.InflateParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParametersList
 
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.ParametersList
Energy term specific method to create a Parameters object from a line of the parameters file.
createParameters(String) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParametersList
 
createParameters(String) - Method in class meshi.energy.solvate.SolvateParametersList
 
createParameters(String) - Method in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
createParameters(String) - Method in class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
createParameters(String) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParametersList
 
createQuickAndDirtyTorsionList(Protein, DistanceMatrix) - Static method in class meshi.geometry.TorsionList
 
createQuickAndDirtyTorsionPairList(Protein, DistanceMatrix) - Static method in class meshi.geometry.TorsionPairList
 
createQuickAndDirtyTorsionPairList(Protein, DistanceMatrix, Filter) - Static method in class meshi.geometry.TorsionPairList
 
createR() - Static method in class meshi.util.overlap.Overlap
Building the R matrix according to equation 7
at the Kabsch paper (1976)
createTorsionList(Protein, DistanceMatrix) - Static method in class meshi.geometry.TorsionList
 
createTorsionPairList(Protein, DistanceMatrix) - Static method in class meshi.geometry.TorsionPairList
Create a torsion pair list from a protein.
createUmatrix(double[][]) - Static method in class meshi.util.overlap.Overlap
Creating the U matrix, the rotation matrix.
creator - Static variable in class meshi.molecularElements.ca.CaResidue
 
creator - Static variable in class meshi.molecularElements.extendedAtoms.BackboneResidue
 
creator - Static variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
creator - Static variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtomsCreator
 
creator - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
creator() - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
creators - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
cross123x - Variable in class meshi.geometry.Torsion
 
cross123y - Variable in class meshi.geometry.Torsion
 
cross123z - Variable in class meshi.geometry.Torsion
 
cross234x - Variable in class meshi.geometry.Torsion
 
cross234y - Variable in class meshi.geometry.Torsion
 
cross234z - Variable in class meshi.geometry.Torsion
 
CSAonly_FILES_LOCATION_PATH - Static variable in interface meshi.util.KeyWords
 
cTerm - Static variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
cType - Variable in enum meshi.parameters.ResidueType
 
cType() - Method in enum meshi.parameters.ResidueType
 
current - Variable in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
current - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
current - Variable in class meshi.geometry.DistanceList.DistanceIterator
 
current - Variable in class meshi.geometry.DistanceMatrix.RowIterator
 
current - Variable in class meshi.geometry.OldDistanceMatrix.RowIterator
 
currentMolecularSystem - Static variable in class meshi.molecularElements.atoms.MolecularSystem
 
currentMolecularSystem() - Static method in class meshi.molecularElements.atoms.MolecularSystem
 
currentResidueIndex - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
currentTemperature - Variable in class meshi.optimizers.TemperatureGenerator
 
currentTemperature() - Method in class meshi.optimizers.TemperatureGenerator
 
curv - Variable in class meshi.optimizers.LBFGS.Element
 
cutoff - Variable in class meshi.applications.hubbard.HubbardPosition
 
CUTOFF - Static variable in interface meshi.util.KeyWords
 
CUTOFF_GLY - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
CUTOFF_NON_GLY - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
CvalAtp1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
cValAtp1 - Variable in class meshi.energy.solvate.SolvateParametersList
 
CvalAtp1 - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
CvalAtp2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
cValAtp2 - Variable in class meshi.energy.solvate.SolvateParametersList
 
CvalAtp2 - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
cx - Variable in class meshi.geometry.Torsion
 
cy - Variable in class meshi.geometry.Torsion
 
cyclicMidTor - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
CYLINDER_ENERGY - Static variable in interface meshi.util.KeyWords
 
CylinderCreator - Class in meshi.symmetryComplex.energy.cylinder
This energy function penalizes atoms which are outside a given cylinder.
CylinderCreator() - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
CylinderCreator(double) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
CylinderCreator(double, double, double, Filter) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
CylinderCreator(double, double, double) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
CylinderCreator(CommandList, String, Filter) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
CylinderEnergy - Class in meshi.symmetryComplex.energy.cylinder
Cylinder energy term.
CylinderEnergy(AtomList, DistanceMatrix, ParametersList, double, Filter) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderEnergy
 
CylinderEnergyElement - Class in meshi.symmetryComplex.energy.cylinder
Responsible for energy and forces calculations of the Cylinder energy function on a single atom.
The atom's cartesian coordinates are transformed to Cylindrical Coordinates and forces are transformed back to cartesian coordinates.
CylinderEnergyElement(Atom, CylinderParameters, double) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
Constructs an energy elements for the given atom.
CylinderParameters - Class in meshi.symmetryComplex.energy.cylinder
 
CylinderParameters(double, double, double) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderParameters
 
CylinderParametersList - Class in meshi.symmetryComplex.energy.cylinder
 
CylinderParametersList() - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
CylinderParametersList(double, double, double) - Constructor for class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
Cys - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | SG
Cys(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Cys
 
cz - Variable in class meshi.geometry.Torsion
 
CZ - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
CZ - Variable in class meshi.molecularElements.extendedAtoms.Phe
 
CZ - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
CZ2 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
CZ3 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 

D

d - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
d - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Arrays for internal storage of eigenvalues.
d2 - Static variable in class meshi.geometry.DistanceMatrixBondedOnly
 
d2 - Static variable in class meshi.geometry.FreeDistance
 
d2 - Static variable in class meshi.geometry.MatrixRow
 
DahiyatImplementationConstants - Interface in meshi.energy.solvate.hydrogenBonds
See what these constants means in heading of the HydrogenBondDahiyat class.
dangleDx1 - Variable in class meshi.geometry.Angle
 
dangleDx1() - Method in class meshi.geometry.Angle
 
dangleDx2 - Variable in class meshi.geometry.Angle
 
dangleDx2() - Method in class meshi.geometry.Angle
 
dangleDx3 - Variable in class meshi.geometry.Angle
 
dangleDx3() - Method in class meshi.geometry.Angle
 
dangleDy1 - Variable in class meshi.geometry.Angle
 
dangleDy1() - Method in class meshi.geometry.Angle
 
dangleDy2 - Variable in class meshi.geometry.Angle
 
dangleDy2() - Method in class meshi.geometry.Angle
 
dangleDy3 - Variable in class meshi.geometry.Angle
 
dangleDy3() - Method in class meshi.geometry.Angle
 
dangleDz1 - Variable in class meshi.geometry.Angle
 
dangleDz1() - Method in class meshi.geometry.Angle
 
dangleDz2 - Variable in class meshi.geometry.Angle
 
dangleDz2() - Method in class meshi.geometry.Angle
 
dangleDz3 - Variable in class meshi.geometry.Angle
 
dangleDz3() - Method in class meshi.geometry.Angle
 
dAngleEnergyDAngle - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDxHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDxOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDxTheidAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDyHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDyOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDyTheidAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDzHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDzOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dAngleEnergyDzTheidAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
data - Static variable in class HomologyModeling
 
date - Variable in class HomologyModeling.TimeTerminator
 
dAtomEnergydEnvior - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
dAtomEnergydEnvior - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
dCdD - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
dCdD - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dCdD - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dCdX - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dCdX - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dCdY - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dCdY - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dCdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dCdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dCosTorsionDx1 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDx1() - Method in class meshi.geometry.Torsion
 
dCosTorsionDx2 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDx2() - Method in class meshi.geometry.Torsion
 
dCosTorsionDx3 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDx3() - Method in class meshi.geometry.Torsion
 
dCosTorsionDx4 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDx4() - Method in class meshi.geometry.Torsion
 
dCosTorsionDy1 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDy1() - Method in class meshi.geometry.Torsion
 
dCosTorsionDy2 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDy2() - Method in class meshi.geometry.Torsion
 
dCosTorsionDy3 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDy3() - Method in class meshi.geometry.Torsion
 
dCosTorsionDy4 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDy4() - Method in class meshi.geometry.Torsion
 
dCosTorsionDz1 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDz1() - Method in class meshi.geometry.Torsion
 
dCosTorsionDz2 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDz2() - Method in class meshi.geometry.Torsion
 
dCosTorsionDz3 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDz3() - Method in class meshi.geometry.Torsion
 
dCosTorsionDz4 - Variable in class meshi.geometry.Torsion
 
dCosTorsionDz4() - Method in class meshi.geometry.Torsion
 
dDistanceDx() - Method in class meshi.geometry.Distance
The derivative of the distance between atom1 & atom2 by the X coordinate of atom1.
dDistanceDx() - Method in class meshi.geometry.DistanceMirror
 
dDistanceDy() - Method in class meshi.geometry.Distance
The derivative of the distance between atom1 & atom2 by the Y coordinate of atom1.
dDistanceDy() - Method in class meshi.geometry.DistanceMirror
 
dDistanceDz() - Method in class meshi.geometry.Distance
The derivative of the distance between atom1 & atom2 by the Z coordinate of atom1.
dDistanceDz() - Method in class meshi.geometry.DistanceMirror
 
dDistanceEnergy_Ddistance - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDx - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDxHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDxOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDy - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDyHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDyOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDz - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDzHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dDistanceEnergyDzOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
de - Variable in class meshi.optimizers.TemperatureGenerator
 
dead() - Method in class meshi.geometry.Distance
 
dead() - Method in class meshi.geometry.DistanceMirror
 
dead - Variable in enum meshi.geometry.DistanceMode
 
dead - Variable in class meshi.util.Terminator
 
dead() - Method in class meshi.util.Terminator
 
debug - Static variable in class AbInitio
 
debug - Static variable in class HydrogenTest
 
debug - Variable in class meshi.applications.prediction.PredictionSequenceAlignment
A sequenceAlignment is extracted from a file whose name is referred to by the command line starting with key.
debug - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
debug - Static variable in class meshi.geometry.ArcCos
 
debug - Variable in class meshi.geometry.DistanceMatrix
 
debug - Variable in class meshi.geometry.OldDistanceMatrix
 
debug - Variable in class meshi.util.CommandList
 
debug() - Static method in class meshi.util.MeshiProgram
Gets the boolean value associated with the keyword debug.
debug - Static variable in class meshi.util.Rms
 
DebugOFF() - Method in class meshi.geometry.DistanceMatrix
Exit DistanceMatrix debug mode.
DebugOFF() - Method in class meshi.geometry.OldDistanceMatrix
Exit DistanceMatrix debug mode.
debugON() - Method in class meshi.geometry.DistanceMatrix
Enter DistanceMatrix debug mode.
debugON() - Method in class meshi.geometry.OldDistanceMatrix
Enter DistanceMatrix debug mode.
dEdD - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
dEdD - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
dEdD - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdD - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
dEdD - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
dEdD - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
dEdD - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dEdD - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dEdD - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
dEdD - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
dEdX - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
dEdX - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdX - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
dEdX - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
dEdX - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
dEdX - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dEdX - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dEdX - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
dEdXAtom(int) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdXAtom(int) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
deDxHAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
deDxHAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDxHAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDxHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
deDxHAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDxHAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDxOAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
deDxOAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDxOAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDxOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
deDxOAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDxOAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDxTheidAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dEdY - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
dEdY - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdY - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
dEdY - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
dEdY - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
dEdY - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dEdY - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dEdY - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
dEdYAtom(int) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdYAtom(int) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
deDyHAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
deDyHAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDyHAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDyHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
deDyHAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDyHAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDyOAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
deDyOAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDyOAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDyOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
deDyOAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDyOAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDyTheidAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
dEdZ - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
dEdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
dEdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
dEdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
dEdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dEdZ - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
dEdZ - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
dEdZAtom(int) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
dEdZAtom(int) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
deDzHAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
deDzHAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDzHAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDzHAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
deDzHAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDzHAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDzOAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
deDzOAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDzOAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
deDzOAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
deDzOAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDzOAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
deDzTheidAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
DEFAULT_ALLOWED_MAX_H_FACTOR - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_ALLOWED_MAX_R_FACTOR - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_BONDED_LIST_DEPTH - Static variable in class meshi.geometry.DistanceMatrix
 
DEFAULT_BONDED_LIST_DEPTH - Static variable in class meshi.geometry.OldDistanceMatrix
 
DEFAULT_BUFFER - Static variable in class meshi.geometry.DistanceMatrix
 
DEFAULT_BUFFER - Static variable in class meshi.geometry.OldDistanceMatrix
 
DEFAULT_C1 - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_C1 - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_C1 - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_C2 - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_C2 - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_C2 - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_CHAIN - Static variable in class meshi.molecularElements.ResidueIdentifier
 
DEFAULT_EDGE(double, double) - Static method in class meshi.geometry.DistanceMatrix
 
DEFAULT_EXTENDED_ALPHA_FACTOR_WOLF_SEARCH - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_EXTENDED_ALPHA_FACTOR_WOLF_SEARCH - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_EXTENDED_ALPHA_FACTOR_WOLF_SEARCH - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_INIT_STEP_STEEPEST_DECENT - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_INIT_STEP_STEEPEST_DECENT - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_INITIAL_STEP_LENGTH - Static variable in class meshi.optimizers.SteepestDecent
 
DEFAULT_M - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_MAX_ITERATION - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_MAX_ITERATION - Static variable in class meshi.optimizers.SteepestDecent
 
DEFAULT_MAX_NUM_EVALUATIONS_WOLF_SEARCH - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_MAX_NUM_EVALUATIONS_WOLF_SEARCH - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_MAX_NUM_EVALUATIONS_WOLF_SEARCH - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_MAX_NUM_KICK_STARTS - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_MAX_NUM_KICK_STARTS - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_NUM_STEP_STEEPEST_DECENT - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_NUM_STEP_STEEPEST_DECENT - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_REPORT_EVERY - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_REPORT_EVERY - Static variable in class meshi.optimizers.SteepestDecent
 
DEFAULT_RESTART_EVERY - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_RMAX - Static variable in class meshi.geometry.DistanceMatrix
 
DEFAULT_RMAX - Static variable in class meshi.geometry.OldDistanceMatrix
 
DEFAULT_STEP_SIZE_EXPENTION - Static variable in class meshi.optimizers.SteepestDecent
 
DEFAULT_STEP_SIZE_EXPENTION_STEEPEST_DECENT - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_STEP_SIZE_EXPENTION_STEEPEST_DECENT - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_STEP_SIZE_REDUCTION - Static variable in class meshi.optimizers.SteepestDecent
 
DEFAULT_STEP_SIZE_REDUCTION_STEEPEST_DECENT - Static variable in class meshi.optimizers.BFGS
 
DEFAULT_STEP_SIZE_REDUCTION_STEEPEST_DECENT - Static variable in class meshi.optimizers.LBFGS
 
DEFAULT_TOLERANCE - Static variable in class meshi.optimizers.ConjugateGradient
 
DEFAULT_TOLERANCE - Static variable in class meshi.optimizers.SteepestDecent
 
DEFAULT_USE_GAMA - Static variable in class meshi.optimizers.LBFGS
 
defaultCell - Variable in class meshi.geometry.Grid
 
defaultCell - Variable in class meshi.geometry.OldGrid
 
defaultExceptionHandler - Static variable in class meshi.util.Utils
 
defrost() - Method in class meshi.molecularElements.atoms.Atom
 
defrost() - Method in class meshi.molecularElements.atoms.AtomList
 
defrost() - Method in class meshi.molecularElements.Protein
Allow all atoms to move.
defrost() - Method in class meshi.molecularElements.Residue
 
defrostedAtoms() - Method in class meshi.molecularElements.atoms.AtomList
 
deg2rad(double) - Static method in class meshi.geometry.Angle
 
deletion(Iterator, List<HomologyModeling.Loop>, HomologyModeling.Loop, HomologyModeling.Three) - Static method in class HomologyModeling
 
deletionFromList - Variable in class meshi.energy.hydrogenBond.HBondList
 
deletions - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
DELTA_ANGLE - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
den - Variable in class meshi.geometry.Torsion
 
derivativeAng1Zero - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
derivativeAng2Zero - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
derivatives - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
derivatives[i][0] is the derivative of the HB value relative to the X coordinate of atom i.
derivatives(int, int) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
derivatives() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
det() - Method in class meshi.util.mathTools.Jama.LUDecomposition
Determinant
det() - Method in class meshi.util.mathTools.Jama.Matrix
Matrix determinant
detectAndCorrectRottenResidues(Protein) - Method in class meshi.applications.corpus.CorrectRottenRamachandrans
This correct the rotten-ramach residues as mentioned on top.
detectRottenResidues(Protein) - Method in class meshi.applications.corpus.CorrectRottenRamachandrans
This method returns an array with the residue numbers of the rotten-ramach residues.
dformat - Variable in class meshi.energy.TotalEnergy
 
dFormatSrt - Static variable in class meshi.energy.EnergyElement
 
dFormatStd - Static variable in class meshi.energy.EnergyElement
 
dGdD - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
dGdD - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
DhbAngScoreDx1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDx2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDx3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDx4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDy1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDy2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDy3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDy4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDz1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDz2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDz3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbAngScoreDz4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDx1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDx2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDx3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDx4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDy1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDy2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDy3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDy4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDz1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDz2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDz3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DhbDisScoreDz4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
dictionary - Static variable in class Pdb2Fasta
 
DICTIONARY_KEY - Static variable in interface meshi.util.KeyWords
 
DIELECTRIC_CONSTANT - Static variable in interface meshi.util.KeyWords
 
dielectricConstant - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
diff - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
diff - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
diff1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
diff1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
diff1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
diff2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
diff2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
diff2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
Differs - Class in meshi.util.filters
 
Differs(Object) - Constructor for class meshi.util.filters.Differs
 
diffSigma - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
diffSigma - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
diffSigma - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
DIFULT_HPUNISHMENT - Static variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
DIFULT_PUNISHMENT - Static variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
dis - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
dis - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dis - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
disAng1atoms12 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
disAng1atoms32 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
disAng2atoms23 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
disAng2atoms43 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
disDivaidedByDisPlusEpsilon - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
disDivaidedByDisPlusEpsilon - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
disDonorAcceptor - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
disPlusEpsilon - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
disPlusEpsilon - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
distance - Variable in class CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute
 
distance - Variable in class ColorByEnergy.DistanceFromCatalyticAttribute
 
distance - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
distance - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
distance - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
distance - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
distance - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
distance - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
distance - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
distance - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
distance - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
distance() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
distance - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
distance - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
distance - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
distance - Variable in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
distance - Variable in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
distance - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
distance - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
Distance - Class in meshi.geometry
The distance between two meshi.molecularElements.atoms
.
Distance(AtomCore, AtomCore, double, double, double, double) - Constructor for class meshi.geometry.Distance
 
distance - Variable in class meshi.geometry.Distance
The distance between atom1 & atom2
Not that the public accessability of of this variable improves computational efficiency but opens a wide door for bugs.
distance() - Method in class meshi.geometry.Distance
Get the distance between atom1 and atom2.
distance(Atom, Atom) - Method in class meshi.geometry.DistanceMatrix
Returns the Distance object of the parameters.
distance(AtomPair) - Method in class meshi.geometry.DistanceMatrix
 
distance(int, int) - Method in class meshi.geometry.DistanceMatrix
Returns the Distance object of the parameters.
distance(Atom, Atom) - Method in class meshi.geometry.DistanceMatrixBondedOnly
Returns the Distance object of the parameters.
distance(AtomPair) - Method in class meshi.geometry.DistanceMatrixBondedOnly
 
distance(int, int) - Method in class meshi.geometry.DistanceMatrixBondedOnly
 
distance() - Method in class meshi.geometry.DistanceMirror
 
distance - Static variable in class meshi.geometry.MatrixRow
 
distance(Atom, Atom) - Method in class meshi.geometry.OldDistanceMatrix
Returns the Distance object of the parameters.
distance(AtomPair) - Method in class meshi.geometry.OldDistanceMatrix
 
distance(int, int) - Method in class meshi.geometry.OldDistanceMatrix
Returns the Distance object of the parameters.
distance(CaResidue) - Method in class meshi.molecularElements.ca.CaResidue
 
DISTANCE1 - Variable in class meshi.geometry.Angle
 
distance1 - Variable in class meshi.geometry.Torsion
 
DISTANCE2 - Variable in class meshi.geometry.Angle
 
distance2 - Variable in class meshi.geometry.Torsion
 
distance3 - Variable in class meshi.geometry.Torsion
 
DISTANCE_AS_NEIGHBOUR_CHAINS - Static variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
DISTANCE_BetweenLoops - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
DISTANCE_CONSTRAINT_PCA - Static variable in interface meshi.util.KeyWords
 
DISTANCE_CONSTRAINTS_ENERGY - Static variable in interface meshi.util.KeyWords
 
DISTANCE_CONSTRAINTS_MASK - Static variable in interface meshi.util.KeyWords
 
DISTANCE_FROM_CATALYTIC_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
DISTANCE_FROM_CENTROID_ENERGY - Static variable in interface meshi.util.KeyWords
 
distanceArray - Variable in class meshi.geometry.DistanceMatrixBondedOnly
 
distanceAttributes1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
distanceAttributes2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
DistanceConstrainsDialog - Class in meshi.applications.prediction.homology.gui
 
DistanceConstrainsDialog() - Constructor for class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
DistanceConstrainsDialogLayout - Class in meshi.applications.prediction.homology.gui
 
DistanceConstrainsDialogLayout() - Constructor for class meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout
 
distanceEnergy - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
distanceFrom(Coordinates) - Method in class meshi.geometry.Coordinates
 
distanceFrom(Atom) - Method in class meshi.molecularElements.atoms.Atom
The distance between this atom and the parameter.
DistanceList - Class in meshi.geometry
 
DistanceList(int) - Constructor for class meshi.geometry.DistanceList
 
DistanceList(int, Filter) - Constructor for class meshi.geometry.DistanceList
 
DistanceList.DistanceIterator - Class in meshi.geometry
 
DistanceList.DistanceIterator(Distance[], int) - Constructor for class meshi.geometry.DistanceList.DistanceIterator
 
distanceMatrix - Static variable in class HeliumClusterMinimization
of the atoms.
distanceMatrix - Variable in class meshi.energy.hydrogenBond.HBondList
 
distanceMatrix - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
distanceMatrix - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
distanceMatrix - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
distanceMatrix - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
distanceMatrix - Variable in class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
 
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergy
 
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergy
The constructor associates any bond with its parameters.
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
distanceMatrix - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergy
 
distanceMatrix - Variable in class meshi.energy.TotalEnergy
 
distanceMatrix() - Method in class meshi.energy.TotalEnergy
 
distanceMatrix - Variable in class meshi.geometry.Angle
 
DistanceMatrix - Class in meshi.geometry
Where all the headache of distances is handled.
DistanceMatrix(MolecularSystem) - Constructor for class meshi.geometry.DistanceMatrix
 
DistanceMatrix(MolecularSystem, double, double, double, int) - Constructor for class meshi.geometry.DistanceMatrix
 
distanceMatrix - Variable in class meshi.geometry.Torsion
 
DistanceMatrix.Indicator - Class in meshi.geometry
 
DistanceMatrix.Indicator() - Constructor for class meshi.geometry.DistanceMatrix.Indicator
 
DistanceMatrix.RowIterator - Class in meshi.geometry
 
DistanceMatrix.RowIterator() - Constructor for class meshi.geometry.DistanceMatrix.RowIterator
 
DistanceMatrixBondedOnly - Class in meshi.geometry
 
DistanceMatrixBondedOnly(MolecularSystem, int) - Constructor for class meshi.geometry.DistanceMatrixBondedOnly
 
DistanceMatrixBondedOnly.DistanceComparator - Class in meshi.geometry
 
DistanceMatrixBondedOnly.DistanceComparator() - Constructor for class meshi.geometry.DistanceMatrixBondedOnly.DistanceComparator
 
DistanceMatrixCaOnly - Class in meshi.geometry
A Distance Matrix specifically tailored for Calpha model.
DistanceMatrixCaOnly(MolecularSystem, double, int) - Constructor for class meshi.geometry.DistanceMatrixCaOnly
 
DistanceMatrixNoImageAtoms - Class in meshi.symmetryComplex.geometryImage
 
DistanceMatrixNoImageAtoms(MolecularSystem, double, double, double, int, ResidueList) - Constructor for class meshi.symmetryComplex.geometryImage.DistanceMatrixNoImageAtoms
 
DistanceMatrixWhichUpdateOnlyMovingAtoms - Class in meshi.molecularElements.allAtoms
 
DistanceMatrixWhichUpdateOnlyMovingAtoms(AtomList, double, int) - Constructor for class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
DistanceMirror - Class in meshi.geometry
 
DistanceMirror(Distance) - Constructor for class meshi.geometry.DistanceMirror
 
DistanceMode - Enum in meshi.geometry
 
DistanceMode(boolean, boolean, boolean, boolean, boolean) - Constructor for enum meshi.geometry.DistanceMode
 
distanceValue() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
distanceValue - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
distanceValue2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
distEnergy - Variable in class meshi.applications.corpus.LoopResults
 
DIVERSITY_RMS_IN_LIB - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
dm - Variable in class meshi.energy.CooperativeEnergyTerm
 
dm - Variable in class meshi.energy.hydrogenBond.HBondList.IsAlive
 
dm - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
dm - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
dm - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
DMinusSig - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
DMinusSig3 - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
DMinusSig4 - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
doIter() - Method in class meshi.applications.hubbard.HubbardPosition
 
doneDistanceConstrainsWin - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
doneInflateParameters - Variable in class meshi.applications.prediction.homology.gui.InflateParametersDialog
 
doneMinimizeParametersFullDialog - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
doneMiniParaShort - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
doneParaForChainCompleteWin - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
doneWeightsForEnergyTerms - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
doNothing() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
doNothing - Static variable in class meshi.util.Utils
 
DoNothingExceptionHandler - Class in meshi.util
 
DoNothingExceptionHandler() - Constructor for class meshi.util.DoNothingExceptionHandler
 
doNotUpdateNonBondedList() - Method in class meshi.geometry.DistanceMatrix
 
doNotUpdateNonBondedList() - Method in class meshi.geometry.OldDistanceMatrix
 
dot(double, double, double, double, double, double) - Static method in class meshi.geometry.Torsion
 
double2DToMatrix(double[][]) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
double2DToMatrix(double[][]) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
doubleValue() - Method in class meshi.util.Pair
 
DpMatrix - Class in meshi.sequences.aligner
Created by IntelliJ IDEA.
DpMatrix(Sequence, Sequence, CellScorer) - Constructor for class meshi.sequences.aligner.DpMatrix
 
DRESSER_FRAGMENTS - Static variable in interface meshi.util.KeyWords
 
DresserFullFrag - Class in meshi.geometry.fragments
 
DresserFullFrag(String) - Constructor for class meshi.geometry.fragments.DresserFullFrag
 
dressFrag(AtomList) - Method in class meshi.geometry.fragments.DresserFullFrag
 
dressProt(AtomList) - Method in class meshi.geometry.fragments.DresserFullFrag
 
dsigmCa1dx1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
dsigmCa1dx1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
dsigmCa1dx1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa1dx2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa1dy1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
dsigmCa1dy1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
dsigmCa1dy1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa1dy2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa1dz1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
dsigmCa1dz1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
dsigmCa1dz1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa1dz2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa2dx1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
dsigmCa2dx1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
dsigmCa2dx1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa2dx2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa2dy1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
dsigmCa2dy1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
dsigmCa2dy1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa2dy2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa2dz1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
dsigmCa2dz1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
dsigmCa2dz1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
dsigmCa2dz2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
DsigmCosAng1Dx1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dx2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dx3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dy1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dy2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dy3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dz1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dz2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng1Dz3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dx2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dx3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dx4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dy2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dy3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dy4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dz2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dz3 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
DsigmCosAng2Dz4 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
dSplineDCNC - Variable in class meshi.energy.solvate.SolvateEnergy
 
dSplineDHBC - Variable in class meshi.energy.solvate.SolvateEnergy
 
dSplineVals - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
dssp - Variable in class HydrogenTest.ResWithSSFilter
 
DSSP - Class in meshi.util.dssp
 
DSSP(String) - Constructor for class meshi.util.dssp.DSSP
 
dsspFileName - Static variable in class HydrogenTest
 
dTorsionDx1 - Variable in class meshi.geometry.Torsion
 
dTorsionDx1() - Method in class meshi.geometry.Torsion
 
dTorsionDx2 - Variable in class meshi.geometry.Torsion
 
dTorsionDx2() - Method in class meshi.geometry.Torsion
 
dTorsionDx3 - Variable in class meshi.geometry.Torsion
 
dTorsionDx3() - Method in class meshi.geometry.Torsion
 
dTorsionDx4 - Variable in class meshi.geometry.Torsion
 
dTorsionDx4() - Method in class meshi.geometry.Torsion
 
dTorsionDy1 - Variable in class meshi.geometry.Torsion
 
dTorsionDy1() - Method in class meshi.geometry.Torsion
 
dTorsionDy2 - Variable in class meshi.geometry.Torsion
 
dTorsionDy2() - Method in class meshi.geometry.Torsion
 
dTorsionDy3 - Variable in class meshi.geometry.Torsion
 
dTorsionDy3() - Method in class meshi.geometry.Torsion
 
dTorsionDy4 - Variable in class meshi.geometry.Torsion
 
dTorsionDy4() - Method in class meshi.geometry.Torsion
 
dTorsionDz1 - Variable in class meshi.geometry.Torsion
 
dTorsionDz1() - Method in class meshi.geometry.Torsion
 
dTorsionDz2 - Variable in class meshi.geometry.Torsion
 
dTorsionDz2() - Method in class meshi.geometry.Torsion
 
dTorsionDz3 - Variable in class meshi.geometry.Torsion
 
dTorsionDz3() - Method in class meshi.geometry.Torsion
 
dTorsionDz4 - Variable in class meshi.geometry.Torsion
 
dTorsionDz4() - Method in class meshi.geometry.Torsion
 
dummy - Static variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
dummy() - Method in class meshi.molecularElements.Residue
 
dunbrack - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
DunbrackLib - Class in meshi.geometry.rotamers
Reading and working with Dunbrack's backbone dependent rotamer library.
DunbrackLib(CommandList) - Constructor for class meshi.geometry.rotamers.DunbrackLib
The default constructor reads up to 15 rotamers or until they cover 98% of the cases.
DunbrackLib(CommandList, double, int) - Constructor for class meshi.geometry.rotamers.DunbrackLib
The constructors needs 2 parameters to decide how many rotamers to load from the library.
DunbrackLib(String) - Constructor for class meshi.geometry.rotamers.DunbrackLib
 
duplicateInAnewMolecularSystem(AtomList) - Static method in class meshi.util.Utils
 
DX - Variable in class meshi.energy.CooperativeEnergyTerm
 
DX - Static variable in class meshi.energy.EnergyElement
 
dx - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
DX - Static variable in class meshi.energy.TotalEnergy
 
dx - Variable in class meshi.geometry.Distance
atom1.x - atom2.x Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.
dx() - Method in class meshi.geometry.Distance
 
dx - Static variable in class meshi.geometry.DistanceMatrixBondedOnly
 
dx() - Method in class meshi.geometry.DistanceMirror
 
dx1 - Variable in class meshi.geometry.Torsion
 
dy - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dy - Variable in class meshi.geometry.Distance
atom1.y - atom2.y Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.
dy() - Method in class meshi.geometry.Distance
 
dy - Static variable in class meshi.geometry.DistanceMatrixBondedOnly
 
dy() - Method in class meshi.geometry.DistanceMirror
 
dy1 - Variable in class meshi.geometry.Torsion
 
dz - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
dz - Variable in class meshi.geometry.Distance
atom1.z - atom2.z Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.
dz() - Method in class meshi.geometry.Distance
 
dz - Static variable in class meshi.geometry.DistanceMatrixBondedOnly
 
dz() - Method in class meshi.geometry.DistanceMirror
 
dz1 - Variable in class meshi.geometry.Torsion
 

E

e - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
e - Variable in class meshi.optimizers.LBFGS
 
e - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Arrays for internal storage of eigenvalues.
e0 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
edge - Static variable in class meshi.geometry.DistanceMatrix
 
edge - Variable in class meshi.geometry.Grid
 
edge - Static variable in class meshi.geometry.OldDistanceMatrix
 
edge - Variable in class meshi.geometry.OldGrid
 
EDM_ENERGY - Static variable in interface meshi.util.KeyWords
 
EDM_ENERGY_FILE_NAME - Static variable in interface meshi.util.KeyWords
 
EDMEnergy - Class in meshi.symmetryComplex.energy.edmEnergy
 
EDMEnergy(Protein, EDMEnergyParametersList, double, String, Filter) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergy
 
EDMEnergyCreator - Class in meshi.symmetryComplex.energy.edmEnergy
The EDM energy class loads a splined polynomial for an electron density map and attempts to fit the protein to that map.
EDMEnergyCreator() - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator
 
EDMEnergyCreator(double) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator
 
EDMEnergyCreator(Filter) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator
 
EDMEnergyCreator(double, Filter) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator
 
EDMEnergyElement - Class in meshi.symmetryComplex.energy.edmEnergy
 
EDMEnergyElement(Atom, EDMEnergyParameters, double) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
 
EDMEnergyParameters - Class in meshi.symmetryComplex.energy.edmEnergy
A dummy parameters class that always includes a splined polynomial.
EDMEnergyParameters(EDMSplinedPolynomial) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParameters
 
EDMEnergyParametersList - Class in meshi.symmetryComplex.energy.edmEnergy
 
EDMEnergyParametersList(String) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParametersList
 
EDMSplinedPolynomial - Class in meshi.symmetryComplex.energy.edmEnergy
 
EDMSplinedPolynomial(double[][], double[]) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
Create a new EDMSplinedPolynomial from parameters.
EDMSplinedPolynomial(String) - Constructor for class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
Create a new EDMSplinedPolynomial from a file.
eI - Variable in class meshi.optimizers.WolfConditionLineSearch
 
eI1 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
eig() - Method in class meshi.util.mathTools.Jama.Matrix
Eigenvalue Decomposition
eigenv - Static variable in class meshi.util.overlap.Overlap
 
EigenvalueDecomposition - Class in meshi.util.mathTools.Jama
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class meshi.util.mathTools.Jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
eigenVectors - Static variable in class meshi.util.overlap.Overlap
 
ELECTROSTATICS - Static variable in interface meshi.util.KeyWords
 
ELECTROSTATICS_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
element - Variable in enum meshi.parameters.AtomType
 
Element - Enum in meshi.parameters
 
Element() - Constructor for enum meshi.parameters.Element
 
elementEvalCounter - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
elementEvalCounter - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
elements - Static variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
elements - Static variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
elements - Static variable in class meshi.energy.templateEnergy.TemplateEnergy
 
elementsList - Variable in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
 
elementsList() - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
 
emptyBonded() - Method in class meshi.molecularElements.atoms.Atom
 
end - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
end - Variable in class meshi.energy.solvate.SigmaParameters
 
END - Static variable in interface meshi.util.KeyWords
 
endAlphaALL - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
endAlphaCOIL - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
endAlphaHELIX - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
endAlphaHELIX - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
endAlphaSHEET - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
endAlphaSHEET - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
endDis - Variable in class meshi.geometry.fragments.DresserFullFrag
 
energies - Variable in class meshi.applications.corpus.Corpus
 
energy - Static variable in class HeliumClusterMinimization
function to minimize;
energy - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
energy - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
energy - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
energy() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
energy - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
energy - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
energy - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
energy - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
energy - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
energy - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
energy - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
energy - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
energy - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
energy() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
energy - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
energy - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
energy() - Method in class meshi.energy.TotalEnergy
 
energy - Variable in class meshi.molecularElements.atoms.Atom
 
energy() - Method in class meshi.molecularElements.atoms.Atom
 
energy - Variable in class meshi.optimizers.LineSearch
 
energy - Variable in class meshi.optimizers.MCM
 
energy - Variable in class meshi.optimizers.Optimizer
 
energy() - Method in class meshi.optimizers.Optimizer
 
energy - Variable in class meshi.optimizers.Perturbation
 
energy - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
energy0 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
energy1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
EnergyCreator - Class in meshi.energy
Factory classes that generate energy terms.
EnergyCreator(Key) - Constructor for class meshi.energy.EnergyCreator
Constructs an energy creator object.
EnergyCreator(Key, CommandList) - Constructor for class meshi.energy.EnergyCreator
Constructs an energy creator object.
EnergyCreator(double) - Constructor for class meshi.energy.EnergyCreator
Construct a somewhat degenerate creator object that cannot read commands from the commands list.
energyCreators(CommandList) - Static method in class EnergyStatistics
 
energyCreators(CommandList) - Static method in class EnergyStatisticsForAtom
 
energyCreators - Static variable in class TestElectrostatics
 
energyCreators1(CommandList) - Static method in class Refine
 
energyCreators2(CommandList, ResidueAlignment) - Static method in class Refine
 
energyCreatorsAll(CommandList) - Static method in class HomologyModeling
 
energyCreatorsAllTetherOriginalAtoms(CommandList, ResidueAlignment) - Static method in class HomologyModeling
 
energyCreatorsBondedTermsEVandRamachandran - Static variable in class HomologyModeling
 
energyCreatorsBondedTermsOnly - Static variable in class HomologyModeling
 
energyCreatorsBondedTermsPlusEV - Static variable in class HomologyModeling
 
EnergyElement - Class in meshi.energy
The essence of an energy term - its application to a minimal set of atoms.
EnergyElement() - Constructor for class meshi.energy.EnergyElement
 
energyElement - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
energyElement - Variable in class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
Must be initialized on subclass construction.
energyNames - Variable in class meshi.applications.corpus.Corpus
 
EnergyStatistics - Class in <Unnamed>
 
EnergyStatistics() - Constructor for class EnergyStatistics
 
EnergyStatisticsForAtom - Class in <Unnamed>
Created by IntelliJ IDEA.
EnergyStatisticsForAtom() - Constructor for class EnergyStatisticsForAtom
 
energyTerms - Variable in class meshi.energy.TotalEnergy
 
energyTerms() - Method in class meshi.energy.TotalEnergy
 
energyTermsDistanceLists - Variable in class meshi.geometry.DistanceMatrix
List of DistanceLists Every DistanceList contains distances needed for one EnergyTerm, selected by its filter For example: - Distances of good hydrogen bonds candidate that were added in the current update opperation - Applicable distances between nonBonded C-N candidate that were added in the current update opperation
energyTermsDistanceLists() - Method in class meshi.geometry.DistanceMatrix
 
energyTermsDistanceLists - Variable in class meshi.geometry.OldDistanceMatrix
List of DistanceLists Every DistanceList contains distances needed for one EnergyTerm, selected by its filter For example: - Distances of good hydrogen bonds candidate that were added in the current update opperation - Applicable distances between nonBonded C-N candidate that were added in the current update opperation
energyTermsDistanceLists() - Method in class meshi.geometry.OldDistanceMatrix
 
energyValues - Variable in class meshi.energy.TotalEnergy
 
energyValues() - Method in class meshi.energy.TotalEnergy
 
ep - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
 
ep - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParametersList
 
eps - Static variable in class meshi.util.overlap.Overlap
 
EPSILON - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
epsilon - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
epsilon - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
epsilon - Variable in class meshi.energy.hydrogenBond.LennardJonesParameters
 
epsilon - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
EPSILON - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
EPSILON - Static variable in class meshi.symmetryComplex.transformations.Matrix1D
 
equals(Object, Object) - Method in class HomologyModeling.LoopComperator
 
equals(Object, Object) - Method in class meshi.applications.prediction.AbitSmarterLoopBuilder.LoopComperator
 
equals(Object) - Method in class meshi.geometry.Coordinates
 
equals(Object) - Method in class meshi.molecularElements.atoms.AtomPair
 
equals(Object) - Method in class meshi.molecularElements.Residue
 
equals(Object) - Method in class meshi.molecularElements.ResidueIdentifier
Returns true if and only if this ResidueIdentifier is equal to some other object.
equals(Object) - Method in class meshi.sequences.SequenceAlignmentCell
 
equals(Object) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
equals(Object) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
equals(Matrix) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
Equals - Class in meshi.util.filters
 
Equals(Object) - Constructor for class meshi.util.filters.Equals
 
equals(Object, Object) - Static method in class meshi.util.Utils
Static version of equals.
equivalent(Torsion) - Method in class meshi.geometry.Torsion
 
equivalentExists(Torsion) - Method in class meshi.geometry.TorsionList
 
esp - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParameters
 
evalCounter - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
evalCounter - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
evaluate() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
evaluate() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
evaluate() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
evaluate() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
evaluate() - Method in class meshi.energy.AbstractEnergy
Evaluates the energy term and update the derivatives.
evaluate() - Method in class meshi.energy.EnergyElement
 
evaluate() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
evaluate(double) - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
evaluate() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
evaluate() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
evaluate() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
energy calculation and atom forces updating.
evaluate(double) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
evaluate() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
evaluate() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
evaluate() - Method in class meshi.energy.linearRG.LinearRgEnergy
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
Evaluates energy for each distance
evaluate(boolean) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
evaluate(double) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
Calculate value of polynomial spline and first derivative for given distance value.
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
evaluate(boolean) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
evaluate(boolean) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
evaluate(boolean) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
evaluate - 1) Invokes updateEnergy() - updates the energy, 2) Invokes updateAtoms() - updates the atoms' position.
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
evaluate(boolean) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVol
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolOLD
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
evaluate() - Method in class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
Evaluates energy for each distance
evaluate() - Method in class meshi.energy.RG.RgEnergy
 
evaluate() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
evaluate(boolean, double, double) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
Angle energy calculation and atom forces updating.
evaluate() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
Angle energy calculation and atom forces updating.
evaluate() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
evaluate(boolean) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
evaluate(boolean) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParameters
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
evaluate(boolean) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
evaluate(boolean) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi0
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi1
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi2
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi3
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi4
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
evaluates parameters for residue torsions.
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi0
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi1
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi2
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi3
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi4
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi0
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi1
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi2
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi3
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi4
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
evaluates parameters for residue torsions.
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi0
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi1
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi2
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi3
 
evaluate(int, ResidueTorsions) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi4
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
evaluate() - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
Evaluates the current value of the energy function and update the derivatives.
evaluate() - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
evaluate() - Method in class meshi.energy.solvate.SolvateEnergy
Calculates Esolv with the weights given in the constructor.
evaluate(boolean, double, double, double) - Method in class meshi.energy.solvate.SolvateEnergy
Calculates Esolv with the weights you give as parameters!
evaluate() - Method in class meshi.energy.solvateRot1.SolvateRot1Energy
 
evaluate(boolean) - Method in class meshi.energy.solvateRot1.SolvateRot1Energy
 
evaluate() - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
evaluate() - Method in class meshi.energy.templateEnergy.TemplateEnergyElement
 
evaluate() - Method in class meshi.energy.TotalEnergy
 
evaluate() - Method in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
Calculates the cylinder energy and updates forces on the atom.
evaluate() - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
 
evaluate(int, double...) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParameters
Return value of polynomial at given points, derive given variable.
evaluate() - Method in class meshi.symmetryComplex.energy.SymmetryEnergyElement
 
evaluateAtoms() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
evaluateAtoms() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
evaluateAtoms() - Method in class meshi.energy.AbstractEnergy
Evaluates the energy term and devides the energy between the atoms.
evaluateAtoms() - Method in class meshi.energy.EnergyElement
 
evaluateAtoms() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
evaluateAtoms() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
evaluateAtoms() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
evaluateAtoms() - Method in class meshi.energy.linearRG.LinearRgEnergy
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
Describe evaluateAtoms method here.
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
 
evaluateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
Describe evaluateAtoms method here.
evaluateAtoms() - Method in class meshi.energy.RG.RgEnergy
 
evaluateAtoms() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
evaluateAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
evaluateAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
evaluateAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
evaluateAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
evaluateAtoms() - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
 
evaluateAtoms() - Method in class meshi.energy.solvate.SolvateEnergy
 
evaluateAtoms() - Method in class meshi.energy.solvateRot1.SolvateRot1Energy
 
evaluateAtoms() - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
evaluateAtoms() - Method in class meshi.energy.TotalEnergy
 
evaluatedAtom - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
evaluatedX - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
evaluatedY - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
evaluatedZ - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
evaluateElement(Distance, boolean) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
evenBreaks - Variable in class meshi.util.mathTools.Spline1D
 
evenBreaks - Variable in class meshi.util.mathTools.Spline2D
 
evEnergy - Variable in class meshi.applications.corpus.BasicLoopResult
 
evEnergy - Variable in class meshi.applications.corpus.LoopResults
 
event(double) - Method in class meshi.util.histogram.Histogram
 
EVRot1BBCreator - Class in meshi.energy.pairwiseNonBondedTerms.evRot1BB
 
EVRot1BBCreator(double, double[][], double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBCreator
 
EVRot1BBCreator(double[][], double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBCreator
 
EVRot1BBEnergy - Class in meshi.energy.pairwiseNonBondedTerms.evRot1BB
 
EVRot1BBEnergy() - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
EVRot1BBEnergy(AtomList, DistanceMatrix, EVRot1BBParameterList, double[][], double, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
EVRot1BBParameterList - Class in meshi.energy.pairwiseNonBondedTerms.evRot1BB
 
EVRot1BBParameterList(String) - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameterList
 
EVRot1BBParameters - Class in meshi.energy.pairwiseNonBondedTerms.evRot1BB
 
EVRot1BBParameters() - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
EVRot1BBParameters(StringTokenizer) - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
EVRot1BBParameters.isA - Class in meshi.energy.pairwiseNonBondedTerms.evRot1BB
 
EVRot1BBParameters.isA() - Constructor for class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters.isA
 
ExceptionHandler - Interface in meshi.util
 
EXCLUDED_VOL - Static variable in interface meshi.util.KeyWords
 
EXCLUDED_VOL_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
excludedProteinsFromUngapped - Variable in class meshi.applications.corpus.Corpus
 
ExcludedVol - Class in meshi.energy.pairwiseNonBondedTerms.excludedVol
 
ExcludedVol - Class in meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
ExcludedVol() - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
 
ExcludedVol(DistanceMatrix, double, double, Filter, double[][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
 
ExcludedVol() - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVol
 
ExcludedVol(DistanceMatrix, ExcludedVolParametersList, int, double, double, Filter) - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVol
 
excludedVolCreator - Static variable in class Beautify
 
ExcludedVolCreator - Class in meshi.energy.pairwiseNonBondedTerms.excludedVol
 
ExcludedVolCreator - Class in meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
ExcludedVolCreator(double, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
ExcludedVolCreator(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
ExcludedVolCreator() - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
ExcludedVolCreator(Filter, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
ExcludedVolCreator(double, int) - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
ExcludedVolCreator(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
ExcludedVolCreator() - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
ExcludedVolCreatorOLD - Class in meshi.energy.pairwiseNonBondedTerms.excludedVolOLD
 
ExcludedVolCreatorOLD(double, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
ExcludedVolCreatorOLD(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
ExcludedVolCreatorOLD() - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
ExcludedVolCreatorOLD(Filter, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
ExcludedVolEnergyElement - Class in meshi.energy.pairwiseNonBondedTerms.excludedVol
 
ExcludedVolEnergyElement - Class in meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
ExcludedVolEnergyElement() - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
ExcludedVolEnergyElement(DistanceMatrix, double, double, double[][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
ExcludedVolEnergyElement() - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
ExcludedVolEnergyElement(ExcludedVolParametersList, DistanceMatrix, int, double, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
ExcludedVolEnergyElementOLD - Class in meshi.energy.pairwiseNonBondedTerms.excludedVolOLD
 
ExcludedVolEnergyElementOLD() - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
ExcludedVolEnergyElementOLD(DistanceMatrix, double, double, double[][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
ExcludedVolOLD - Class in meshi.energy.pairwiseNonBondedTerms.excludedVolOLD
 
ExcludedVolOLD() - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolOLD
 
ExcludedVolOLD(DistanceMatrix, double, double, Filter, double[][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolOLD
 
ExcludedVolParameters - Class in meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
ExcludedVolParameters() - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
ExcludedVolParameters(StringTokenizer) - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
ExcludedVolParameters.isA - Class in meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
ExcludedVolParameters.isA() - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters.isA
 
ExcludedVolParametersList - Class in meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
ExcludedVolParametersList(String) - Constructor for class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParametersList
 
excludedVolumeWeight - Static variable in class meshi.util.Scmod
 
expandToSquareFour(double[][]) - Method in class meshi.symmetryComplex.transformations.Transformation
 
extendAlphaFactor - Variable in class meshi.optimizers.WolfConditionLineSearch
 
extendAlphaFactorWolfSearch - Variable in class meshi.optimizers.BFGS
 
extendAlphaFactorWolfSearch - Variable in class meshi.optimizers.ConjugateGradient
 
extendAlphaFactorWolfSearch - Variable in class meshi.optimizers.LBFGS
 
ExtendedAtomsProtein - Class in meshi.molecularElements.extendedAtoms
An extended atoms model of a protein.
ExtendedAtomsProtein(String, CommandList) - Constructor for class meshi.molecularElements.extendedAtoms.ExtendedAtomsProtein
The parameter is expected to be a PDB formatted file.
ExtendedAtomsProtein(String, CommandList, List<String>) - Constructor for class meshi.molecularElements.extendedAtoms.ExtendedAtomsProtein
 
extendedCaEnergyCreators - Static variable in class Beautify
 
extendedDistance - Static variable in class Beautify
 
ExtractChain - Class in <Unnamed>
 
ExtractChain() - Constructor for class ExtractChain
 
extractCoordinatesOfRes(Residue, double[][]) - Static method in class meshi.applications.corpus.Corpus
 
extractResidueEnergy(Protein, double[][], TotalEnergy, AbstractEnergy, int) - Static method in class ChooseTemplate
 
extractResidueEnergy(Protein, double[][], TotalEnergy, AbstractEnergy, int) - Static method in class ModelRanker
 

F

f(Object) - Method in class meshi.util.formats.Fdouble
 
f(double) - Method in class meshi.util.formats.Fdouble
 
f(Object) - Method in class meshi.util.formats.Fint
 
f(int) - Method in class meshi.util.formats.Fint
 
f(Object) - Method in class meshi.util.formats.Format
 
f2a(String) - Static method in class meshi.util.file.File2StringArray
 
factor - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
factor - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
factor - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
factor - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
factor - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
factor - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
factor1 - Variable in class meshi.geometry.Torsion
 
factor4 - Variable in class meshi.geometry.Torsion
 
FACTOR_LARGE_CONTIG_RMS_CUTOFF_IN_OVERLAP - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
failToBuild - Variable in class meshi.geometry.Grid
 
failToBuild() - Method in class meshi.geometry.Grid
 
failToBuild - Variable in class meshi.geometry.OldGrid
 
failToBuild() - Method in class meshi.geometry.OldGrid
 
FAR_AWAY - Static variable in class Beautify
 
FastaList - Class in meshi.sequences
 
FastaList(String) - Constructor for class meshi.sequences.FastaList
 
FastaReader - Class in aligner
Text Files: read, write:

this class covers some importent topics of cs such as text-files:
Note: this code contains a wrong exception handling!!
FastaReader() - Constructor for class aligner.FastaReader
 
FastaReader(String) - Constructor for class aligner.FastaReader
 
Fdouble - Class in meshi.util.formats
 
Fdouble(int, int, int) - Constructor for class meshi.util.formats.Fdouble
 
fdouble(double, int, int) - Static method in class meshi.util.formats.Format
 
fdoubleL(double, int, int) - Static method in class meshi.util.formats.Format
 
fdoubleR(double, int, int) - Static method in class meshi.util.formats.Format
 
FIELD - Variable in class meshi.util.formats.Format
 
fifthWordDouble() - Method in class meshi.util.Command
 
File2StringArray - Class in meshi.util.file
 
File2StringArray() - Constructor for class meshi.util.file.File2StringArray
 
fileName - Static variable in class meshi.applications.corpus.MergeCorpora
A string with the name of the pdb file to minimize.
fileName - Variable in class meshi.sequences.SequenceList
 
fileName() - Method in class meshi.sequences.SequenceList
 
fileName - Variable in class meshi.util.dssp.DSSP
 
fileName() - Method in class meshi.util.file.MeshiLineReader
 
FileToString - Class in aligner
Created by IntelliJ IDEA.
FileToString() - Constructor for class aligner.FileToString
 
FileToString(String) - Constructor for class aligner.FileToString
 
filter - Static variable in class meshi.applications.prediction.OriginalAtom
 
filter - Static variable in class meshi.energy.AbstractEnergy
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVol
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolOLD
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
 
filter - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
filter - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
filter - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherCreator
 
filter - Variable in class meshi.geometry.DistanceList
 
filter(Filter) - Method in class meshi.geometry.TorsionList
 
filter(Filter) - Method in class meshi.geometry.TorsionPairList
 
filter(Filter) - Method in class meshi.molecularElements.atoms.AtomList
Extracts the list elements that pass the filter.
filter(Filter) - Method in class meshi.molecularElements.atoms.AtomPairList
 
filter(Filter) - Method in class meshi.molecularElements.Chain
Extracts the residues accepted by the filter.
filter(Filter) - Method in class meshi.molecularElements.ChainList
 
filter(Filter) - Method in class meshi.molecularElements.ResidueList
Extracts the residues accepted by the filter.
filter - Static variable in class meshi.PDB.PdbLineATOM
 
filter(Filter) - Method in class meshi.sequences.ResidueAlignment
 
filter - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
filter - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator
 
filter - Static variable in class meshi.util.filters.BackboneFilter
 
filter - Static variable in class meshi.util.filters.CaFilter
 
Filter - Interface in meshi.util.filters
 
filter - Variable in class meshi.util.histogram.Histogram.RepresentativesIterator
 
filter(Filter) - Method in class meshi.util.string.StringList
 
filter(ArrayList, Filter, ArrayList) - Static method in class meshi.util.Utils
 
filter(DistanceList, Filter, DistanceList) - Static method in class meshi.util.Utils
 
filter(ModelDataList, ModelData, double) - Static method in class SelectModels
 
filterCompleteResidues() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
A method to filter residues that have all torsions
filteredEnergy(double) - Method in class meshi.energy.TotalEnergy
 
filterEndsWith(String) - Method in class meshi.util.string.StringList
 
filterEndsWith(StringList) - Method in class meshi.util.string.StringList
 
filterEquivalents() - Method in class meshi.geometry.TorsionList
 
filterGrep(String) - Method in class meshi.util.string.StringList
 
filterGrep(StringList) - Method in class meshi.util.string.StringList
 
filterIncompleteResidues() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
A method to filter for incomplete residues.
filterPhiPsiResidues() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
A method to filter residues that have {PHI,PSI} torsions.
filters - Variable in class meshi.symmetryComplex.utils.GJFilters.AndFilter
 
filterStartsWith(String) - Method in class meshi.util.string.StringList
 
filterStartsWith(StringList) - Method in class meshi.util.string.StringList
 
FINAL_TEMPERATURE - Static variable in interface meshi.util.KeyWords
 
finalTemperature - Variable in class meshi.optimizers.TemperatureGenerator
 
find(AtomList, int) - Method in class meshi.geometry.fragments.DresserFullFrag
 
find(AtomList, String, int) - Method in class meshi.geometry.fragments.DresserFullFrag
 
find(AtomList, BBatom) - Static method in class meshi.molecularElements.Residue
 
find(AtomList, String) - Static method in class meshi.molecularElements.Residue
 
find_best_conformation(int) - Method in class meshi.applications.hubbard.HubbardPosition
 
findBin(double[], double) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
Find break index (bin) for torsion angle.
findBin(double[], double) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
Find break index (bin) for value.
findBondByPolars(Atom, Atom) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
This method returns a pointer to the hydrogen bond that exists between two POLAR atoms (hydrogens are not consider polar) If no such object exists then null is returned.
findBondByPolars(int, int) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
findCriminalAtom() - Method in class meshi.energy.TotalEnergy
Searching for a `criminal' atom
findCriminalEnergyTerm(Atom) - Method in class meshi.energy.TotalEnergy
Searching for a `criminal' energy term , with specific atom
findDisDist(int) - Method in class meshi.applications.corpus.Corpus
Find the distributaion of distances between ends.
findEigenval(double[]) - Static method in class meshi.util.overlap.Overlap
In order to find the 3 eigenValues of P, which is
a positive definite matrix, we are solving a cubic equation
findEigenvec1(double[]) - Static method in class meshi.util.overlap.Overlap
Incase all 3 eigenvalues are different (most cases) in order to derive the eigenvectors we use the Gauss elimination procedure with scaled pivoting
findEigenvec2(double[]) - Static method in class meshi.util.overlap.Overlap
FIND EIGEN VEC 2
findInd(double) - Method in class meshi.geometry.rotamers.DunbrackLib
 
findInUngapped(String, int) - Method in class meshi.applications.corpus.Corpus
 
findLowestEnergy(int[], double[], boolean, int) - Method in class meshi.applications.corpus.LocalFragmentLib
This method finds the lowest energy fragment that is not too similar to the rest of the lib
findMax(double, double) - Static method in class meshi.util.overlap.Overlap
 
findMaxAbs(double, double) - Static method in class meshi.util.overlap.Overlap
some help functions
findMin(double, double) - Static method in class meshi.util.overlap.Overlap
 
findPhiPsiRelations(int) - Method in class meshi.applications.corpus.Corpus
Find the relation between Delta{phi,psi} and RMS
findPolynomial(int, int[], int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
Finds polynomial of given type in vector.
findProblematicShotgunResidues(Protein, CommandList) - Static method in class Beautify
 
findProblematicShotgunResidues(ResidueAlignment) - Static method in class Beautify
 
findResidueInList(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
 
findStepLength(double[][]) - Method in class meshi.optimizers.LineSearch
 
findStepLength(double[][]) - Method in class meshi.optimizers.SimpleStepLength
 
findStepLength(double[][]) - Method in class meshi.optimizers.WolfConditionLineSearch
 
finish(Protein) - Static method in class HomologyModeling
 
finishAndPrint(int, int) - Method in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
FiniteExcludedVol - Class in meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol
 
FiniteExcludedVol() - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
 
FiniteExcludedVol(DistanceMatrix, double, double, Filter, double[][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
 
FiniteExcludedVolCreator - Class in meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol
 
FiniteExcludedVolCreator(double, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
FiniteExcludedVolCreator(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
FiniteExcludedVolCreator() - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
FiniteExcludedVolCreator(Filter, double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
FiniteExcludedVolEnergyElement - Class in meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol
 
FiniteExcludedVolEnergyElement() - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
FiniteExcludedVolEnergyElement(DistanceMatrix, double, double, double[][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
Fint - Class in meshi.util.formats
 
Fint(int, int) - Constructor for class meshi.util.formats.Fint
 
fint(int, int) - Static method in class meshi.util.formats.Format
 
fintL(int, int) - Static method in class meshi.util.formats.Format
 
fintR(int, int) - Static method in class meshi.util.formats.Format
 
first - Variable in class HomologyModeling.Three
 
first - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
FIRST - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
FIRST - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
firstHBSeqGap - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
Key values: firstHBSeqGap = the gap between the two atoms in the first HB (O1-H1) secondHBSeqGap = the gap between the two atoms in the second HB (O2-H2) h1h2SeqGap = the gap between the two Hydrogens o1o2SeqGap = the gap between the two Oxygens h1o2SeqGap = the gap between the H of the first HB and the O of the second HB o1h2SeqGap = the gap between the O of the first HB and the H of the second HB value is proportionaly to the friquency of such pair of HBs in the data base
firstNonDummyResidue() - Method in class meshi.molecularElements.Chain
 
firstPassOverTheNonBondedList() - Method in class meshi.energy.solvate.SolvateEnergy
 
firstRes(AtomList) - Method in class meshi.geometry.fragments.DresserFullFrag
 
firstResidueIndex - Variable in class meshi.molecularElements.Protein
 
firstResidueIndex() - Method in class meshi.molecularElements.Protein
For users who need this signature.
firstResidues() - Method in class meshi.molecularElements.Protein
An array of the Residue Identifiers of the first residues in each chain In most cases it is residue 1 but in many other cases some n > 1 typicaly because the N-terminus is not present in the PDB file
firstRun - Variable in class meshi.optimizers.WolfConditionLineSearch
 
firstTimeWornning - Variable in class meshi.energy.hydrogenBond.GoodResiduesForHB
 
firstTimeWornning - Variable in class meshi.energy.hydrogenBond.HBondList.IsAlive
 
firstWord() - Method in class meshi.util.Command
 
firstWord(Key) - Method in class meshi.util.CommandList
Returns the first command that start with the given keyword.
firstWord(String) - Method in class meshi.util.CommandList
Returns the first command that start with the given keyword.
firstWordFilter(Key) - Method in class meshi.util.CommandList
 
firstWordFilter(String) - Method in class meshi.util.CommandList
Generates a list including only the commands starting with a given keyword.
FIX_C_TERMINAL - Static variable in interface meshi.util.KeyWords
 
FIX_N_TERMINAL - Static variable in interface meshi.util.KeyWords
 
fixTorsionToBin(double[], double, int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
Fixes a torsion to be inside its bin.
fixZero(long) - Static method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
FLAT_RAMACH_ENERGY - Static variable in interface meshi.util.KeyWords
 
FLAT_RAMACH_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
forAlign1 - Variable in class meshi.applications.corpus.Corpus
 
forAlign2 - Variable in class meshi.applications.corpus.Corpus
 
force - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
force - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
force - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
force - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
force - Variable in class meshi.energy.simpleEnergyTerms.bond.BondParameters
The force constant for this type of bond.
force - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
force - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
force - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
force - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
force - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
force - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
Force constants.
force2 - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondParameters
The square of the force constant.
force2 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
force2 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
force2 - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
Force constants.
forceMagnitude - Variable in class meshi.optimizers.Minimizer
 
forceSmooth - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
forceX - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
forceX - Variable in class meshi.energy.solvate.SolvateEnergy
 
forceX - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
forceY - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
forceY - Variable in class meshi.energy.solvate.SolvateEnergy
 
forceY - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
forceZ - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
forceZ - Variable in class meshi.energy.solvate.SolvateEnergy
 
forceZ - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
Format - Class in meshi.util.formats
 
Format(int, int) - Constructor for class meshi.util.formats.Format
 
fourthWordDouble() - Method in class meshi.util.Command
 
fourthWordPositiveInt() - Method in class meshi.util.Command
 
fracBelowRMS(double[], double, int) - Static method in class meshi.util.GDTcalculator
 
fractionOfOccurrences - Variable in class meshi.util.histogram.HistogramBin
 
fractionOfOccurrences(int) - Method in class meshi.util.histogram.HistogramBin
 
fractionOfOccurrences() - Method in class meshi.util.histogram.HistogramBin
 
fragCoors - Variable in class meshi.applications.corpus.LocalFragmentLib
 
fragL - Variable in class meshi.applications.corpus.LocalFragmentLib
 
fragL - Static variable in class meshi.applications.corpus.RunThreadingExperiment
 
FRAGMENT_LENGTH - Static variable in class Beautify
 
fragRank - Variable in class meshi.applications.corpus.BasicLoopResult
 
free - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
free - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
free - Variable in enum meshi.geometry.DistanceMode
 
FREE_FINAL_MINIMIZATION - Static variable in interface meshi.util.KeyWords
 
FreeDistance - Class in meshi.geometry
The distance between two Atoms
.
FreeDistance(Atom, Atom) - Constructor for class meshi.geometry.FreeDistance
 
freeElement() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
freeElenet() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
freeze() - Method in class meshi.geometry.Torsion
 
freeze() - Method in class meshi.geometry.TorsionList
 
freeze() - Method in class meshi.molecularElements.atoms.Atom
 
freeze() - Method in class meshi.molecularElements.atoms.AtomList
 
freeze(Filter) - Method in class meshi.molecularElements.atoms.AtomList
 
freeze() - Method in class meshi.molecularElements.Protein
 
freeze(Filter) - Method in class meshi.molecularElements.Protein
 
freezeReliableCAs(ResidueAlignment, Protein) - Static method in class Beautify
 
frozen - Variable in class meshi.energy.EnergyElement
 
frozen() - Method in class meshi.energy.EnergyElement
 
frozen - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
frozen - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
frozen - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
frozen - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
frozen - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
frozen - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
frozen() - Method in class meshi.geometry.Angle
 
frozen - Variable in enum meshi.geometry.DistanceMode
 
frozen() - Method in class meshi.geometry.Torsion
 
frozen() - Method in class meshi.molecularElements.atoms.Atom
 
frozen() - Method in class meshi.molecularElements.atoms.AtomPair
 
frozen() - Method in enum meshi.molecularElements.atoms.AtomStatus
 
frozenAtom - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
frozenAtoms() - Method in class meshi.molecularElements.atoms.AtomList
 
frozenAtomsExist() - Method in class meshi.energy.TotalEnergy
 
frozenAtomsExist() - Method in class meshi.molecularElements.atoms.AtomList
 
FrozenCoordinates - Class in meshi.geometry
 
FrozenCoordinates(Coordinates) - Constructor for class meshi.geometry.FrozenCoordinates
 
FrozenDistance - Class in meshi.geometry
 
FrozenDistance(AtomCore, AtomCore, double, double, double, double) - Constructor for class meshi.geometry.FrozenDistance
 
frozenFlag - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
frozenMap - Static variable in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
frozenMap() - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
frozenMap(int) - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
frozenResiduesFilter - Static variable in class meshi.symmetryComplex.utils.GJFilters
 
fstring(String, int) - Static method in class meshi.util.formats.Format
 
fstringL(String, int) - Static method in class meshi.util.formats.Format
 
fstringR(String, int) - Static method in class meshi.util.formats.Format
 
fullMinimization() - Method in class meshi.symmetryComplex.proteinsGJ.FullModeller
 
FullModeller - Class in meshi.symmetryComplex.proteinsGJ
 
FullModeller(String, String, CommandList, String) - Constructor for class meshi.symmetryComplex.proteinsGJ.FullModeller
 
fullOccupancyFilter() - Method in class meshi.molecularElements.atoms.AtomList
 
fullSol - Variable in class meshi.util.dssp.DSSP
 
FWriter - Class in aligner
 
FWriter(String) - Constructor for class aligner.FWriter
 
fx - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
fx - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.SummaAttribute
 
fx() - Method in class meshi.geometry.Coordinates
 
fx() - Method in class meshi.molecularElements.atoms.Atom
Returns the force operating on the atom in the X direction.
fy - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
fy - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.SummaAttribute
 
fy() - Method in class meshi.geometry.Coordinates
 
fy() - Method in class meshi.molecularElements.atoms.Atom
Returns the force operating on the atom in the Y direction.
fz - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
fz - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.SummaAttribute
 
fz() - Method in class meshi.geometry.Coordinates
 
fz() - Method in class meshi.molecularElements.atoms.Atom
Returns the force operating on the atom in the Z direction.

G

g - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
g - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
G - Variable in class meshi.optimizers.BFGS
 
G - Variable in class meshi.optimizers.ConjugateGradient
 
G - Variable in class meshi.optimizers.LBFGS
 
gama - Variable in class meshi.optimizers.LBFGS
 
gap() - Method in class meshi.sequences.AlignmentCell
 
gap() - Method in class meshi.sequences.AtomAlignmentCell
 
gap() - Method in class meshi.sequences.ResidueAlignmentCell
 
GAP - Static variable in class meshi.sequences.SequenceAlignmentCell
 
gap() - Method in class meshi.sequences.SequenceAlignmentCell
 
GAP_CHAR - Static variable in class meshi.sequences.SequenceAlignmentCell
 
gapPenalty - Variable in class meshi.sequences.aligner.Identity
 
gapPenalty - Variable in class meshi.sequences.aligner.StructureBasedMatrix
 
GAUSSIAN_ALPHA - Static variable in interface meshi.util.MeshiAttribute
 
GAUSSIAN_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
gDividedByGplusBETA - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
gDividedByGplusBETA - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
gdt(ResidueAlignment, int) - Static method in class meshi.util.GDTcalculator
 
gdt(ResidueAlignment, int, MeshiWriter) - Static method in class meshi.util.GDTcalculator
 
gdt(AtomList, AtomList, int) - Static method in class meshi.util.GDTcalculator
 
gdt(Protein, Protein) - Static method in class meshi.util.Rms
 
gdt(ResidueAlignment, int) - Static method in class meshi.util.Rms
 
gdt(Protein, CommandList) - Static method in class meshi.util.Rms
 
gdt(Protein, CommandList, Filter) - Static method in class meshi.util.Rms
 
gdt(ResidueAlignment, Filter, int) - Static method in class meshi.util.Rms
 
GDT_INDEX - Static variable in class meshi.applications.prediction.ModelData
 
GDTcalculator - Class in meshi.util
 
GDTcalculator() - Constructor for class meshi.util.GDTcalculator
 
GeneralThreadingExperiment(int, int, String, int, int) - Method in class meshi.applications.corpus.Corpus
This is a method for general ungapped threading.
generateData(String) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
generateFiles(SymmetricComplex, ResidueCreator) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
generateImageChains() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
generateLoopData(String) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
GENERIC_CHAIN_NAME - Static variable in class meshi.molecularElements.Chain
 
get(int) - Method in class meshi.geometry.DistanceList
 
get(String) - Method in class meshi.molecularElements.Residue
Fetches an atom by its name.
get(int, int) - Method in class meshi.util.mathTools.Jama.Matrix
Get a single element.
get(String) - Method in class meshi.util.MeshiProgram.GlobalElementList
 
get2ndString(String, String) - Static method in class meshi.util.MeshiProgram
 
getAA() - Method in class meshi.util.dssp.DSSP
 
getACC() - Method in class meshi.util.dssp.DSSP
 
getAngle() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
getAngle(AtomPair, AtomPair, DistanceMatrix) - Method in class meshi.geometry.AngleList
 
getAngle(AtomPair, AtomPair, DistanceMatrix) - Method in class meshi.geometry.QuickAndDirtyAngleList
 
getAngle(Coordinates, Coordinates) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
getAngleCode() - Method in class meshi.geometry.Angle
 
getAngleName() - Method in class meshi.geometry.Angle
 
getAngleParameters(CommandList) - Static method in class meshi.util.Utils
 
getAngleResName() - Method in class meshi.geometry.Angle
 
getAngleResNum() - Method in class meshi.geometry.Angle
 
getAntiParalel() - Method in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
getArray() - Method in class meshi.util.mathTools.Jama.Matrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class meshi.util.mathTools.Jama.Matrix
Copy the internal two-dimensional array.
getAtom(AtomList, String) - Static method in class meshi.geometry.ResidueBuilder
Returns the specified atom from a residue.
getAtom(String, AtomType, AtomList, Residue) - Static method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
getAtom(String, ResidueIdentifier, String) - Method in class meshi.molecularElements.Protein
Returns the specified atom.
getAtom(String) - Method in class meshi.molecularElements.Residue
 
getAtom(CaResidue, CaResidue, int) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getAtom(CaResidue, CaResidue, Loop) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getAtom(AtomList, String) - Static method in class meshi.util.alignmentTools.AlignmentTools
 
getAtom(AtomList, int, String) - Static method in class meshi.util.alignmentTools.AlignmentTools
 
getAtom_xyza(double[], double, double, double, Atom, Atom, Atom) - Static method in class meshi.geometry.ResidueBuilder
 
getAtomAlignment(Protein, CommandList, Filter) - Static method in class meshi.util.Rms
 
getAtomList(CommandList) - Static method in class HeliumClusterMinimization
 
getAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
returns a list of all atoms in this residue torsions
getAtoms(int[]) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
getAttribute(int) - Method in class meshi.energy.AbstractEnergy
 
getAttribute(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
getAttribute(int) - Method in class meshi.geometry.Distance
 
getAttribute(int) - Method in class meshi.molecularElements.atoms.Atom
 
getAttribute(int) - Method in class meshi.molecularElements.Residue
 
getAttribute(int) - Method in class meshi.sequences.AlignmentCell
 
getAttribute() - Method in class meshi.sequences.SequenceAlignmentCell
 
getAttribute(int) - Method in interface meshi.util.Attributable
 
getAttribute(int) - Method in class meshi.util.AttributesRack
 
getAverageAngleForLoop(AtomList, int) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
getAverageAngleForLoopParts(AtomList, int, int) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
getAverageDistanceBetweenCysCBconnexin(String, AtomList) - Static method in class meshi.symmetryComplex.utils.LoopUtils
Returns the average distance between C-Beta atoms of cysteines which are thought to be bonded by disulfide links.
getAverageForce(double[][]) - Static method in class meshi.energy.TotalEnergy
 
getB(String) - Static method in class meshi.util.MeshiProgram
Gets the Boolean value associated with the keyword key.
getb(String) - Static method in class meshi.util.MeshiProgram
Gets the boolean value associated with the keyword key.
getBack() - Method in class meshi.sequences.aligner.Cell
 
getBBcoors() - Method in class meshi.applications.corpus.LoopResults
 
getBeautifyAttribute(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
getBestCaModel(ResidueSequence, Protein, CommandList, Beautify.BeautifyLogger) - Static method in class Beautify
 
getBonded(Atom, int) - Static method in class meshi.geometry.DistanceMatrix
 
getBonded(Atom, int, AtomList, int) - Static method in class meshi.geometry.DistanceMatrix
 
getBonded(Atom, int) - Static method in class meshi.geometry.DistanceMatrixBondedOnly
 
getBonded(Atom, int, AtomList, int) - Static method in class meshi.geometry.DistanceMatrixBondedOnly
 
getBonded(Atom, int) - Static method in class meshi.geometry.OldDistanceMatrix
 
getBonded(Atom, int, AtomList, int) - Static method in class meshi.geometry.OldDistanceMatrix
 
getBondedList(MolecularSystem, int, MatrixRow[]) - Static method in class meshi.geometry.DistanceMatrix
 
getBondedList(MolecularSystem, int) - Static method in class meshi.geometry.DistanceMatrixBondedOnly
 
getBondedList(Object[], int, MatrixRow[]) - Static method in class meshi.geometry.OldDistanceMatrix
 
getBondParameters(CommandList) - Static method in class meshi.util.Utils
 
getCaAngles(Protein, DistanceMatrix) - Static method in class meshi.geometry.AngleList
 
getCaAnglesQuickAndDirty(Protein, DistanceMatrix) - Static method in class meshi.geometry.QuickAndDirtyAngleList
 
getCaAtomList(char, Coordinates) - Static method in class meshi.molecularElements.Chain
 
getCaList(int) - Method in class meshi.sequences.ResidueAlignment
 
getCatalyticResPosFromCSAonlyFile(String, String) - Static method in class CalculateEnergyFromStructuresListAverages
This method reads the catalytic residue positions stated in a CSAonly file for the current protein.
getCatalyticResPosFromCSAonlyFile(String, String) - Static method in class ColorByEnergy
This method reads the catalytic residue positions stated in a CSAonly file for the current protein.
getCell(AtomCore) - Method in class meshi.geometry.Grid
 
getCell(Atom) - Method in class meshi.geometry.OldGrid
 
getCell(int, int) - Method in class meshi.sequences.aligner.DpMatrix
 
getCenterOfMass0() - Method in class meshi.util.Rms
 
getCenterOfMass1() - Method in class meshi.util.Rms
 
getChainAtoms(String) - Method in class meshi.molecularElements.atoms.AtomList
 
getChainLetters(boolean[]) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
getChainSequence(Chain) - Static method in class meshi.sequences.Sequence
 
getChar(int) - Method in class meshi.sequences.Sequence
 
getChar() - Method in class meshi.sequences.SequenceAlignmentCell
 
getChar(int) - Method in class meshi.sequences.SequenceAlignmentColumn
 
getCharAsString(int) - Method in class meshi.sequences.Sequence
 
getCharAsString() - Method in class meshi.sequences.SequenceAlignmentCell
 
getChiMax(int) - Method in class meshi.geometry.rotamers.DunbrackLib
Gives the number of Chi torsion for a specific residue type (parameter #1).
getClashes(Atom, ArrayList<Atom>, double) - Static method in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
getClashes(Coordinates, Residue, ResidueList, double) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
Modified by Oren Wolfshtat.
getClashes(Atom, List<Atom>, double) - Static method in class meshi.util.Utils
 
getColumn(int, int) - Method in class meshi.sequences.SequenceAlignment
Fetches a column with a specific cell number in a specific row.
getColumnDimension() - Method in class meshi.util.mathTools.Jama.Matrix
Get column dimension.
getColumnPackedCopy() - Method in class meshi.util.mathTools.Jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getColumns() - Method in interface meshi.symmetryComplex.transformations.Matrix
 
getColumns() - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
getColumnVector(int) - Method in class meshi.util.mathTools.Jama.Matrix
 
getCommandLine(String[]) - Static method in class meshi.util.MeshiProgram
Assembles the command-line string from an array of command-line-words.
getContacts(ResidueList, double) - Method in class meshi.molecularElements.ca.CaResidue
 
getCoolAtomsEnergy(Protein, int) - Static method in class meshi.applications.prediction.ModelData
 
getCoordinates() - Method in class meshi.energy.TotalEnergy
 
getCoordinates(AtomList) - Static method in class meshi.energy.TotalEnergy
Reduce the Atom coordinates of an atom list to an array.
getCovalentNeighbor(Atom) - Static method in class meshi.util.Utils
 
getCovalentNeighborUp(Atom) - Static method in class meshi.util.Utils
May be used only by getCovalentNeighbor(Atom atom)
getCSAonlyFilesLocationPath(CommandList) - Static method in class CalculateEnergyFromStructuresListAverages
This method reads the location path where the CSAonly files are found.
getCSAonlyFilesLocationPath(CommandList) - Static method in class ColorByEnergy
This method reads the location path where the CSAonly files are found.
getCummSum(int, double, double) - Method in class meshi.geometry.rotamers.DunbrackLib
Gives the coverage of the rotamers available for a specific residue type (parameter #1) at a certain phi/psi (parameters #2,3).
getD() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getD(String) - Static method in class meshi.util.MeshiProgram
Gets the Double value associated with the keyword key.
getd(String) - Static method in class meshi.util.MeshiProgram
Gets the double value associated with the keyword key.
getDEdD() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
getDEdX() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
getDEdY() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
getDEdZ() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
getDescription() - Method in class meshi.applications.prediction.homology.gui.HomologyFileFilter
 
getDielectricConstant(CommandList) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticCreator
This takes the value of the dielectricConstant from the commands file (the user may choose to change it)
getDistance(Atom, Atom) - Static method in class meshi.geometry.FreeDistance
 
getDistanceBetween2Residues(Residue, Residue) - Static method in class CalculateEnergyFromStructuresListAverages
This method calculates the distance between two residues.
getDistanceBetween2Residues(Residue, Residue) - Static method in class ColorByEnergy
This method calculates the distance between two residues.
getDistanceGrade(Atom, Atom) - Static method in class HomologyModeling
 
getDistanceMatrix() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
getDistanceMatrix() - Method in class meshi.energy.TotalEnergy
 
getDistanceMatrix(AtomList, CommandList) - Static method in class meshi.util.Utils
A standard method to build distance matrices.
getDistancesBetweenCysCBofConnexin(String, AtomList) - Static method in class meshi.symmetryComplex.utils.LoopUtils
Returns distances between C-Beta atoms of some special cysteines pattern for connexin
getDistancesBetweenCysCBofConnexons(String, AtomList, AtomList, AtomList, AtomList) - Static method in class meshi.symmetryComplex.utils.LoopUtils
Returns distances between C-Beta atoms of some special cysteines pattern
getDistancesBetweenEveryResidueAndItsClosestFunctionalNeighbour(Protein, String) - Static method in class CalculateEnergyFromStructuresListAverages
 
getDistancesBetweenEveryResidueAndItsClosestFunctionalNeighbour(Protein, String) - Static method in class ColorByEnergy
 
getDoublePivot() - Method in class meshi.util.mathTools.Jama.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getDx(Atom, Atom) - Static method in class meshi.geometry.FreeDistance
 
getDy(Atom, Atom) - Static method in class meshi.geometry.FreeDistance
 
getDz(Atom, Atom) - Static method in class meshi.geometry.FreeDistance
 
getEnergy(AtomList, DistanceMatrix, CommandList) - Static method in class HeliumClusterMinimization
 
getEnergyOnCommon(ResidueAlignment, double[][], double[][], int) - Static method in class ChooseTemplate
 
getEnergyOnCommon(ResidueAlignment, double[][], double[][], int) - Static method in class ModelRanker
 
getEnergyTerm(AbstractEnergy) - Method in class meshi.energy.TotalEnergy
 
getEnergyTerms(AbstractEnergy) - Method in class meshi.energy.TotalEnergy
 
getEnergyTermsNames(TotalEnergy) - Static method in class meshi.util.Utils
 
getEnergyValues(TotalEnergy) - Static method in class meshi.util.Utils
 
getFile(CommandList, Key, Key) - Static method in class meshi.util.file.MeshiWriter
 
getFile(CommandList, Key, Key, String) - Static method in class meshi.util.file.MeshiWriter
 
getFinalModel(Protein, CommandList, Protein, Beautify.BeautifyLogger) - Static method in class Beautify
 
getFirstPolar() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
getFlag(String, String[]) - Static method in class meshi.util.MeshiProgram
Get a boolean flag Searcheds for a the keyword key in args.
getFlagedArgument(String, String[]) - Static method in class meshi.util.MeshiProgram
Searcheds for a the keyword key in args.
getFragment(Protein, int, int) - Static method in class meshi.util.Utils
 
getGdt(Protein, Protein) - Static method in class CalcGDT
 
getGradMagnitude() - Method in class meshi.energy.TotalEnergy
Finds the maximal component (in magnitude) of the gradient vecor in coordinates ( coordinates[][1] ).
getH() - Method in class meshi.util.mathTools.Jama.QRDecomposition
Return the Householder vectors
getHydrogenBondsEnergy() - Method in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
getI(String) - Static method in class meshi.util.MeshiProgram
Gets the Integer value associated with the keyword key.
geti(String) - Static method in class meshi.util.MeshiProgram
Gets the int value associated with the keyword key.
getID(AtomList, String) - Static method in class Pdb2Fasta.MyResidue
 
getImage() - Method in class aligner.FastaReader
 
getImagEigenvalues() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getKey(Object) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
getKey(Object) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
getKoehlLines(MeshiLineReader) - Static method in class RoisFirstMeshiProgram
 
getL() - Method in class meshi.util.mathTools.Jama.CholeskyDecomposition
Return triangular factor.
getL() - Method in class meshi.util.mathTools.Jama.LUDecomposition
Return lower triangular factor
getLastEnergy() - Method in class meshi.energy.TotalEnergy
Returns the last enrgy value that was calculated
getLBFGS(TotalEnergy, CommandList) - Static method in class meshi.util.Utils
 
getLBFGS(TotalEnergy, CommandList, Key) - Static method in class meshi.util.Utils
 
getLine() - Method in class meshi.util.Command
 
getLoops(Protein, List<HomologyModeling.Loop>) - Static method in class HomologyModeling
 
getLoops(Protein, double, int, int) - Static method in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
getLoopsBefore(Iterator, List<HomologyModeling.Loop>, HomologyModeling.Three) - Static method in class HomologyModeling
 
getMatrix(int, int, int, int) - Method in class meshi.util.mathTools.Jama.Matrix
Get a submatrix.
getMatrix(int[], int[]) - Method in class meshi.util.mathTools.Jama.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class meshi.util.mathTools.Jama.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class meshi.util.mathTools.Jama.Matrix
Get a submatrix.
getMatrix() - Method in class meshi.util.Rms
 
getMCM(Protein, TotalEnergy, CommandList, SimpleInflate) - Static method in class AbInitio
 
getMCM(Protein, TotalEnergy, CommandList, SimpleInflate) - Method in class meshi.symmetryComplex.proteinsGJ.BackboneMCM
 
getMCM(Protein, TotalEnergy, CommandList, SimpleInflate) - Method in class meshi.symmetryComplex.proteinsGJ.FullModeller
 
getMCM(Protein, TotalEnergy, CommandList, SimpleInflate) - Static method in class Optimize
 
getMean(int, double, int) - Static method in class meshi.util.rotamericTools.RotamericTools
 
getMember(int, int) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
getMember(int, int) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
getMinimizer(TotalEnergy, CommandList) - Static method in class HeliumClusterMinimization
 
getMode() - Method in class meshi.molecularElements.Residue
 
getModel() - Method in class meshi.PDB.PdbLine
 
getModelNumber(MeshiLineReader) - Method in class meshi.molecularElements.Protein
Extracts the model number from the filename.
getName(AtomList) - Static method in class Pdb2Fasta.MyResidue
 
getNeighbors(Atom, Protein, double) - Static method in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
getNeighbors(ResidueList, Protein, double) - Static method in class meshi.util.Utils
 
getNeighbors(Atom, Protein, double) - Static method in class meshi.util.Utils
 
getNewAtomList(AtomList, ResidueType) - Static method in class meshi.molecularElements.ca.CaResidue
 
getNewAtomList(AtomList, MeshiLog) - Static method in class Pdb2Fasta
 
getNewResidue(Residue, String) - Static method in class Pdb2Fasta.MyAtom
 
getNonWeightedHBenergy() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
getNumberOfBetaResidues() - Method in class meshi.util.dssp.DSSP
 
getNumberOfResiduesWithCoordinates(ResidueList) - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter
 
getNumberOfResiduesWithoutCoordinates(ResidueList) - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter
 
getOldCoordinates(TotalEnergy) - Static method in class meshi.optimizers.MCM
 
getOldSize() - Method in class meshi.energy.hydrogenBond.HBondList
 
getOrderedArgument(String[]) - Static method in class meshi.util.MeshiProgram
Removes the first string in args and returns it.
getOriginalAtomsAlignment(ResidueAlignment, OriginalAtoms, int) - Static method in class meshi.util.Utils
Gets a residue alignment as a parameters and returns a new alignment that includes only residues with original atoms.
getOutputFile(CommandList) - Static method in class CalculateEnergyFromStructuresListAverages
 
getOutputFile(CommandList) - Static method in class HeliumClusterMinimization
 
getOutputFile(CommandList) - Static method in class meshi.util.Utils
 
getPairsOfHBEElementsList() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
getPairValue() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
getParameters(Parameters) - Method in class meshi.energy.simpleEnergyTerms.ParametersList
Fetches a parameter from the list.
getParameters(double, int, double, double, double, int, int, double, double, double) - Method in class meshi.optimizers.BFGS
 
getParametersDirectory(CommandList) - Static method in class meshi.energy.EnergyCreator
 
getParametersList() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
getPartialTransformations(double, int, boolean[]) - Static method in class meshi.symmetryComplex.utils.GJUtils
 
getPdbFile(String) - Static method in class meshi.PDB.PdbReader
 
getPdbFile(String, String) - Static method in class meshi.PDB.PdbReader
 
getPivot() - Method in class meshi.util.mathTools.Jama.LUDecomposition
Return pivot permutation vector
getProtein(String, CommandList) - Static method in class CalculateEnergyFromStructuresListAverages
 
getProtein(String, List<String>, CommandList) - Static method in class CalculateEnergyFromStructuresListAverages
 
getProtein(String, CommandList) - Static method in class ColorByEnergy
 
getProtein(String, List<String>, CommandList) - Static method in class ColorByEnergy
 
getProtein(CommandList, Key, ResidueCreator, ExceptionHandler) - Static method in class meshi.util.Utils
Creates a Protein object in a new MolecularSystem.
getProtein(CommandList, String, ResidueCreator, ExceptionHandler) - Static method in class meshi.util.Utils
 
getProtein(CommandList, Key, Key, ResidueCreator, ExceptionHandler) - Static method in class meshi.util.Utils
Reads a protein structure from the file pointed at by the command list.
getProteinName(MeshiLineReader) - Static method in class meshi.molecularElements.Protein
Extract the protein name from the filename.
getProteinName(String) - Static method in class meshi.molecularElements.Protein
 
getProteinNameFromPdbFileName(String) - Static method in class meshi.util.Utils
Reads a protein structure from the file pointed at by the command list.
getQ() - Method in class meshi.util.mathTools.Jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getR() - Method in class meshi.util.mathTools.Jama.QRDecomposition
Return the upper triangular factor
getRandomPointAroundCyllinder(Atom, double, int, double[]) - Static method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getRandomPointOnSphere(double) - Static method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
Returns a point on a sphere (more precisely, on a shell) of a given radius.
getRandomPointOnSphereBiasDirection(double, double[], double[]) - Static method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getRealEigenvalues() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getReferenceProtein(CommandList) - Static method in class meshi.util.Utils
 
getRelativeACC() - Method in class meshi.util.dssp.DSSP
 
getResidue() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
returns residue
getResidue(Iterator, Atom) - Method in class Pdb2Fasta.MyChain
 
getResidueNumber() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
returns residue's number
getResidueSequence(String, String) - Static method in class AbInitio
 
getResidueSequence(CommandList) - Static method in class Beautify
 
getResidueSequence(String) - Method in class meshi.sequences.SequenceList
 
getResidueSequence() - Method in class meshi.sequences.SequenceList
 
getResidueSequence(CommandList, Key) - Method in class meshi.sequences.SequenceList
 
getResidueSequence(CommandList, Key) - Static method in class meshi.util.Utils
 
getResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters
returns rotamer's residue type
getResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters
returns rotamer's residue type
getResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParameters
returns rotamer's residue type
getResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
returns rotamer's residue type
getResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
returns residue type
getResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
returns rotamer's residue type
getRms(AtomList) - Method in class meshi.molecularElements.atoms.AtomList
 
getRms() - Method in class meshi.util.Rms
 
getRotamer(int, double, double, int) - Method in class meshi.geometry.rotamers.DunbrackLib
Gives the array of a rotamer Chi angle for a specific residue type (parameter #1) at a certain phi/psi (parameters #2,3).
getRotamerNum(int, double, double) - Method in class meshi.geometry.rotamers.DunbrackLib
Gives the number of rotamers available for a specific residue type (parameter #1) at a certain phi/psi (parameters #2,3)
getRotamerProb(int, double, double, int) - Method in class meshi.geometry.rotamers.DunbrackLib
Gives the probablity for a certain rotamer (whose index is given as parameter #4) for a specific residue type (parameter #1) at a certain phi/psi (parameters #2,3).
getRowDimension() - Method in class meshi.util.mathTools.Jama.Matrix
Get row dimension.
getRowPackedCopy() - Method in class meshi.util.mathTools.Jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getRows() - Method in interface meshi.symmetryComplex.transformations.Matrix
 
getRows() - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
getRowVector(int) - Method in class meshi.util.mathTools.Jama.Matrix
 
getS() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getS(String) - Static method in class meshi.util.MeshiProgram
Gets the String value associated with the keyword key.
getS(String, StringList, String) - Static method in class meshi.util.MeshiProgram
 
getScore(char, char) - Method in class aligner.AminoAcidSubstitutionMatrix
 
getScore(char, char) - Method in interface aligner.SubstitutionMatrix
 
getScore(Cell) - Method in interface meshi.sequences.aligner.CellScorer
 
getScore(Cell) - Method in class meshi.sequences.aligner.Identity
 
getScore(Cell) - Method in class meshi.sequences.aligner.StructureBasedMatrix
 
getSecondPolar() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
getSeqOfProt(Protein, int, int) - Static method in class meshi.util.Utils
 
getSequence(int) - Static method in class HydrogenTest.PolyAla
 
getSequence() - Method in class meshi.molecularElements.Protein
 
getSequence(String) - Method in class meshi.sequences.SequenceList
 
getSingularValues() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSource() - Method in class aligner.FastaReader
 
getSource() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
getSourceAtoms() - Method in class meshi.molecularElements.atoms.AtomList
 
getSpecialDis() - Method in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
getSpecialDisArray() - Method in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
getSplinedPolynomial(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
retrieves specific polynomial.
getSplinedPolynomial(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
retrieves specific polynomial.
getSs(int) - Method in class meshi.sequences.Sequence
 
getSSInOneLine() - Method in class meshi.util.dssp.DSSP
 
getSSInOneLineConventional() - Method in class meshi.util.dssp.DSSP
 
getStructureNames(CommandList) - Static method in class CalculateEnergyFromStructuresListAverages
 
getStructureNames(CommandList) - Static method in class ColorByEnergy
 
getStructureNames(CommandList) - Static method in class meshi.util.Utils
 
getSubmatrix(int, int, int, int) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
getSubmatrix(int, int, int, int) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
getText() - Method in class aligner.FileToString
 
getTo(int) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getTo(Residue, int, int) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getToNull(int, int, int) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
getTorsion() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
getTorsion(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
returns torsion of type torsionType.
getTorsion(Angle, Angle, DistanceMatrix) - Method in class meshi.geometry.QuickAndDirtyTorsionList
 
getTorsion(Angle, Angle, DistanceMatrix) - Method in class meshi.geometry.TorsionList
 
getTorsionCode() - Method in class meshi.geometry.Torsion
 
getTorsionName() - Method in class meshi.geometry.Torsion
 
getTorsionResName() - Method in class meshi.geometry.Torsion
 
getTorsionResNum() - Method in class meshi.geometry.Torsion
 
getTransformations() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
getTransformations(double, int) - Static method in class meshi.symmetryComplex.utils.GJUtils
 
getType(int) - Static method in class meshi.geometry.ResidueBuilder
 
getType(AtomList) - Static method in class Pdb2Fasta.MyResidue
 
getU() - Method in class meshi.util.mathTools.Jama.LUDecomposition
Return upper triangular factor
getU() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Return the left singular vectors
getUnitMatrix(int) - Static method in class meshi.symmetryComplex.transformations.Matrix1D
 
getV() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Return the right singular vectors
getWarpThreshold(CommandList) - Static method in class Beautify
 
getWeight(CommandList) - Method in class meshi.energy.EnergyCreator
Get the weight of the energy term.
getWeight(Key) - Method in class meshi.util.CommandList
Gets energy term weight getWeight.
getWeight(String) - Method in class meshi.util.CommandList
Gets energy term weight getWeight.
getWeightedEnergy(Protein, int) - Static method in class meshi.applications.prediction.ModelData
 
gj - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
gj - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
GJFilters - Class in meshi.symmetryComplex.utils
Created by IntelliJ IDEA.
GJFilters() - Constructor for class meshi.symmetryComplex.utils.GJFilters
 
GJFilters.AcceptChainFilter - Class in meshi.symmetryComplex.utils
Accepts atoms whose chain is identical to the one given to the constructor.
GJFilters.AcceptChainFilter(String) - Constructor for class meshi.symmetryComplex.utils.GJFilters.AcceptChainFilter
 
GJFilters.AndFilter - Class in meshi.symmetryComplex.utils
 
GJFilters.AndFilter(Filter...) - Constructor for class meshi.symmetryComplex.utils.GJFilters.AndFilter
 
GJFilters.RejectChainFilter - Class in meshi.symmetryComplex.utils
Accepts only atoms whose chain is different than the one given to the constructor.
GJFilters.RejectChainFilter(String) - Constructor for class meshi.symmetryComplex.utils.GJFilters.RejectChainFilter
 
GJFilters.ResidueRangeFilter - Class in meshi.symmetryComplex.utils
Accepts residues and atoms whose residue numbers are within the ranges given in the constructor.
GJFilters.ResidueRangeFilter(int[][]) - Constructor for class meshi.symmetryComplex.utils.GJFilters.ResidueRangeFilter
 
GJFilters.ResidueRangeFilter(int[]) - Constructor for class meshi.symmetryComplex.utils.GJFilters.ResidueRangeFilter
 
GJFilters.ResidueRangeFilter(int, int) - Constructor for class meshi.symmetryComplex.utils.GJFilters.ResidueRangeFilter
 
GJModeller - Class in meshi.symmetryComplex.proteinsGJ
Created by IntelliJ IDEA.
GJModeller(String, CommandList, String) - Constructor for class meshi.symmetryComplex.proteinsGJ.GJModeller
 
GJModeller(String, String, CommandList, String) - Constructor for class meshi.symmetryComplex.proteinsGJ.GJModeller
 
GJModeller.HBRangesAndGoodResiduesFilter - Class in meshi.symmetryComplex.proteinsGJ
 
GJModeller.HBRangesAndGoodResiduesFilter() - Constructor for class meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesAndGoodResiduesFilter
 
GJModeller.HBRangesFilter - Class in meshi.symmetryComplex.proteinsGJ
 
GJModeller.HBRangesFilter() - Constructor for class meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesFilter
 
GJModeller.SpecialHBPairs - Class in meshi.symmetryComplex.proteinsGJ
 
GJModeller.SpecialHBPairs() - Constructor for class meshi.symmetryComplex.proteinsGJ.GJModeller.SpecialHBPairs
 
GJUtils - Class in meshi.symmetryComplex.utils
This class contains utils for work on gap junctions.
GJUtils() - Constructor for class meshi.symmetryComplex.utils.GJUtils
 
Gln - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - CD - NE2 - HE21 | | OE1 HE22
Gln(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Gln
 
globalTable - Static variable in class meshi.util.MeshiProgram
After program initiation, stores all the information needed for program execution.
Glu - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - CD - OE2 | (-) OE1
Glu(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Glu
 
Gly - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | H
Gly(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Gly
 
GoodBonds - Class in meshi.energy.simpleEnergyTerms
 
GoodBonds() - Constructor for class meshi.energy.simpleEnergyTerms.GoodBonds
 
GoodResiduesForHB - Class in meshi.energy.hydrogenBond
 
GoodResiduesForHB() - Constructor for class meshi.energy.hydrogenBond.GoodResiduesForHB
 
GoodResiduesForHB(DistanceList) - Constructor for class meshi.energy.hydrogenBond.GoodResiduesForHB
 
goodResiduesForHB - Variable in class meshi.energy.hydrogenBond.HBdistanceList
 
goodResiduesForHB - Variable in class meshi.energy.hydrogenBond.HBondList
 
GoodResiduesForHB.GoodSS - Class in meshi.energy.hydrogenBond
 
GoodResiduesForHB.GoodSS() - Constructor for class meshi.energy.hydrogenBond.GoodResiduesForHB.GoodSS
 
GoodResiduesForHB.IsNot13 - Class in meshi.energy.hydrogenBond
 
GoodResiduesForHB.IsNot13() - Constructor for class meshi.energy.hydrogenBond.GoodResiduesForHB.IsNot13
 
goodSS - Variable in class meshi.energy.hydrogenBond.GoodResiduesForHB
 
grad0 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
gradI - Variable in class meshi.optimizers.WolfConditionLineSearch
 
gradI1 - Variable in class meshi.optimizers.WolfConditionLineSearch
 
gravityCenter() - Static method in class meshi.util.overlap.Overlap
Uniting the gravity center of both proteins to (0,0,0)
grid - Variable in class meshi.geometry.DistanceMatrix
 
Grid - Class in meshi.geometry
 
Grid(double, double) - Constructor for class meshi.geometry.Grid
 
Grid(MolecularSystem, double, double) - Constructor for class meshi.geometry.Grid
 
grid - Variable in class meshi.geometry.OldDistanceMatrix
 
GRID_EDGE - Static variable in interface meshi.util.KeyWords
 
GridCell - Class in meshi.geometry
 
GridCell(int) - Constructor for class meshi.geometry.GridCell
 

H

H - Variable in class meshi.geometry.fragments.DresserFullFrag
 
H - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
h() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
H - Variable in class meshi.optimizers.BFGS
 
H - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Array for internal storage of nonsymmetric Hessenberg form.
h1h2SeqGap - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
Key values: firstHBSeqGap = the gap between the two atoms in the first HB (O1-H1) secondHBSeqGap = the gap between the two atoms in the second HB (O2-H2) h1h2SeqGap = the gap between the two Hydrogens o1o2SeqGap = the gap between the two Oxygens h1o2SeqGap = the gap between the H of the first HB and the O of the second HB o1h2SeqGap = the gap between the O of the first HB and the H of the second HB value is proportionaly to the friquency of such pair of HBs in the data base
h1o2SeqGap - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
Key values: firstHBSeqGap = the gap between the two atoms in the first HB (O1-H1) secondHBSeqGap = the gap between the two atoms in the second HB (O2-H2) h1h2SeqGap = the gap between the two Hydrogens o1o2SeqGap = the gap between the two Oxygens h1o2SeqGap = the gap between the H of the first HB and the O of the second HB o1h2SeqGap = the gap between the O of the first HB and the H of the second HB value is proportionaly to the friquency of such pair of HBs in the data base
halfEnergy0 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
halfNumberOfChains - Static variable in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
handle(Exception) - Method in class meshi.util.DoNothingExceptionHandler
 
handle(Exception) - Method in interface meshi.util.ExceptionHandler
 
handle(Exception) - Method in class meshi.util.Utils.DefaultExceptionHandler
 
handle(Exception) - Method in class meshi.util.Utils.DoNothingExceptionHandler
 
handleMissingParameters(Object) - Method in class meshi.energy.AbstractEnergy
 
handleMissingParameters(Object) - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
handleMissingParameters(Object) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
handleMissingParameters(Object) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
hasAllTorsions() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
verifies all the torsions used by this residue are available.
hasGap() - Method in class meshi.sequences.AlignmentColumn
 
hasGaps() - Method in class meshi.sequences.AtomAlignment
Does the alignemnt include gaps? .
hasNext() - Method in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
hasNext() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
hasNext() - Method in class meshi.geometry.DistanceList.DistanceIterator
 
hasNext() - Method in class meshi.geometry.DistanceMatrix.RowIterator
 
hasNext() - Method in class meshi.geometry.OldDistanceMatrix.RowIterator
 
hasNext() - Method in class meshi.util.histogram.Histogram.RepresentativesIterator
 
hasNowhereAtoms(Chain) - Static method in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
hasProblematicNeighbor() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
hasProblematicNeighbor(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
hasSecondWord() - Method in class meshi.util.Command
 
hAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
hAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
hAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
hAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
hAtom(Distance) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
hAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
hAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
haveAllAtoms(Residue) - Static method in class CalculateEnergyFromStructuresListAverages
 
haveAllAtoms(Residue) - Static method in class ColorByEnergy
 
haveAllBackboneAtoms(Residue) - Static method in class meshi.applications.corpus.Corpus
 
HB_AtomAttribute - Class in meshi.energy.hydrogenBond
 
HB_AtomAttribute(boolean, boolean) - Constructor for class meshi.energy.hydrogenBond.HB_AtomAttribute
 
hb_Attribute - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
HB_DistanceAttribute - Class in meshi.energy.hydrogenBond
 
HB_DistanceAttribute(boolean) - Constructor for class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
HB_PAIR_CAPACITY - Static variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hbAngScore - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
hbAngScore() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
hbAngScore - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
HBC - Variable in class meshi.energy.solvate.SolvateEnergy
 
HBCforHBenergy - Variable in class meshi.energy.solvate.SolvateEnergy
 
hbDisScore - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
HBdistanceList - Class in meshi.energy.hydrogenBond
 
HBdistanceList(Filter) - Constructor for class meshi.energy.hydrogenBond.HBdistanceList
 
HBend - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
hbEnd - Variable in class meshi.energy.solvate.SolvateParametersList
 
hbEnergy - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
HBondList - Class in meshi.energy.hydrogenBond
 
HBondList(DistanceMatrix, HydrogenBondsParametersList) - Constructor for class meshi.energy.hydrogenBond.HBondList
 
HBondList(DistanceMatrix, HydrogenBondsParametersList, DistanceList) - Constructor for class meshi.energy.hydrogenBond.HBondList
 
hBondList - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
hBondList() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
hBondList - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
hBondList - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
hBondList() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
HBondList.IsAlive - Class in meshi.energy.hydrogenBond
 
HBondList.IsAlive(DistanceMatrix) - Constructor for class meshi.energy.hydrogenBond.HBondList.IsAlive
 
HBondList.IsWithInRmax - Class in meshi.energy.hydrogenBond
 
HBondList.IsWithInRmax() - Constructor for class meshi.energy.hydrogenBond.HBondList.IsWithInRmax
 
HBondList.WithinRmaxIterator - Class in meshi.energy.hydrogenBond
 
HBondList.WithinRmaxIterator(DistanceList) - Constructor for class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
hBondsCreator - Static variable in class meshi.symmetryComplex.utils.GJUtils
Residue number ranges of the gap junction's parts.
hbondsPunishHOCAngleCreator - Static variable in class Beautify
 
HbondsPunishHOCAngleCreator - Class in meshi.energy.hydrogenBondsAngle
Created by IntelliJ IDEA.
HbondsPunishHOCAngleCreator(HydrogenBondsCreator) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleCreator
 
HbondsPunishHOCAngleCreator(double, HydrogenBondsCreator) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleCreator
 
hBondsPunishHOCAngleEnergy - Variable in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleCreator
 
HbondsPunishHOCAngleEnergy - Class in meshi.energy.hydrogenBondsAngle
Created by IntelliJ IDEA.
HbondsPunishHOCAngleEnergy() - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
 
HbondsPunishHOCAngleEnergy(DistanceMatrix, HBondList, double, DistanceList) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
 
HbondsPunishHOCAngleEnergy(DistanceMatrix, HBondList, double, DistanceList, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
 
HbondsPunishHOCAngleEnergy(DistanceMatrix, HBondList, double, DistanceList, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
 
HbondsPunishHOCAngleEnergyElement - Class in meshi.energy.hydrogenBondsAngle
Created by IntelliJ IDEA.
HbondsPunishHOCAngleEnergyElement(DistanceMatrix, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
HbondsPunishHOCAngleEnergyElement(DistanceMatrix, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
HbondsPunishHOCAngleEnergyElement(DistanceMatrix, double, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
hBondsPunishOHNAngleCreator - Static variable in class Beautify
 
HBondsPunishOHNAngleCreator - Class in meshi.energy.hydrogenBondsAngle
 
HBondsPunishOHNAngleCreator(HydrogenBondsCreator) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleCreator
 
HBondsPunishOHNAngleCreator(double, HydrogenBondsCreator) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleCreator
 
hBondsPunishOHNAngleEnergy - Variable in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleCreator
 
HBondsPunishOHNAngleEnergy - Class in meshi.energy.hydrogenBondsAngle
 
HBondsPunishOHNAngleEnergy() - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
 
HBondsPunishOHNAngleEnergy(DistanceMatrix, HBondList, double, DistanceList) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
 
HBondsPunishOHNAngleEnergy(DistanceMatrix, HBondList, double, DistanceList, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
 
HBondsPunishOHNAngleEnergy(DistanceMatrix, HBondList, double, DistanceList, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
 
HBondsPunishOHNAngleEnergyElement - Class in meshi.energy.hydrogenBondsAngle
 
HBondsPunishOHNAngleEnergyElement(DistanceMatrix, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
HBondsPunishOHNAngleEnergyElement(DistanceMatrix, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
HBondsPunishOHNAngleEnergyElement(DistanceMatrix, double, double, double) - Constructor for class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
HBp1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
hbP1 - Variable in class meshi.energy.solvate.SolvateParametersList
 
HBp2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
hbP2 - Variable in class meshi.energy.solvate.SolvateParametersList
 
hbParameters - Static variable in class meshi.energy.solvate.SolvateParametersList
 
hbPrecentage - Variable in class meshi.util.dssp.DSSP
 
hbVal - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
hbVal() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
HBvalAtp1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
hbValAtp1 - Variable in class meshi.energy.solvate.SolvateParametersList
 
HBvalAtp2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
hbValAtp2 - Variable in class meshi.energy.solvate.SolvateParametersList
 
HD1 - Variable in class meshi.molecularElements.extendedAtoms.His
 
HD21 - Variable in class meshi.molecularElements.extendedAtoms.Asn
 
HD22 - Variable in class meshi.molecularElements.extendedAtoms.Asn
 
HE - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
HE1 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
HE2 - Variable in class meshi.molecularElements.extendedAtoms.His
 
HE21 - Variable in class meshi.molecularElements.extendedAtoms.Gln
 
HE22 - Variable in class meshi.molecularElements.extendedAtoms.Gln
 
head() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
head - Variable in class meshi.molecularElements.Residue
First atom of the residue (typicaly N).
head() - Method in class meshi.molecularElements.Residue
 
heavy - Variable in class meshi.geometry.putH.PutHposLog
 
HeavyAtomsFilter - Class in meshi.util.filters
 
HeavyAtomsFilter() - Constructor for class meshi.util.filters.HeavyAtomsFilter
 
height - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
height - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The cylinder's dimensions.
height - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderParameters
 
height - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
HeliumClusterMinimization - Class in <Unnamed>
A program for the generation and energy minimization of a Helium atoms cluster.
HeliumClusterMinimization() - Constructor for class HeliumClusterMinimization
 
HeliumClusterMinimization.HeliumLennardJonesCreator - Class in <Unnamed>
 
HeliumClusterMinimization.HeliumLennardJonesCreator(double) - Constructor for class HeliumClusterMinimization.HeliumLennardJonesCreator
 
HELIX - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
HELIX - Static variable in interface meshi.parameters.MeshiPotential
 
HELIX_OR_COIL - Static variable in interface meshi.parameters.MeshiPotential
 
helixPair - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
helixPair(Distance) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
HelixParametersList - Class in meshi.energy.hydrogenBondsPairs
Created by IntelliJ IDEA.
HelixParametersList() - Constructor for class meshi.energy.hydrogenBondsPairs.HelixParametersList
 
HelixParametersList(String) - Constructor for class meshi.energy.hydrogenBondsPairs.HelixParametersList
 
helixParametersList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
 
helixParametersList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
helixParametersList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
HelixParametersList.IsHydrogenBondsPairsParameters - Class in meshi.energy.hydrogenBondsPairs
 
HelixParametersList.IsHydrogenBondsPairsParameters() - Constructor for class meshi.energy.hydrogenBondsPairs.HelixParametersList.IsHydrogenBondsPairsParameters
 
helixSheetPair(Distance) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
help - Static variable in class meshi.util.overlap.Overlap
 
hFactor - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
hFactor - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
hhSeqDistance - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hhSeqDistance() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hiAng - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
hide() - Method in class meshi.molecularElements.atoms.Atom
 
hideAllBut(AtomList) - Static method in class meshi.util.Utils
 
highBound - Variable in class meshi.util.histogram.Histogram
 
highBound() - Method in class meshi.util.histogram.Histogram
 
highestEnergyAtoms(double) - Method in class meshi.energy.TotalEnergy
 
highestEnergyAtoms(double) - Method in class meshi.energy.TotalEnergy.SortedAtoms
 
highestPeak() - Method in class meshi.util.histogram.Histogram
 
hinge(Angle) - Method in class meshi.geometry.Angle
 
His - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - CD2 - NE2 - HE2 | | HD1 - ND1 ------ CE1
His(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.His
 
histFactor - Variable in class meshi.util.histogram.Histogram
 
Histogram - Class in meshi.util.histogram
 
Histogram(double, double, int) - Constructor for class meshi.util.histogram.Histogram
 
histogram - Variable in class meshi.util.histogram.HistogramBin
 
Histogram.BinCreator - Class in meshi.util.histogram
 
Histogram.BinCreator() - Constructor for class meshi.util.histogram.Histogram.BinCreator
 
Histogram.IsBin - Class in meshi.util.histogram
 
Histogram.IsBin() - Constructor for class meshi.util.histogram.Histogram.IsBin
 
Histogram.RepresentativesIterator - Class in meshi.util.histogram
 
Histogram.RepresentativesIterator(double) - Constructor for class meshi.util.histogram.Histogram.RepresentativesIterator
 
Histogram.RepresentativesIterator.ThresholdFilter - Class in meshi.util.histogram
 
Histogram.RepresentativesIterator.ThresholdFilter(double) - Constructor for class meshi.util.histogram.Histogram.RepresentativesIterator.ThresholdFilter
 
HistogramBin - Class in meshi.util.histogram
 
HistogramBin(double, int) - Constructor for class meshi.util.histogram.HistogramBin
 
HistogramBin(double, int, Histogram) - Constructor for class meshi.util.histogram.HistogramBin
 
HistogramBinAt(int) - Method in class meshi.util.histogram.Histogram
 
HistogramBinAt(double) - Method in class meshi.util.histogram.Histogram
 
hiTor - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
HOelement1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
HOelement1 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
HOelement1() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
HOelement2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
HOelement2 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
HOelement2() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
HomologyFileFilter - Class in meshi.applications.prediction.homology.gui
Created by IntelliJ IDEA.
HomologyFileFilter(String) - Constructor for class meshi.applications.prediction.homology.gui.HomologyFileFilter
 
HomologyFrame - Class in meshi.applications.prediction.homology.gui
 
HomologyFrame() - Constructor for class meshi.applications.prediction.homology.gui.HomologyFrame
 
HomologyFrame11Layout - Class in meshi.applications.prediction.homology.gui
 
HomologyFrame11Layout() - Constructor for class meshi.applications.prediction.homology.gui.HomologyFrame11Layout
 
HomologyModeling - Class in <Unnamed>
 
HomologyModeling() - Constructor for class HomologyModeling
 
HomologyModeling.HomologyLogger - Class in <Unnamed>
 
HomologyModeling.HomologyLogger(MeshiWriter, Protein, CommandList) - Constructor for class HomologyModeling.HomologyLogger
 
HomologyModeling.Loop - Class in <Unnamed>
 
HomologyModeling.Loop() - Constructor for class HomologyModeling.Loop
 
HomologyModeling.LoopAttribute - Class in <Unnamed>
 
HomologyModeling.LoopAttribute() - Constructor for class HomologyModeling.LoopAttribute
 
HomologyModeling.LoopComperator - Class in <Unnamed>
 
HomologyModeling.LoopComperator() - Constructor for class HomologyModeling.LoopComperator
 
HomologyModeling.LoopMode - Enum in <Unnamed>
 
HomologyModeling.LoopMode() - Constructor for enum HomologyModeling.LoopMode
 
HomologyModeling.Three - Class in <Unnamed>
 
HomologyModeling.Three() - Constructor for class HomologyModeling.Three
 
HomologyModeling.TimeTerminator - Class in <Unnamed>
 
HomologyModeling.TimeTerminator(long) - Constructor for class HomologyModeling.TimeTerminator
 
hoSeqDistance - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hoSeqDistance() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
hpunish - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
hqr2() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
hType - Variable in enum meshi.parameters.ResidueType
 
hType() - Method in enum meshi.parameters.ResidueType
 
HubbardPosition - Class in meshi.applications.hubbard
 
HubbardPosition(int, int, double, double[][], double[][]) - Constructor for class meshi.applications.hubbard.HubbardPosition
gets the protein size and the size of subunit we first sent to the rms function
hydrogen - Variable in class meshi.geometry.putH.PutHposLog
 
HYDROGEN_BONDS - Static variable in interface meshi.util.KeyWords
 
HYDROGEN_BONDS_ANGLES - Static variable in interface meshi.util.KeyWords
 
HYDROGEN_BONDS_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
HYDROGEN_BONDS_PAIRS - Static variable in interface meshi.util.KeyWords
 
HYDROGEN_BONDS_PAIRS_BETA_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
HYDROGEN_BONDS_PAIRS_HELIX_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
HYDROGEN_BONDS_PAIRS_PARAMETERS_SURFACE - Static variable in interface meshi.parameters.MeshiPotential
 
HYDROGEN_BONDS_PLANE - Static variable in interface meshi.util.KeyWords
 
HydrogenBondDahiyat - Class in meshi.energy.solvate.hydrogenBonds
A specific hydrogen bond description following: Dahiyat et al.
HydrogenBondDahiyat() - Constructor for class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
HydrogenBondDahiyat(DistanceMatrix, AtomList, double, double, double, double, double) - Constructor for class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
HydrogenBondDahiyatList - Class in meshi.energy.solvate.hydrogenBonds
This class describe a list of hydrogen bonds in a protein.
HydrogenBondDahiyatList() - Constructor for class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
 
HydrogenBondDahiyatList(DistanceMatrix, AtomList, SolvateParametersList) - Constructor for class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
 
hydrogenBondsCreator - Static variable in class Beautify
 
HydrogenBondsCreator - Class in meshi.energy.hydrogenBond
 
HydrogenBondsCreator() - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
HydrogenBondsCreator(double) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
HydrogenBondsCreator(double, int[], Protein, DistanceMatrix, boolean) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
HydrogenBondsCreator(int[], Protein, DistanceMatrix, boolean) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
hydrogenBondsCreator - Variable in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleCreator
 
hydrogenBondsCreator - Variable in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleCreator
 
hydrogenBondsCreator - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
 
hydrogenBondsEnergy - Variable in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
HydrogenBondsEnergy - Class in meshi.energy.hydrogenBond
 
HydrogenBondsEnergy() - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
HydrogenBondsEnergy(DistanceMatrix, HydrogenBondsParametersList, double, HBondList) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
HydrogenBondsEnergy(DistanceMatrix, HydrogenBondsParametersList, double, HBondList, DistanceList) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
HydrogenBondsEnergyElement - Class in meshi.energy.hydrogenBond
 
HydrogenBondsEnergyElement() - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
HydrogenBondsEnergyElement(double) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
hydrogenBondsPairsCreator - Static variable in class Beautify
 
HydrogenBondsPairsCreator - Class in meshi.energy.hydrogenBondsPairs
 
HydrogenBondsPairsCreator(HydrogenBondsCreator) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
 
HydrogenBondsPairsCreator(double, HydrogenBondsCreator) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
 
HydrogenBondsPairsEnergy - Class in meshi.energy.hydrogenBondsPairs
 
HydrogenBondsPairsEnergy() - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
HydrogenBondsPairsEnergy(DistanceMatrix, HelixParametersList, BetaParametersList, PairsOfHBEElementsList, double) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
HydrogenBondsPairsEnergy(DistanceMatrix, HelixParametersList, BetaParametersList, PairsOfHBEElementsList, double, int[], boolean) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
HydrogenBondsPairsEnergy(DistanceMatrix, HelixParametersList, BetaParametersList, PairsOfHBEElementsList, double, double, double) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
HydrogenBondsPairsEnergy(DistanceMatrix, HelixParametersList, BetaParametersList, PairsOfHBEElementsList, double, double, double, int[], boolean) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
HydrogenBondsPairsEnergyElement - Class in meshi.energy.hydrogenBondsPairs
 
HydrogenBondsPairsEnergyElement() - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
HydrogenBondsPairsEnergyElement(HelixParametersList, BetaParametersList, double, double, double) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
HydrogenBondsPairsEnergyElement(HelixParametersList, BetaParametersList, double, double, double, int[], boolean) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
HydrogenBondsPairsParameters - Class in meshi.energy.hydrogenBondsPairs
 
HydrogenBondsPairsParameters(String) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
HydrogenBondsPairsParameters(StringTokenizer) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
HydrogenBondsPairsParameters(int, int, int, int, int, int) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
HydrogenBondsPairsParameters(int, int, int, int, int, int, int) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
HydrogenBondsPairsParametersList - Class in meshi.energy.hydrogenBondsPairs
 
HydrogenBondsPairsParametersList() - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
HydrogenBondsPairsParametersList(String) - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
HydrogenBondsPairsParametersList.NoElements - Class in meshi.energy.hydrogenBondsPairs
 
HydrogenBondsPairsParametersList.NoElements() - Constructor for class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList.NoElements
 
HydrogenBondsParameters - Class in meshi.energy.hydrogenBond
 
HydrogenBondsParameters() - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsParameters
 
HydrogenBondsParameters(StringTokenizer) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsParameters
 
HydrogenBondsParametersList - Class in meshi.energy.hydrogenBond
 
HydrogenBondsParametersList(String, AtomList) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsParametersList
 
HydrogenBondsParametersList(String) - Constructor for class meshi.energy.hydrogenBond.HydrogenBondsParametersList
 
HydrogenTest - Class in <Unnamed>
Created by IntelliJ IDEA.
HydrogenTest() - Constructor for class HydrogenTest
 
HydrogenTest.PolyAla - Class in <Unnamed>
 
HydrogenTest.PolyAla(int, String, CommandList) - Constructor for class HydrogenTest.PolyAla
 
HydrogenTest.ResWithSSFilter - Class in <Unnamed>
 
HydrogenTest.ResWithSSFilter(DSSP) - Constructor for class HydrogenTest.ResWithSSFilter
 
hypot(double, double) - Static method in class meshi.util.mathTools.Jama.Maths
sqrt(a^2 + b^2) without under/overflow.

I

i - Variable in class meshi.optimizers.SimpleStepLength
 
i - Variable in class meshi.optimizers.WolfConditionLineSearch
 
i1w1 - Static variable in class meshi.util.Scmod
 
i1w2 - Static variable in class meshi.util.Scmod
 
i1w3 - Static variable in class meshi.util.Scmod
 
i1w4 - Static variable in class meshi.util.Scmod
 
i1w5 - Static variable in class meshi.util.Scmod
 
i1w6 - Static variable in class meshi.util.Scmod
 
i2w1 - Static variable in class meshi.util.Scmod
 
i2w2 - Static variable in class meshi.util.Scmod
 
i2w3 - Static variable in class meshi.util.Scmod
 
i2w4 - Static variable in class meshi.util.Scmod
 
i2w5 - Static variable in class meshi.util.Scmod
 
i2w6 - Static variable in class meshi.util.Scmod
 
ID - Variable in class meshi.molecularElements.atoms.Atom
A unique identifier of the atom in the MolecularSystem.
ID - Variable in class meshi.molecularElements.atoms.MolecularSystem
 
ID - Variable in class meshi.molecularElements.Residue
A unique identifier.
ID() - Method in class meshi.molecularElements.Residue
Returns the ResidueIdentifier of this Residue or throws an exception if (this != ID.RESIDUE).
Identity - Class in meshi.sequences.aligner
 
Identity(double) - Constructor for class meshi.sequences.aligner.Identity
 
identity(int, int) - Static method in class meshi.util.mathTools.Jama.Matrix
Generate identity matrix
identityAlignment(Sequence, Sequence) - Static method in class meshi.sequences.SequenceAlignment
 
ifCrossing(Atom, Atom, Atom, Atom, boolean) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
iformat - Variable in class meshi.energy.TotalEnergy
 
ignoreLoopResidues() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
ignoreLoopResidues() - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
ignoreUnhappyResidues(double) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
ignoreUnhappyResidues(double) - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
Ile - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB - CG1 - CD1 | CG2
Ile(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Ile
 
image() - Method in enum meshi.molecularElements.atoms.AtomStatus
 
ImageAtom - Class in meshi.symmetryComplex.molecularImageElements
Created by IntelliJ IDEA.
ImageAtom(Atom, Transformation) - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
ImageAtomList - Class in meshi.symmetryComplex.molecularImageElements
A list of ImageAtoms
ImageAtomList(AtomList, Transformation) - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageAtomList
 
ImageAtomList(Residue, Transformation) - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageAtomList
 
ImageAtomList(ImageChain, Transformation) - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageAtomList
 
ImageChain - Class in meshi.symmetryComplex.molecularImageElements
Created by IntelliJ IDEA.
ImageChain(Protein, Chain, String, Transformation) - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageChain
 
ImageChain.IsImageChain - Class in meshi.symmetryComplex.molecularImageElements
 
ImageChain.IsImageChain() - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageChain.IsImageChain
 
ImageResidue - Class in meshi.symmetryComplex.molecularImageElements
 
ImageResidue(Residue, String, Transformation) - Constructor for class meshi.symmetryComplex.molecularImageElements.ImageResidue
 
imageResidues - Variable in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
imageResidues() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
imortal - Variable in class meshi.molecularElements.atoms.AtomPair
 
imortal() - Method in class meshi.molecularElements.atoms.AtomPair
 
inactivateFarFromAtom(Atom, double) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
inactive - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
inactiveAtConstructor - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
includesNowhereAtoms() - Method in class meshi.molecularElements.atoms.AtomList
 
increment() - Method in class meshi.util.histogram.HistogramBin
 
INDENT - Variable in class meshi.util.formats.Format
 
indicatorToUpdateHB - Variable in class meshi.geometry.DistanceMatrix
 
indicatorToUpdateHB() - Method in class meshi.geometry.DistanceMatrix
 
indicatorToUpdateHB - Variable in class meshi.geometry.OldDistanceMatrix
 
indicatorToUpdateHB - Variable in class meshi.symmetryComplex.geometryImage.DistanceMatrixNoImageAtoms
 
infForce - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
infForce - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
infForce3 - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
infForce3 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
INFINITE_DISTANCE - Static variable in class meshi.geometry.Distance
 
INFINITY - Static variable in class meshi.energy.AbstractEnergy
1/0 good for dubugging.
INFINITY - Static variable in class meshi.energy.TotalEnergy
 
INFINITY - Variable in class meshi.geometry.FrozenCoordinates
 
INFINITY - Variable in class meshi.optimizers.SimpleStepLength
 
INFLATE_ENERGY - Static variable in interface meshi.util.KeyWords
 
InflateParameters - Class in meshi.energy.simpleEnergyTerms.inflate
 
InflateParameters() - Constructor for class meshi.energy.simpleEnergyTerms.inflate.InflateParameters
 
InflateParametersDialog - Class in meshi.applications.prediction.homology.gui
 
InflateParametersDialog() - Constructor for class meshi.applications.prediction.homology.gui.InflateParametersDialog
 
InflateParametersLayout - Class in meshi.applications.prediction.homology.gui
 
InflateParametersLayout() - Constructor for class meshi.applications.prediction.homology.gui.InflateParametersLayout
 
InflateParametersList - Class in meshi.energy.simpleEnergyTerms.inflate
 
InflateParametersList() - Constructor for class meshi.energy.simpleEnergyTerms.inflate.InflateParametersList
 
init(String[]) - Static method in class AbInitio
 
init(String[]) - Static method in class ChooseTemplate
 
init(String[]) - Static method in class HydrogenTest
 
init(String[]) - Static method in class meshi.applications.corpus.MergeCorpora
================================= init ========================================= A static function for parsing of the command line arguments and assigning the variables commandsFileName, modelFileName and randomNumberSeed with the right inputs.
init(String[]) - Static method in class meshi.applications.corpus.RunThreadingExperiment
================================= init ========================================= A static function for parsing of the command line arguments and assigning the variables commandsFileName, modelFileName and randomNumberSeed with the right inputs.
init() - Method in class meshi.optimizers.BFGS
 
init() - Method in class meshi.optimizers.ConjugateGradient
 
init() - Method in class meshi.optimizers.LBFGS
 
init() - Method in class meshi.optimizers.Minimizer
 
init() - Method in class meshi.optimizers.SteepestDecent
 
init(AtomList, AtomList) - Static method in class meshi.util.GDTcalculator
 
init(String[], String) - Static method in class meshi.util.Utils
A standard method to create the commands list.
init(String[], int, String) - Static method in class meshi.util.Utils
 
init(String[], int, int, String) - Static method in class meshi.util.Utils
 
init(CommandList) - Static method in class MinimizeProtein
 
init(String[]) - Static method in class ModelRanker
 
init(String[]) - Static method in class SimplestMinimizeProtein
================================= init ========================================= A static function for parsing of the command line arguments and assigning the variables commandsFileName, modelFileName and randomNumberSeed with the right inputs.
initFields(int, int) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
initHessian() - Method in class meshi.optimizers.BFGS
 
INITIAL_TEMPERATURE - Static variable in interface meshi.util.KeyWords
 
InitialEvaluation - Class in <Unnamed>
 
InitialEvaluation() - Constructor for class InitialEvaluation
 
initialize(HubbardPosition[]) - Static method in class meshi.util.GDTcalculator
 
initialLocationsMatrix - Variable in class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
The constructor associates any bond with its parameters.
initialModel(Protein, ResidueAlignment, List<HomologyModeling.Loop>, CommandList) - Static method in class HomologyModeling
 
initialRmsGdt() - Method in class Beautify.BeautifyLogger
 
initialStepLength - Variable in class meshi.optimizers.SteepestDecent
 
initialTemperature - Variable in class meshi.optimizers.TemperatureGenerator
 
initiateAtoms() - Method in class meshi.molecularElements.Residue
 
initiateFields(double[][], double[][], int, String, String) - Static method in class meshi.util.overlap.Overlap
A function that initializes all the class fields so that
all the other functions can use them
initPreviousCoordinates() - Method in class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
initRandom() - Static method in class meshi.util.MeshiProgram
Initializes the random number generator.
initRandom(int) - Static method in class meshi.util.MeshiProgram
 
initRandom(String[]) - Static method in class meshi.util.MeshiProgram
 
initStepSteepestDecent - Variable in class meshi.optimizers.BFGS
 
initStepSteepestDecent - Static variable in class meshi.optimizers.ConjugateGradient
 
initStepSteepestDecent - Variable in class meshi.optimizers.LBFGS
 
inList(int, char[]) - Method in class meshi.util.dssp.DSSP
 
inLoop(Residue) - Method in class meshi.symmetryComplex.topologyMap.Topology
 
inLoop(int) - Method in class meshi.symmetryComplex.topologyMap.Topology
 
innerBarrelFilter - Static variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
innerBarrelHeight - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
innerBarrelInnerR - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
innerBarrelOuterR - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
innerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
innerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The cylinder's dimensions.
innerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderParameters
 
innerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
INPUT_FILE - Static variable in interface meshi.util.KeyWords
 
inputNewHBList - Static variable in class meshi.energy.hydrogenBond.HBondList
 
inputNewHBList() - Static method in class meshi.energy.hydrogenBond.HBondList
 
inRadiusFromNonFrozen(Atom) - Method in class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
insert(int, AtomCore, AtomCore, int, double, double, double, double, DistanceList, ArrayList<DistanceList>) - Method in class meshi.geometry.MatrixRow
 
insert(ResidueAlignmentColumn) - Method in class meshi.sequences.ResidueAlignment
 
insertFragToProt(DunbrackLib, int) - Method in class meshi.applications.corpus.LocalFragmentLib
It is assumed that isFragCompatible was run before this method was called, so that fragCoors is updated.
insertFragToProt(DunbrackLib, int, Protein, int, int, int) - Method in class meshi.applications.corpus.LocalFragmentLib
It is assumed that isFragCompatible was run before this method was called, so that fragCoors is updated.
insertion(Iterator, List<HomologyModeling.Loop>, HomologyModeling.Loop, HomologyModeling.Three) - Static method in class HomologyModeling
 
insertion - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
insertionEnd(Iterator, List<HomologyModeling.Loop>, HomologyModeling.Loop, HomologyModeling.Three) - Static method in class HomologyModeling
 
insertionToList - Variable in class meshi.energy.hydrogenBond.HBondList
 
INTER_SEGMENT_FACTOR - Static variable in interface meshi.util.KeyWords
 
INTER_SEGMENT_TOLERANCE - Static variable in interface meshi.util.KeyWords
 
interestingTorsion(Torsion) - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
checks whether a given torsion angle is in [PHI,PSI,CHI_1-CHI_4].
intermediateCAModel(int, Protein, double, int) - Method in class Beautify.BeautifyLogger
 
internal - Variable in class meshi.util.histogram.Histogram.RepresentativesIterator
 
internalArray - Variable in class meshi.geometry.DistanceList
 
internalArray - Variable in class meshi.util.AttributesRack
 
interSafeGuard - Variable in class meshi.optimizers.WolfConditionLineSearch
 
interSafeGuardFactor - Variable in class meshi.optimizers.WolfConditionLineSearch
 
INTRA_SEGMENT_FACTOR - Static variable in interface meshi.util.KeyWords
 
INTRA_SEGMENT_TOLERANCE - Static variable in interface meshi.util.KeyWords
 
INV_BUFF - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
INV_BUFF - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
invBB - Variable in class meshi.geometry.Torsion
 
invDistance - Variable in class meshi.geometry.Distance
The inverse of the distance between atom1 & atom2.
invDistance() - Method in class meshi.geometry.Distance
Get the inverse of the distance between atom1 and atom2.
invDistance() - Method in class meshi.geometry.DistanceMirror
 
inverse() - Method in class meshi.util.mathTools.Jama.Matrix
Matrix inverse or pseudoinverse
invWCDMinusSig4PlusBETA - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
isA() - Method in class meshi.energy.hydrogenBond.LennardJonesParameters
 
isA() - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
isA() - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
isA() - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
isA() - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
isA() - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
isAComment() - Method in class meshi.PDB.PdbLine
 
isAHeteroAtom() - Method in class meshi.PDB.PdbLine
 
isAlive - Variable in class meshi.energy.hydrogenBond.HBondList
 
isAModel() - Method in class meshi.PDB.PdbLine
 
isAnAtom() - Method in class meshi.PDB.PdbLine
 
isAnAtomOrHeteroAtom() - Method in class meshi.PDB.PdbLine
 
isAPdbFile - Class in meshi.PDB
 
isAPdbFile() - Constructor for class meshi.PDB.isAPdbFile
 
isBackbone() - Method in class meshi.molecularElements.atoms.Atom
 
isBetaPair() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
isCarbon() - Method in class meshi.molecularElements.atoms.Atom
 
isCarbon() - Method in enum meshi.parameters.AtomType
 
isChi1(Torsion) - Static method in class meshi.geometry.TorsionList
 
isChi2(Torsion) - Static method in class meshi.geometry.TorsionList
 
isChi3(Torsion) - Static method in class meshi.geometry.TorsionList
 
isChi4(Torsion) - Static method in class meshi.geometry.TorsionList
 
isChi5(Torsion) - Static method in class meshi.geometry.TorsionList
 
isCimp(Torsion) - Static method in class meshi.geometry.TorsionList
 
IsClass - Class in meshi.util.filters
 
IsClass(Class) - Constructor for class meshi.util.filters.IsClass
 
isConnectedToNonFrozen(Atom, int) - Method in class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
isDistanceBetweenLoops - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
isEmpty() - Method in class meshi.geometry.DistanceList
 
isExactMach() - Method in class meshi.sequences.SequenceAlignment
 
isExactMach() - Method in class meshi.sequences.SequenceAlignmentColumn
 
isExactMachWithGaps() - Method in class meshi.sequences.SequenceAlignment
 
isExactMachWithGaps() - Method in class meshi.sequences.SequenceAlignmentColumn
 
isFasta(String) - Static method in class meshi.sequences.FastaList
 
isFirstStructure - Static variable in class CalculateEnergyFromStructuresListAverages
 
isFirstStructure - Static variable in class ColorByEnergy
 
isFirstStructure - Static variable in class TestElectrostatics
 
isFragCompatible(int, Protein, int, int, int, double) - Method in class meshi.applications.corpus.LocalFragmentLib
This method check whether the fragment 'indInLib' in the lib can overlap the given coordinates bellow a certain RMS cut off.
isFragCompatible(int, double) - Method in class meshi.applications.corpus.LocalFragmentLib
The 'prot', 'overlap', 'manner' and 'residueFragStart' are from the class's fields.
isFragCompatibleForConstruction(int, double) - Method in class meshi.applications.corpus.LocalFragmentLib
This method is used only during the construction when 'libOrig' is not yet ready.
isFullRank() - Method in class meshi.util.mathTools.Jama.QRDecomposition
Is the matrix full rank?
isH - Variable in class meshi.energy.hydrogenBond.HB_AtomAttribute
 
isHbond - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
isHelixPair() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
isHO - Variable in class meshi.energy.hydrogenBond.GoodResiduesForHB
 
IsHO - Class in meshi.energy.hydrogenBond
 
IsHO() - Constructor for class meshi.energy.hydrogenBond.IsHO
 
isHydrogen() - Method in class meshi.molecularElements.atoms.Atom
 
isHydrogen() - Method in enum meshi.parameters.AtomType
 
isItGzipped(File) - Static method in class meshi.util.file.MeshiLineReader
 
isKnot(Protein, CommandList) - Static method in class Beautify
 
isLegalIndices(int, int) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
isLegalIndices(int, int) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
isLegalMatrixObject(Object) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
isLegalMatrixObject(Object) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
isLegalSubmatrixBoundaries(int, int, int, int) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
isLegalSubmatrixBoundaries(int, int, int, int) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
isLegalTransformation(Matrix) - Static method in class meshi.symmetryComplex.transformations.Transformation
A legal transformation is composed of translation and/or rotation only.
Such matrices have the following attribute: The 3x3 submatrix [0..2]x[0..2] is orthogonal.
Orthogonality is tested in this way: A given matrix is orthogonal iff when multiplying it by its transposed matrix the result is the unit matrix.
isLoop() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isLoop(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isLoopCloseToAnyInTheVector(LoopResults, double) - Method in class meshi.applications.corpus.LoopResultVector
 
isNamed(Angle) - Method in class meshi.geometry.AngleList
 
isNamed(Torsion) - Static method in class meshi.geometry.TorsionList
 
isNimp(Torsion) - Static method in class meshi.geometry.TorsionList
 
isNitrogen() - Method in class meshi.molecularElements.atoms.Atom
 
isNitrogen() - Method in enum meshi.parameters.AtomType
 
isNonsingular() - Method in class meshi.util.mathTools.Jama.LUDecomposition
Is the matrix nonsingular?
isNot13 - Variable in class meshi.energy.hydrogenBond.GoodResiduesForHB
 
isO - Variable in class meshi.energy.hydrogenBond.HB_AtomAttribute
 
isOmega(Torsion) - Static method in class meshi.geometry.TorsionList
 
isOn() - Method in class meshi.energy.AbstractEnergy
 
isOn() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
isOn() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
isOn() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
isOneBetta() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
isOneHelix() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
isOOP(Torsion) - Static method in class meshi.geometry.TorsionList
 
isOrthogonal() - Method in interface meshi.symmetryComplex.transformations.Matrix
 
isOrthogonal() - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
isOxygen() - Method in class meshi.molecularElements.atoms.Atom
 
isOxygen() - Method in enum meshi.parameters.AtomType
 
isPhi(Torsion) - Static method in class meshi.geometry.TorsionList
 
isPointInCylinder(Coordinates, double, double, double) - Static method in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
For loops building.
isPolynomialNeeded(int, int[], int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
checks whether this polynomial is of the parameters needed.
isPP - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
isPP() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
isProblematic() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isProblematic(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isProblematicOrHasProblematicNeighbor(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isProblematicOrLoop(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isPsi(Torsion) - Static method in class meshi.geometry.TorsionList
 
isSecondaryStructure(char) - Static method in enum meshi.parameters.SecondaryStructure
 
isSEQRES() - Method in class meshi.PDB.PdbLine
 
isspd - Variable in class meshi.util.mathTools.Jama.CholeskyDecomposition
Symmetric and positive definite flag.
isSPD() - Method in class meshi.util.mathTools.Jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
isSteps - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
isStrictClashes - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
isSulfur() - Method in class meshi.molecularElements.atoms.Atom
 
isSulfur() - Method in enum meshi.parameters.AtomType
 
issymmetric - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Symmetry flag.
isVisible(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
isWithInRmax - Variable in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
isWithinRmax - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
isWithInRmax - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
isZero(double) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
isZero(double) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
iterationNum - Variable in class meshi.optimizers.BFGS
 
iterationNum - Variable in class meshi.optimizers.ConjugateGradient
 
iterationNum - Variable in class meshi.optimizers.LBFGS
 
iterationNum - Variable in class meshi.optimizers.SteepestDecent
 
ITERATIONS_ALLATOM - Static variable in interface meshi.util.KeyWords
 
ITERATIONS_BACKBONE - Static variable in interface meshi.util.KeyWords
 
ITERATIONS_CA - Static variable in interface meshi.util.KeyWords
 
iterator() - Method in class meshi.energy.simpleEnergyTerms.ParametersList
 
iterator() - Method in class meshi.geometry.DistanceList
 

J

join(String, String) - Static method in class Pdb2Fasta
 
jumble(Protein) - Static method in class meshi.util.rotamericTools.RotamericTools
 

K

key() - Method in class CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute
 
key() - Method in class CalculateEnergyFromStructuresListAverages.GaussianAttributes
 
key() - Method in class ColorByEnergy.DistanceFromCatalyticAttribute
 
key() - Method in class ColorByEnergy.GaussianAttributes
 
key() - Method in class HomologyModeling.LoopAttribute
 
key() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
key - Variable in class meshi.applications.prediction.ModelData.TermComparator
 
key() - Method in class meshi.applications.prediction.OriginalAtom
 
key - Variable in class meshi.energy.EnergyCreator
The keyword for the energy term.
key - Static variable in class meshi.energy.hydrogenBond.HB_AtomAttribute
 
key() - Method in class meshi.energy.hydrogenBond.HB_AtomAttribute
 
key - Static variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
key() - Method in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
key - Static variable in class meshi.energy.hydrogenBond.LennardJonesParameters
 
key() - Method in class meshi.energy.hydrogenBond.LennardJonesParameters
 
key() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.SummaAttribute
 
key() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
key() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.ResidueTorsionsPropensityAttribute
 
key() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
key() - Method in class meshi.energy.solvate.SolvateDistanceAttribute
 
key() - Method in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
key() - Method in class meshi.molecularElements.Residue
 
key() - Method in enum meshi.parameters.SecondaryStructure
 
key() - Method in class meshi.sequences.SequenceAlignmentCell
 
key() - Method in class meshi.sequences.SequenceAlignmentColumn
 
Key - Class in meshi.util
Key is a semantic sugar for a String that is used as a key to the ComandList class.
Key(String) - Constructor for class meshi.util.Key
 
key - Variable in class meshi.util.Key
 
key() - Method in interface meshi.util.MeshiAttribute
 
key - Variable in class meshi.util.MeshiProgram.GlobalElement
 
key() - Method in class meshi.util.MeshiProgram.GlobalElement
 
key - Variable in class meshi.util.Pair
 
key - Variable in class SelectModels.ModelComparator
 
KEY_KEY - Static variable in interface meshi.util.KeyWords
 
keyExists(Key) - Method in class meshi.util.CommandList
Testing if some key exists
keyExists(String) - Method in class meshi.util.CommandList
Testing if some key is exists
keyExists(Key, Key) - Method in class meshi.util.CommandList
Testing if a combined key exists
keyExists(String, String) - Method in class meshi.util.CommandList
Testing if a combined key exists
keys - Static variable in class meshi.util.Key
 
keys - Variable in class meshi.util.string.StringFilter
 
KeyWords - Interface in meshi.util
 
kickStart() - Method in class meshi.optimizers.BFGS
 
kickStart() - Method in class meshi.optimizers.ConjugateGradient
 
kickStart() - Method in class meshi.optimizers.LBFGS
 
kickStart() - Method in class meshi.optimizers.Minimizer
 
kickStart() - Method in class meshi.optimizers.SteepestDecent
 
kill(String) - Method in class meshi.util.Terminator
 
knot() - Method in class Beautify.BeautifyLogger
 
knot() - Method in class HomologyModeling.HomologyLogger
 
KOEHL_FILE - Static variable in interface meshi.util.KeyWords
 
KolDichfin - Class in meshi.util.filters
 
KolDichfin() - Constructor for class meshi.util.filters.KolDichfin
 

L

L - Variable in class meshi.util.mathTools.Jama.CholeskyDecomposition
Array for internal storage of decomposition.
LABEL_ATOM_NAMES_BEGIN - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
LABEL_ATOM_NAMES_END - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
LABEL_BINS_BEGIN - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
LABEL_BINS_END - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
LABEL_PMF_BEGIN - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
LABEL_PMF_END - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
labelAlphaAngleEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelAlphaTorsionEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelAngleEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelBondedEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelExcludedVolumeWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelFlatRamachEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelHydrogenBondsPairsWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelHydrogenBondsWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelInflateEnergyRmsTarget - Variable in class meshi.applications.prediction.homology.gui.InflateParametersDialog
 
labelInflateEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.InflateParametersDialog
 
labelLennardJonesCaWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelLennardJonesWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelLoopNIterationsAllAtoms - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
labelLoopNIterationsBackbone - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
labelLoopNIterationsCA - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
labelLoosenEdgeLength - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
labelMinimizeMaxSteps - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
labelMinimizeReportEvery - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
labelMinimizeTolerane - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
labelNonFrozenBondDepth - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
labelNonFrozenRadius - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
labelOutOfPlaneEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelParameters - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
labelPlaneEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelPropensityTorsionEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelSeedNumber - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
labelSolvateCA100EnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelSolventAa40 - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelSolventBb60 - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
labelTargetName - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
labelTwoTorsionsEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
laconic(String) - Method in class meshi.molecularElements.atoms.AtomPair
 
largeNumber - Variable in class meshi.molecularElements.atoms.AtomPair
 
largeNumber() - Method in class meshi.molecularElements.atoms.AtomPair
 
largeType - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
largeType - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
largeType - Variable in class meshi.geometry.Distance
 
largeType - Variable in class meshi.molecularElements.atoms.AtomPair
 
largeType() - Method in class meshi.molecularElements.atoms.AtomPair
 
lastColumn - Variable in class meshi.sequences.ResidueAlignment
 
lastEmpty - Static variable in class meshi.geometry.MatrixRow
 
lastRes(AtomList) - Method in class meshi.geometry.fragments.DresserFullFrag
 
lastStepLength - Variable in class meshi.optimizers.SteepestDecent
 
lastStepLength() - Method in class meshi.optimizers.SteepestDecent
 
lastString() - Method in class meshi.util.string.StringList
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.HomologyFrame11Layout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.InflateParametersLayout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.OptionDialog3Layout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout
 
layoutContainer(Container) - Method in class meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout
 
LBFGS - Class in meshi.optimizers
This class implements a LBFGS minimizer according to the scheme in: Numerical Optimization by J.
LBFGS(TotalEnergy, double, int, int) - Constructor for class meshi.optimizers.LBFGS
 
LBFGS(TotalEnergy, double, int, int, int, int, int, boolean, double, double, double, int, int, double, double, double) - Constructor for class meshi.optimizers.LBFGS
 
LBFGS - Static variable in interface meshi.util.KeyWords
 
LBFGS.Element - Class in meshi.optimizers
 
LBFGS.Element() - Constructor for class meshi.optimizers.LBFGS.Element
 
leftCell - Variable in class meshi.sequences.aligner.Cell
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
verifies residue type is a legal residue types for class.
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi0
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi1
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi2
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi3
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi4
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
verifies residue type is a legal residue types for class.
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi0
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi1
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi2
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi3
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi4
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
verifies residue type is a legal residue types for class.
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi0
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi1
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi2
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi3
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi4
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
verifies residue type is a legal residue types for class.
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi0
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi1
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi2
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi3
 
legalResidueType() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi4
 
len - Static variable in class meshi.util.GDTcalculator
 
length - Static variable in class AbInitio
 
length - Static variable in class HydrogenTest
 
length() - Method in class meshi.PDB.PdbLine
 
LENNARD_JONES - Static variable in interface meshi.util.KeyWords
 
LENNARD_JONES_CA - Static variable in interface meshi.util.KeyWords
 
LENNARD_JONES_ELEMENT_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
LENNARD_JONES_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
LENNARD_JONES_PARAMETERS_BACKBONE - Static variable in interface meshi.parameters.MeshiPotential
 
LENNARD_JONES_PARAMETERS_CA - Static variable in interface meshi.parameters.MeshiPotential
 
LennardJones - Class in meshi.energy.pairwiseNonBondedTerms.LennardJones
 
LennardJones() - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJones
 
LennardJones(DistanceMatrix, double, double[][][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJones
 
LennardJonesCreator - Class in meshi.energy.pairwiseNonBondedTerms.LennardJones
 
LennardJonesCreator(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator
 
LennardJonesCreator() - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator
 
LennardJonesCreatorCa - Class in meshi.energy.pairwiseNonBondedTerms.LennardJones
 
LennardJonesCreatorCa(double) - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreatorCa
 
LennardJonesCreatorCa() - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreatorCa
 
LennardJonesEnergyElement - Class in meshi.energy.pairwiseNonBondedTerms.LennardJones
 
LennardJonesEnergyElement() - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
LennardJonesEnergyElement(DistanceMatrix, double, double[][][]) - Constructor for class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
LennardJonesParameters - Class in meshi.energy.hydrogenBond
 
LennardJonesParameters() - Constructor for class meshi.energy.hydrogenBond.LennardJonesParameters
 
LennardJonesParameters(StringTokenizer) - Constructor for class meshi.energy.hydrogenBond.LennardJonesParameters
 
LennardJonesParameters.isA - Class in meshi.energy.hydrogenBond
 
LennardJonesParameters.isA() - Constructor for class meshi.energy.hydrogenBond.LennardJonesParameters.isA
 
LennardJonesParametersList - Class in meshi.energy.hydrogenBond
 
LennardJonesParametersList(String) - Constructor for class meshi.energy.hydrogenBond.LennardJonesParametersList
 
Leu - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB - CG - CD1 | CD2
Leu(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Leu
 
lib - Static variable in class InitialEvaluation
 
lib - Static variable in class meshi.util.Scmod
The implemented interfaces defines the names of atom and residue types.
libEnergy - Variable in class meshi.applications.corpus.LocalFragmentLib
 
libOrig - Variable in class meshi.applications.corpus.LocalFragmentLib
 
libOrig(int) - Method in class meshi.applications.corpus.LocalFragmentLib
 
libSize - Variable in class meshi.applications.corpus.LocalFragmentLib
 
libSize() - Method in class meshi.applications.corpus.LocalFragmentLib
 
line - Variable in class meshi.PDB.PdbLine
 
line - Variable in class meshi.util.Command
 
LINEAR_RG - Static variable in interface meshi.util.KeyWords
 
LinearRgCreator - Class in meshi.energy.linearRG
An implicit solvation energy term for all-atom models, modeling a 4.0 angs solvation shell around each atom.
LinearRgCreator() - Constructor for class meshi.energy.linearRG.LinearRgCreator
 
LinearRgCreator(double) - Constructor for class meshi.energy.linearRG.LinearRgCreator
 
LinearRgEnergy - Class in meshi.energy.linearRG
 
LinearRgEnergy() - Constructor for class meshi.energy.linearRG.LinearRgEnergy
 
LinearRgEnergy(AtomList, double, double, RgCalculator) - Constructor for class meshi.energy.linearRG.LinearRgEnergy
 
lineSearch - Variable in class meshi.optimizers.BFGS
 
lineSearch - Variable in class meshi.optimizers.ConjugateGradient
 
lineSearch - Variable in class meshi.optimizers.LBFGS
 
LineSearch - Class in meshi.optimizers
An abstract class of the common function calls in all the Line-Search procedure.
LineSearch(TotalEnergy) - Constructor for class meshi.optimizers.LineSearch
 
lineSearch - Variable in class meshi.optimizers.SteepestDecent
 
LineSearchException - Exception in meshi.optimizers
 
LineSearchException(int, String) - Constructor for exception meshi.optimizers.LineSearchException
 
list - Variable in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
list - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
listSize - Variable in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
listSize - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
LJ_ENVIRONMENT_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
LJ_ENVIRONMENT_PARAMETERS_BACKBONE - Static variable in interface meshi.parameters.MeshiPotential
 
LJ_ENVIRONMENT_PARAMETERS_CA - Static variable in interface meshi.parameters.MeshiPotential
 
loadingParametersFailed(String) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
Throws exception.
loAng - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
LocalFragmentLib - Class in meshi.applications.corpus
The purpose of this class is is class is to build a fragment library that is compatible with a certain sequence.
LocalFragmentLib(Corpus, int[], int, double, int, int, Protein, int, int, int, double) - Constructor for class meshi.applications.corpus.LocalFragmentLib
 
LocalFragmentLib(Corpus, int[], int, double, int, int) - Constructor for class meshi.applications.corpus.LocalFragmentLib
 
localSigma - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
log - Variable in class meshi.optimizers.MCM
 
Logger - Interface in meshi.util
 
lookAtThisPair - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
LOOKUP_SIZE - Static variable in class meshi.geometry.ArcCos
 
loop - Variable in class meshi.applications.prediction.beautify.BeautifyAttribute
 
Loop - Class in meshi.symmetryComplex.topologyMap
Created by IntelliJ IDEA.
Loop(CommandList, int) - Constructor for class meshi.symmetryComplex.topologyMap.Loop
 
LOOP - Variable in class meshi.symmetryComplex.topologyMap.Topology
 
loop(int) - Method in class meshi.symmetryComplex.topologyMap.Topology
 
LOOP1 - Static variable in interface meshi.util.KeyWords
 
LOOP1_IN_BARREL_RESIDUES - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
loop1Filter - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesFilter
 
LOOP2 - Static variable in interface meshi.util.KeyWords
 
LOOP2_IN_BARREL_RESIDUES - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
loop2Filter - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesFilter
 
loop_over_Popo(HubbardPosition[]) - Static method in class meshi.util.GDTcalculator
 
LOOP_RESIDUE - Static variable in interface meshi.util.MeshiAttribute
 
loopBounds(int) - Method in class meshi.symmetryComplex.topologyMap.Topology
 
loopFirstAtomNumber(int) - Method in class meshi.symmetryComplex.topologyMap.Topology
 
loopLastAtomNumber(int) - Method in class meshi.symmetryComplex.topologyMap.Topology
 
loopMap - Static variable in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
loopMap() - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
loopMap(int) - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
loopMap() - Method in class meshi.symmetryComplex.topologyMap.Topology
 
LoopResults - Class in meshi.applications.corpus
 
LoopResults() - Constructor for class meshi.applications.corpus.LoopResults
 
LoopResults(double, double, double, double, double) - Constructor for class meshi.applications.corpus.LoopResults
 
LoopResultVector - Class in meshi.applications.corpus
 
LoopResultVector() - Constructor for class meshi.applications.corpus.LoopResultVector
 
loops - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
loops - Variable in class meshi.symmetryComplex.topologyMap.Topology
 
loops() - Method in class meshi.symmetryComplex.topologyMap.Topology
 
loopsAdded(Protein) - Method in class HomologyModeling.HomologyLogger
 
loopsResiduesFilter - Static variable in class meshi.symmetryComplex.utils.GJFilters
 
LoopUtils - Class in meshi.symmetryComplex.utils
Created by IntelliJ IDEA.
LoopUtils() - Constructor for class meshi.symmetryComplex.utils.LoopUtils
 
LoopUtils.Line - Class in meshi.symmetryComplex.utils
 
LoopUtils.Line() - Constructor for class meshi.symmetryComplex.utils.LoopUtils.Line
 
LoopUtils.Point - Class in meshi.symmetryComplex.utils
 
LoopUtils.Point(double, double) - Constructor for class meshi.symmetryComplex.utils.LoopUtils.Point
 
LOOSEN_EDGE_LENGTH - Static variable in interface meshi.util.KeyWords
 
loTor - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
lowBound - Variable in class meshi.util.histogram.Histogram
 
lowBound() - Method in class meshi.util.histogram.Histogram
 
lowestEnergyAtoms(double) - Method in class meshi.energy.TotalEnergy.SortedAtoms
 
LU - Variable in class meshi.util.mathTools.Jama.LUDecomposition
Array for internal storage of decomposition.
lu() - Method in class meshi.util.mathTools.Jama.Matrix
LU Decomposition
LUDecomposition - Class in meshi.util.mathTools.Jama
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class meshi.util.mathTools.Jama.LUDecomposition
LU Decomposition
lut - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
These fields are for general use in the class
lut - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
These fields are for general use in the class
lut - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
lut - Variable in class meshi.energy.solvate.SolvateEnergy
The look-up table (lut) converts the atom internal number (field of Atom), which is the index of the array, to its index in the atom list given to the constructor.
lut - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
These fields are for general use in the class
lutHB - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
lutHB() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
Lys - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - CD - CE - NZ
Lys(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Lys
 

M

m - Variable in class meshi.optimizers.LBFGS
 
m - Variable in class meshi.util.mathTools.Jama.LUDecomposition
Row and column dimensions, and pivot sign.
m - Variable in class meshi.util.mathTools.Jama.Matrix
Row and column dimensions.
m - Variable in class meshi.util.mathTools.Jama.QRDecomposition
Row and column dimensions.
m - Variable in class meshi.util.mathTools.Jama.SingularValueDecomposition
Row and column dimensions.
magnitude(double[]) - Static method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
magnitudeForce - Variable in class meshi.optimizers.BFGS
 
magnitudeForce - Variable in class meshi.optimizers.ConjugateGradient
 
magnitudeForce - Variable in class meshi.optimizers.LBFGS
 
magnitudeForce - Variable in class meshi.optimizers.SteepestDecent
 
main(String[]) - Static method in class AbInitio
 
main(String[]) - Static method in class Beautify
 
main(String[]) - Static method in class CalcGDT
 
main(String[]) - Static method in class CalculateEnergyFromStructuresListAverages
 
main(String[]) - Static method in class ChooseTemplate
 
main(String[]) - Static method in class ColorByEnergy
 
main(String[]) - Static method in class EnergyStatistics
 
main(String[]) - Static method in class EnergyStatisticsForAtom
 
main(String[]) - Static method in class ExtractChain
 
main(String[]) - Static method in class HeliumClusterMinimization
 
main(String[]) - Static method in class HomologyModeling
 
main(String[]) - Static method in class HydrogenTest
 
main(String[]) - Static method in class InitialEvaluation
 
main(String[]) - Static method in class meshi.applications.corpus.MergeCorpora
 
main(String[]) - Static method in class meshi.applications.corpus.RunThreadingExperiment
 
main(String[]) - Static method in class meshi.applications.prediction.homology.gui.HomologyFrame
 
main(String[]) - Static method in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
main(String[]) - Static method in class meshi.applications.prediction.homology.gui.OptionDialog
 
main(String[]) - Static method in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
main(String[]) - Static method in class meshi.symmetryComplex.proteinsGJ.RunBackboneCompleterAndMinimizer
 
main(String[]) - Static method in class meshi.symmetryComplex.proteinsGJ.RunBackboneMCM
 
main(String[]) - Static method in class meshi.symmetryComplex.proteinsGJ.RunFullModeller
 
main(String[]) - Static method in class MinimizeProtein
the only parameter of the program is expected to be the name of the commands file
main(String[]) - Static method in class ModelRanker
 
main(String[]) - Static method in class Optimize
 
main(String[]) - Static method in class Pdb2Fasta
 
main(String[]) - Static method in class Refine
 
main(String[]) - Static method in class RoisFirstMeshiProgram
 
main(String[]) - Static method in class SCMOD
 
main(String[]) - Static method in class SelectForCASP
 
main(String[]) - Static method in class SelectModels
 
main(String[]) - Static method in class SimplestMinimizeProtein
 
main(String[]) - Static method in class TestElectrostatics
 
majorMutation(ResidueType, ResidueType) - Static method in class HomologyModeling
 
makeActualSymmetryComplex(SymmetricComplex, ResidueCreator) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
manner - Variable in class meshi.applications.corpus.LocalFragmentLib
 
map(CommandList, String) - Static method in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
Maths - Class in meshi.util.mathTools.Jama
 
Maths() - Constructor for class meshi.util.mathTools.Jama.Maths
 
matrix - Variable in class meshi.geometry.DistanceMatrix
Internal data structure.
matrix - Variable in class meshi.geometry.MatrixRow
 
matrix - Variable in class meshi.geometry.OldDistanceMatrix
Internal data structure.
matrix - Variable in class meshi.sequences.aligner.Cell
 
matrix - Variable in class meshi.sequences.aligner.DpMatrix
 
Matrix - Interface in meshi.symmetryComplex.transformations
 
matrix - Variable in class meshi.symmetryComplex.transformations.Matrix1D
 
Matrix - Class in meshi.util.mathTools.Jama
Jama = Java Matrix class.
Matrix(int, int) - Constructor for class meshi.util.mathTools.Jama.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class meshi.util.mathTools.Jama.Matrix
Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class meshi.util.mathTools.Jama.Matrix
Construct a matrix from a 2-D array.
Matrix(double[]) - Constructor for class meshi.util.mathTools.Jama.Matrix
 
Matrix(double[][], int, int) - Constructor for class meshi.util.mathTools.Jama.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class meshi.util.mathTools.Jama.Matrix
Construct a matrix from a one-dimensional packed array
Matrix1D - Class in meshi.symmetryComplex.transformations
An implementation of the Matrix interface as a one-dimesional array.
Matrix1D() - Constructor for class meshi.symmetryComplex.transformations.Matrix1D
 
Matrix1D(int, int) - Constructor for class meshi.symmetryComplex.transformations.Matrix1D
 
Matrix1D(Matrix) - Constructor for class meshi.symmetryComplex.transformations.Matrix1D
 
Matrix1D(double[][]) - Constructor for class meshi.symmetryComplex.transformations.Matrix1D
 
MatrixRow - Class in meshi.geometry
 
MatrixRow(AtomCore, MatrixRow[]) - Constructor for class meshi.geometry.MatrixRow
 
MatrixRowCaOnly - Class in meshi.geometry
 
MatrixRowCaOnly(AtomCore, MatrixRow[], MolecularSystem) - Constructor for class meshi.geometry.MatrixRowCaOnly
 
MatrixRowNoImageAtoms - Class in meshi.symmetryComplex.geometryImage
Created by IntelliJ IDEA.
MatrixRowNoImageAtoms(AtomCore, MatrixRow[]) - Constructor for class meshi.symmetryComplex.geometryImage.MatrixRowNoImageAtoms
 
matrixToDouble2D() - Method in interface meshi.symmetryComplex.transformations.Matrix
 
matrixToDouble2D() - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
max0001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
max001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
max01 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
max1 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
max10 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
MAX_ANGLE - Static variable in interface meshi.util.KeyWords
 
MAX_ATTRIBUTES - Static variable in class meshi.util.AttributesRack
 
MAX_CLASHES - Static variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
MAX_CLASHES - Static variable in interface meshi.util.KeyWords
 
MAX_DISTANCE - Static variable in interface meshi.util.KeyWords
 
MAX_ENERGY - Static variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
MAX_ENERGY - Static variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
MAX_FEATURES - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttributes
 
MAX_FEATURES - Variable in class ColorByEnergy.GaussianAttributes
 
MAX_GRID_SIZE - Variable in class meshi.geometry.Grid
 
MAX_GRID_SIZE - Variable in class meshi.geometry.OldGrid
 
MAX_INER_SEQ_DISTANCE - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
MAX_KICKSTARTS - Variable in class meshi.optimizers.Minimizer
 
MAX_LIB_SIZE_FOR_EACH_ROTTEN - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
MAX_NUM_FRAGS - Variable in class meshi.geometry.fragments.DresserFullFrag
 
MAX_NUM_VARIABLES - Variable in class meshi.optimizers.BFGS
 
MAX_RUN_TIME - Static variable in interface meshi.util.KeyWords
 
MAX_SEQ_PAIRS_DISTANCE - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
MAX_STEPS - Static variable in interface meshi.util.KeyWords
 
MAX_WIDTH_OF_HAIRPIN - Static variable in interface meshi.util.KeyWords
 
maxAtomNum - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
maxAtomNumber(Atom[]) - Static method in class meshi.geometry.OldGrid
 
maxchi - Variable in class meshi.geometry.rotamers.DunbrackLib
 
maxEnd - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameterList
 
maxEnd - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
maxEnd - Variable in class meshi.energy.solvate.SolvateParametersList
 
maxEnd - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
maxEnergy - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
maxes0001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
maxes001 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
maxes01 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
maxes1 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
maxes10 - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
maxFilterList - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
maxFilterListSize - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
maximal_distance - Static variable in class meshi.util.GDTcalculator
 
maximalZ - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBCreator
 
maximalZ - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
maximalZ - Variable in class meshi.energy.solvateRot1.SolvateRot1Creator
 
maximalZ - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
maxListSize - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
maxListSize - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
maxNumberOfClashes - Variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
maxNumberOfClashes - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
maxNumberOfClashesLabel - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
maxNumberOfClashesText - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
maxNumEvaluations - Variable in class meshi.optimizers.WolfConditionLineSearch
 
maxNumEvaluationsWolfSearch - Static variable in class meshi.optimizers.BFGS
 
maxNumEvaluationsWolfSearch - Variable in class meshi.optimizers.ConjugateGradient
 
maxNumEvaluationsWolfSearch - Variable in class meshi.optimizers.LBFGS
 
maxNumKickStarts - Variable in class meshi.optimizers.BFGS
 
maxNumKickStarts - Variable in class meshi.optimizers.LBFGS
 
maxSteepestDecent - Static variable in class meshi.optimizers.ConjugateGradient
 
maxSteps - Variable in class meshi.optimizers.Optimizer
 
maxSteps - Variable in class meshi.optimizers.Perturbation
 
maxWidthOfHairpin - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
maxWidthOfHairpin() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
maxX - Variable in class meshi.geometry.Grid
 
maxX - Variable in class meshi.geometry.OldGrid
 
maxY - Variable in class meshi.geometry.Grid
 
maxY - Variable in class meshi.geometry.OldGrid
 
maxZ - Variable in class meshi.geometry.Grid
 
maxZ - Variable in class meshi.geometry.OldGrid
 
mcm(TotalEnergy, int, String) - Method in class AbInitio.AbInitioLogger
 
mcm(TotalEnergy, int) - Method in class AbInitio.AbInitioLogger
 
mcm(TotalEnergy, int) - Method in class Beautify.BeautifyLogger
 
mcm(Protein, CommandList, Protein, Beautify.BeautifyLogger) - Static method in class Beautify
 
mcm(TotalEnergy, int) - Method in class HomologyModeling.HomologyLogger
 
MCM - Class in meshi.optimizers
 
MCM(TotalEnergy, Minimizer, Perturbation, TemperatureGenerator, int) - Constructor for class meshi.optimizers.MCM
 
MCM(GJModeller, TotalEnergy, Minimizer, Perturbation, TemperatureGenerator, int) - Constructor for class meshi.optimizers.MCM
 
MCM - Static variable in interface meshi.util.KeyWords
 
mcm(TotalEnergy, int) - Method in interface meshi.util.Logger
 
mcm(TotalEnergy, int, String) - Method in class Optimize.OptimizeLogger
 
mcm(TotalEnergy, int) - Method in class Optimize.OptimizeLogger
 
mcm(Protein, CommandList, ResidueAlignment, Refine.RefineLogger) - Static method in class Refine
 
mcm(TotalEnergy, int) - Method in class Refine.RefineLogger
 
MCM_PERTURBATION - Static variable in interface meshi.util.KeyWords
 
mcmModel - Variable in class Beautify.BeautifyLogger
 
mean - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
mean - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaParameters
 
mean - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZParameters
 
mean - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
mean - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
mean - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityParameters
 
mean - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
mean - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranParameters
 
mean - Static variable in interface meshi.util.rotamericTools.Rot1Arrays
 
means - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
means - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
merge(Corpus) - Method in class meshi.applications.corpus.Corpus
 
MergeCorpora - Class in meshi.applications.corpus
 
MergeCorpora() - Constructor for class meshi.applications.corpus.MergeCorpora
 
meshi.applications.corpus - package meshi.applications.corpus
 
meshi.applications.hubbard - package meshi.applications.hubbard
 
meshi.applications.prediction - package meshi.applications.prediction
 
meshi.applications.prediction.beautify - package meshi.applications.prediction.beautify
 
meshi.applications.prediction.beautify.unWarpEnergy - package meshi.applications.prediction.beautify.unWarpEnergy
 
meshi.applications.prediction.beautify.warpEnergy - package meshi.applications.prediction.beautify.warpEnergy
 
meshi.applications.prediction.homology - package meshi.applications.prediction.homology
 
meshi.applications.prediction.homology.gui - package meshi.applications.prediction.homology.gui
 
meshi.energy - package meshi.energy
energy - overview
meshi.energy.hydrogenBond - package meshi.energy.hydrogenBond
 
meshi.energy.hydrogenBondsAngle - package meshi.energy.hydrogenBondsAngle
 
meshi.energy.hydrogenBondsPairs - package meshi.energy.hydrogenBondsPairs
 
meshi.energy.linearRG - package meshi.energy.linearRG
 
meshi.energy.pairwiseNonBondedTerms - package meshi.energy.pairwiseNonBondedTerms
 
meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma - package meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
 
meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics - package meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics
 
meshi.energy.pairwiseNonBondedTerms.evRot1BB - package meshi.energy.pairwiseNonBondedTerms.evRot1BB
 
meshi.energy.pairwiseNonBondedTerms.ExcludedVol - package meshi.energy.pairwiseNonBondedTerms.ExcludedVol
 
meshi.energy.pairwiseNonBondedTerms.excludedVol - package meshi.energy.pairwiseNonBondedTerms.excludedVol
 
meshi.energy.pairwiseNonBondedTerms.excludedVolOLD - package meshi.energy.pairwiseNonBondedTerms.excludedVolOLD
 
meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol - package meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol
 
meshi.energy.pairwiseNonBondedTerms.LennardJones - package meshi.energy.pairwiseNonBondedTerms.LennardJones
 
meshi.energy.RG - package meshi.energy.RG
 
meshi.energy.sideChainModelingSolvate - package meshi.energy.sideChainModelingSolvate
 
meshi.energy.simpleEnergyTerms - package meshi.energy.simpleEnergyTerms
 
meshi.energy.simpleEnergyTerms.alphaAngle - package meshi.energy.simpleEnergyTerms.alphaAngle
 
meshi.energy.simpleEnergyTerms.alphaTorsion - package meshi.energy.simpleEnergyTerms.alphaTorsion
 
meshi.energy.simpleEnergyTerms.angle - package meshi.energy.simpleEnergyTerms.angle
Angle energy term.
meshi.energy.simpleEnergyTerms.bond - package meshi.energy.simpleEnergyTerms.bond
Bond energy term.
meshi.energy.simpleEnergyTerms.compositeTorsions - package meshi.energy.simpleEnergyTerms.compositeTorsions
Estimates probable backbone and sidechain torsion angles using statistical approximations.
meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity - package meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
 
meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP - package meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP
 
meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran - package meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
 
meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain - package meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary - package meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
 
meshi.energy.simpleEnergyTerms.inflate - package meshi.energy.simpleEnergyTerms.inflate
 
meshi.energy.simpleEnergyTerms.inflate.simpleInflate - package meshi.energy.simpleEnergyTerms.inflate.simpleInflate
 
meshi.energy.simpleEnergyTerms.outOfPlane - package meshi.energy.simpleEnergyTerms.outOfPlane
Out of plane energy term.
meshi.energy.simpleEnergyTerms.plane - package meshi.energy.simpleEnergyTerms.plane
Plane energy term.
meshi.energy.simpleEnergyTerms.tether - package meshi.energy.simpleEnergyTerms.tether
 
meshi.energy.solvate - package meshi.energy.solvate
 
meshi.energy.solvate.hydrogenBonds - package meshi.energy.solvate.hydrogenBonds
 
meshi.energy.solvateRot1 - package meshi.energy.solvateRot1
 
meshi.energy.templateEnergy - package meshi.energy.templateEnergy
 
meshi.geometry - package meshi.geometry
Atom distances, angles and torsion angles.
meshi.geometry.fragments - package meshi.geometry.fragments
 
meshi.geometry.putH - package meshi.geometry.putH
 
meshi.geometry.rotamers - package meshi.geometry.rotamers
 
meshi.molecularElements - package meshi.molecularElements
Where all the basic structural elements of molecules are found.
meshi.molecularElements.allAtoms - package meshi.molecularElements.allAtoms
 
meshi.molecularElements.atoms - package meshi.molecularElements.atoms
 
meshi.molecularElements.ca - package meshi.molecularElements.ca
 
meshi.molecularElements.extendedAtoms - package meshi.molecularElements.extendedAtoms
 
meshi.optimizers - package meshi.optimizers
Local minimizers as well as global optimization tools.
meshi.parameters - package meshi.parameters
 
meshi.PDB - package meshi.PDB
Tools for reading and writing PDB formatted files.
meshi.sequences - package meshi.sequences
Sequence manipulation tools.
meshi.sequences.aligner - package meshi.sequences.aligner
 
meshi.symmetryComplex.energy - package meshi.symmetryComplex.energy
 
meshi.symmetryComplex.energy.cylinder - package meshi.symmetryComplex.energy.cylinder
 
meshi.symmetryComplex.energy.edmEnergy - package meshi.symmetryComplex.energy.edmEnergy
 
meshi.symmetryComplex.geometryImage - package meshi.symmetryComplex.geometryImage
 
meshi.symmetryComplex.molecularImageElements - package meshi.symmetryComplex.molecularImageElements
 
meshi.symmetryComplex.proteinsGJ - package meshi.symmetryComplex.proteinsGJ
 
meshi.symmetryComplex.topologyMap - package meshi.symmetryComplex.topologyMap
 
meshi.symmetryComplex.transformations - package meshi.symmetryComplex.transformations
 
meshi.symmetryComplex.utils - package meshi.symmetryComplex.utils
 
meshi.util - package meshi.util
A collection of useful tools.
meshi.util.alignmentTools - package meshi.util.alignmentTools
 
meshi.util.dssp - package meshi.util.dssp
 
meshi.util.file - package meshi.util.file
 
meshi.util.filters - package meshi.util.filters
 
meshi.util.formats - package meshi.util.formats
Text formatting tools.
meshi.util.histogram - package meshi.util.histogram
 
meshi.util.mathTools - package meshi.util.mathTools
 
meshi.util.mathTools.Jama - package meshi.util.mathTools.Jama
 
meshi.util.overlap - package meshi.util.overlap
 
meshi.util.rotamericTools - package meshi.util.rotamericTools
 
meshi.util.string - package meshi.util.string
 
MESHI2SUMMA - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
meshiAtomTypeToSummaAtomName(AtomType) - Static method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
Translates MESHI atom type to Summa atom name.
MeshiAttribute - Interface in meshi.util
 
MeshiException - Exception in meshi.util
 
MeshiException(String) - Constructor for exception meshi.util.MeshiException
 
meshiExplanationLabel - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
MeshiInitException - Exception in meshi.util
 
MeshiInitException(String) - Constructor for exception meshi.util.MeshiInitException
 
MeshiLineReader - Class in meshi.util.file
 
MeshiLineReader(InputStreamReader, String) - Constructor for class meshi.util.file.MeshiLineReader
 
MeshiLineReader(InputStreamReader) - Constructor for class meshi.util.file.MeshiLineReader
 
MeshiLineReader(FileReader, String) - Constructor for class meshi.util.file.MeshiLineReader
 
MeshiLineReader(FileReader) - Constructor for class meshi.util.file.MeshiLineReader
 
MeshiLineReader(String) - Constructor for class meshi.util.file.MeshiLineReader
 
MeshiLineReader(File) - Constructor for class meshi.util.file.MeshiLineReader
 
MESHILOG_KEY - Static variable in interface meshi.util.KeyWords
 
MeshiPotential - Interface in meshi.parameters
 
MeshiProgram - Class in meshi.util
The (suggested) superclass of programs using the meshi package.
MeshiProgram() - Constructor for class meshi.util.MeshiProgram
 
MeshiProgram.GlobalElement - Class in meshi.util
An element of the keyword-value table.
MeshiProgram.GlobalElement(String, Object) - Constructor for class meshi.util.MeshiProgram.GlobalElement
 
MeshiProgram.GlobalElementList - Class in meshi.util
A keyword-value table
MeshiProgram.GlobalElementList() - Constructor for class meshi.util.MeshiProgram.GlobalElementList
 
MeshiWriter - Class in meshi.util.file
 
MeshiWriter(String) - Constructor for class meshi.util.file.MeshiWriter
 
MeshiWriter(CommandList, Key, Key) - Constructor for class meshi.util.file.MeshiWriter
 
MeshiWriter(CommandList, Key, Key, String) - Constructor for class meshi.util.file.MeshiWriter
 
message - Variable in exception meshi.util.MeshiInitException
 
message() - Method in exception meshi.util.MeshiInitException
 
message - Variable in class meshi.util.Terminator
 
message() - Method in class meshi.util.Terminator
 
Met - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - SD - CE
Met(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Met
 
METHOD - Static variable in interface meshi.util.KeyWords
 
mid - Variable in class meshi.applications.corpus.LoopResults
 
midTor - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
MIN_DISTANCE_SQR - Static variable in class HeliumClusterMinimization
 
MIN_WIDTH_OF_HAIRPIN - Static variable in interface meshi.util.KeyWords
 
minAvgSigma - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaParameters
 
minAvgSigma - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityParameters
 
minAvgSigma - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranParameters
 
MINIMIZATION_LOOP - Static variable in interface meshi.util.KeyWords
 
minimizationStep() - Method in class meshi.optimizers.BFGS
 
minimizationStep() - Method in class meshi.optimizers.ConjugateGradient
 
minimizationStep() - Method in class meshi.optimizers.LBFGS
 
minimizationStep() - Method in class meshi.optimizers.Minimizer
 
minimizationStep() - Method in class meshi.optimizers.SteepestDecent
 
minimizationWithEV(Protein, CommandList) - Static method in class HomologyModeling
Minimization of all sidechains accept the original ones.
minimize(Protein, CommandList) - Static method in class InitialEvaluation
 
MINIMIZE - Static variable in interface meshi.util.KeyWords
 
MinimizeParametersFullDialog - Class in meshi.applications.prediction.homology.gui
 
MinimizeParametersFullDialog() - Constructor for class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
MinimizeParametersFullDialogLayout - Class in meshi.applications.prediction.homology.gui
 
MinimizeParametersFullDialogLayout() - Constructor for class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout
 
MinimizeParametersShortDialog - Class in meshi.applications.prediction.homology.gui
 
MinimizeParametersShortDialog() - Constructor for class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
MinimizeParametersShortLayout - Class in meshi.applications.prediction.homology.gui
 
MinimizeParametersShortLayout() - Constructor for class meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout
 
MinimizeProtein - Class in <Unnamed>
A minimalist MESHI program.
MinimizeProtein() - Constructor for class MinimizeProtein
 
minimizer - Static variable in class HeliumClusterMinimization
The optimization engine.
minimizer - Variable in class meshi.optimizers.MCM
 
Minimizer - Class in meshi.optimizers
Minimize energy according to a given set of coordinates and an energy function
Minimizer(TotalEnergy, int, int, double) - Constructor for class meshi.optimizers.Minimizer
 
minimizer - Variable in class meshi.optimizers.Perturbation
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.HomologyFrame11Layout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.InflateParametersLayout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.OptionDialog3Layout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout
 
minimumLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout
 
minSphereRadiusToEdge - Variable in class meshi.geometry.Grid
 
minSphereRadiusToEdge - Variable in class meshi.geometry.OldGrid
 
minus(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
C = A - B
minusEquals(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
A = A - B
minusTwelveSigma6 - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
minusTwelveSigma6 - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
minusTwelveSigma6 - Variable in class meshi.energy.hydrogenBond.LennardJonesParameters
 
minusTwelveSigma6 - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
minusVerySmall - Static variable in class meshi.geometry.ArcCos
 
minWidthOfHairpin - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
minWidthOfHairpin() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
minX - Variable in class meshi.geometry.Grid
 
minX - Variable in class meshi.geometry.OldGrid
 
minY - Variable in class meshi.geometry.Grid
 
minY - Variable in class meshi.geometry.OldGrid
 
minZ - Variable in class meshi.geometry.Grid
 
minZ - Variable in class meshi.geometry.OldGrid
 
mirror - Variable in enum meshi.geometry.DistanceMode
 
missingResidues() - Method in class meshi.molecularElements.Chain
 
missingResidues() - Method in class meshi.molecularElements.Protein
 
mode - Variable in class meshi.geometry.Distance
 
mode() - Method in class meshi.geometry.Distance
 
mode - Static variable in class meshi.geometry.MatrixRow
 
mode - Variable in class meshi.molecularElements.Residue
 
mode - Static variable in class meshi.symmetryComplex.geometryImage.MatrixRowNoImageAtoms
 
MODE - Static variable in interface meshi.util.KeyWords
 
model - Variable in class AbInitio.AbInitioLogger
 
model(Protein, TotalEnergy, String, boolean, int) - Method in class Beautify.BeautifyLogger
 
MODEL - Static variable in interface meshi.util.KeyWords
 
model - Variable in class Optimize.OptimizeLogger
 
model - Variable in class Refine.RefineLogger
 
MODEL_DSSP - Static variable in interface meshi.util.KeyWords
 
MODEL_NUMBER - Static variable in interface meshi.util.KeyWords
 
ModelData - Class in meshi.applications.prediction
 
ModelData() - Constructor for class meshi.applications.prediction.ModelData
 
ModelData(Protein, Protein, TotalEnergy) - Constructor for class meshi.applications.prediction.ModelData
 
ModelData(Protein, Protein, TotalEnergy, String) - Constructor for class meshi.applications.prediction.ModelData
 
ModelData(ModelData) - Constructor for class meshi.applications.prediction.ModelData
 
ModelData.TermComparator - Class in meshi.applications.prediction
 
ModelData.TermComparator(String) - Constructor for class meshi.applications.prediction.ModelData.TermComparator
 
modelFileName - Static variable in class AbInitio
 
modelFileName - Static variable in class CalcGDT
 
modelFileName - Static variable in class HydrogenTest
 
modelFileName - Static variable in class SimplestMinimizeProtein
 
modelHeader(TotalEnergy) - Method in class Beautify.BeautifyLogger
 
modelNumber - Variable in class meshi.molecularElements.Protein
Often many models of the same protein are generated.
modelNumber() - Method in class meshi.molecularElements.Protein
 
ModelRanker - Class in <Unnamed>
 
ModelRanker() - Constructor for class ModelRanker
 
molecularSystem - Variable in class meshi.energy.solvate.SolvateEnergy
 
molecularSystem - Variable in class meshi.geometry.DistanceMatrix
The list of all atoms in the molecular system.
molecularSystem - Static variable in class meshi.geometry.MatrixRowCaOnly
 
molecularSystem - Variable in class meshi.molecularElements.atoms.Atom
 
molecularSystem - Variable in class meshi.molecularElements.atoms.AtomList
 
molecularSystem() - Method in class meshi.molecularElements.atoms.AtomList
 
MolecularSystem - Class in meshi.molecularElements.atoms
 
MolecularSystem() - Constructor for class meshi.molecularElements.atoms.MolecularSystem
 
molecularSystemSize - Variable in class meshi.energy.solvate.SolvateEnergy
 
monitor(double, double...) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
Reports energy values.
monitor(double, double...) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
Reports energy values.
MONOMERS_TO_IGNORE - Static variable in class Pdb2Fasta
 
moveCMtoOrigin() - Method in class meshi.molecularElements.atoms.AtomList
 
moved(Atom, int) - Method in class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
moveHydrogensCloseToHeavy(AtomList, double) - Static method in class meshi.util.Utils
 
moveTo(double, double, double) - Method in class meshi.molecularElements.ca.CaResidue
 
movingAtom - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
movingAtom - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
movingAtoms - Variable in class meshi.geometry.Grid
 
movingAtoms - Variable in class meshi.geometry.OldGrid
 
multiply(Matrix) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
multiply(Matrix) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
myPhiPsi - Variable in class meshi.applications.corpus.BasicLoopResult
 

N

n - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
n - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
N - Variable in class meshi.geometry.fragments.DresserFullFrag
 
N - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
n() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
n - Variable in class meshi.optimizers.BFGS
 
n - Variable in class meshi.optimizers.LBFGS
 
n - Variable in class meshi.optimizers.WolfConditionLineSearch
 
n - Variable in class meshi.util.mathTools.Jama.CholeskyDecomposition
Row and column dimension (square matrix).
n - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Row and column dimension (square matrix).
n - Variable in class meshi.util.mathTools.Jama.LUDecomposition
Row and column dimensions, and pivot sign.
n - Variable in class meshi.util.mathTools.Jama.Matrix
Row and column dimensions.
n - Variable in class meshi.util.mathTools.Jama.QRDecomposition
Row and column dimensions.
n - Variable in class meshi.util.mathTools.Jama.SingularValueDecomposition
Row and column dimensions.
n - Variable in class meshi.util.mathTools.Spline1D
 
N_ATOMS - Static variable in interface meshi.util.KeyWords
 
N_TRIES - Static variable in interface meshi.util.KeyWords
 
N_TSAI - Static variable in class meshi.energy.solvate.SolvateParametersList
 
NAME - Static variable in class AbInitio
 
NAME - Static variable in class Beautify
 
NAME - Static variable in class CalcGDT
 
NAME - Static variable in class EnergyStatistics
 
NAME - Static variable in class EnergyStatisticsForAtom
 
NAME - Static variable in class HomologyModeling
 
name - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
 
name() - Method in class meshi.geometry.Torsion
 
name - Variable in class meshi.molecularElements.atoms.Atom
The atoms name.
name() - Method in class meshi.molecularElements.atoms.Atom
 
name - Variable in class meshi.molecularElements.Chain
The first Non Dummy Residue (may but also may not be number 1).
name() - Method in class meshi.molecularElements.Chain
 
NAME - Static variable in class meshi.molecularElements.extendedAtoms.Asn
 
name - Variable in class meshi.molecularElements.Protein
The protein name.
name() - Method in class meshi.molecularElements.Protein
The protein name.
name - Variable in class meshi.molecularElements.Residue
Residue name.
name - Variable in class meshi.PDB.PdbLine
 
name() - Method in class meshi.PDB.PdbLine
 
NAME - Static variable in class meshi.symmetryComplex.proteinsGJ.RunBackboneCompleterAndMinimizer
 
NAME - Static variable in class meshi.symmetryComplex.proteinsGJ.RunBackboneMCM
 
NAME - Static variable in class meshi.symmetryComplex.proteinsGJ.RunFullModeller
 
name - Variable in class meshi.util.file.MeshiLineReader
 
name() - Method in class meshi.util.file.MeshiLineReader
 
name - Static variable in class meshi.util.MeshiProgram
Program name.
NAME - Static variable in class Optimize
 
NAME - Static variable in class Refine
 
NAME - Static variable in class RoisFirstMeshiProgram
 
NAME_INDEX - Static variable in class meshi.applications.prediction.ModelData
 
nameConverter(String) - Static method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
namedFilter() - Method in class meshi.geometry.AngleList
Returns a sub-list containing angles that have a known name
namedFilter() - Method in class meshi.geometry.TorsionList
Returns a sub-list that is has a known name
namedFilterQD() - Method in class meshi.geometry.QuickAndDirtyAngleList
Returns a sub-list containing angles that have a known name
nameIs(String) - Method in class meshi.molecularElements.atoms.Atom
Returns true if the protein's name is a substring of the String parameter seperated by spaces.
nameIs(StringList) - Method in class meshi.molecularElements.atoms.Atom
Returns true if the protein's name is included in the StringList parameter.
nameOneLetter - Variable in enum meshi.parameters.ResidueType
 
nameOneLetter() - Method in enum meshi.parameters.ResidueType
 
nameOneLetter - Variable in enum meshi.parameters.SecondaryStructure
 
names1 - Static variable in class meshi.molecularElements.Residue
A list of Residue names1 (one letter code).
names3 - Static variable in class meshi.molecularElements.Residue
A list of Residue names3 (three letter code).
namesDone - Static variable in class meshi.molecularElements.Residue
The list of residue names is done.
nameThreeLetters - Variable in enum meshi.parameters.ResidueType
 
nameThreeLetters() - Method in enum meshi.parameters.ResidueType
 
NaN - Static variable in class meshi.energy.AbstractEnergy
sqrt(-1) good for dubugging.
nbins - Variable in class meshi.geometry.rotamers.DunbrackLib
 
nBins - Variable in class meshi.util.histogram.Histogram
 
nBins() - Method in class meshi.util.histogram.Histogram
 
ND1 - Variable in class meshi.molecularElements.extendedAtoms.His
 
ND2 - Variable in class meshi.molecularElements.extendedAtoms.Asn
 
NE - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
NE1 - Variable in class meshi.molecularElements.extendedAtoms.Trp
 
NE2 - Variable in class meshi.molecularElements.extendedAtoms.Gln
 
NE2 - Variable in class meshi.molecularElements.extendedAtoms.His
 
nearestRot(DunbrackLib, Residue, double, double) - Static method in class meshi.util.rotamericTools.RotamericTools
 
needsToBeAnAtom() - Method in class meshi.PDB.PdbLine
 
Nenergies - Variable in class meshi.applications.corpus.Corpus
 
new_e - Variable in class meshi.optimizers.SimpleStepLength
 
new_FileReader(File) - Static method in class meshi.util.file.MeshiLineReader
 
new_InputStreamReader(File) - Static method in class meshi.util.file.MeshiLineReader
 
newConstant - Variable in class meshi.geometry.DistanceMatrix
 
newConstant - Variable in class meshi.geometry.OldDistanceMatrix
 
newE - Variable in class meshi.optimizers.WolfConditionLineSearch
 
newhBondList - Variable in class meshi.energy.hydrogenBond.HBondList
 
newhBondList() - Method in class meshi.energy.hydrogenBond.HBondList
 
newPdbWriter(CommandList, Key, Key, int) - Static method in class meshi.util.Utils
Opens a file for writing (warped by MeshiWriter object) with a name and location specified by the commands and a ...pdb suffix.
newToNonBonded - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
newWithinRmaxIterator() - Method in class meshi.energy.hydrogenBond.HBondList
 
Nexp - Static variable in class meshi.applications.corpus.RunThreadingExperiment
 
next() - Method in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
next() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
next() - Method in class meshi.geometry.DistanceList.DistanceIterator
 
next() - Method in class meshi.geometry.DistanceMatrix.RowIterator
 
next() - Method in class meshi.geometry.OldDistanceMatrix.RowIterator
 
next() - Method in class meshi.optimizers.TemperatureGenerator
 
next() - Method in class meshi.util.histogram.Histogram.RepresentativesIterator
 
nextAtom - Variable in class meshi.molecularElements.Residue
 
nextAtom() - Method in class meshi.molecularElements.Residue
 
NH1 - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
NH2 - Variable in class meshi.molecularElements.extendedAtoms.Arg
 
Ninst - Static variable in class meshi.applications.corpus.RunThreadingExperiment
 
nInstances - Static variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator
 
nitrogens - Variable in class meshi.energy.hydrogenBond.HydrogenBondsParametersList
 
nitrogens() - Method in class meshi.energy.hydrogenBond.HydrogenBondsParametersList
 
nLoops - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
nmcrosprod(double, double, double, double, double, double) - Static method in class meshi.geometry.ViewAt
 
nn - Variable in class meshi.applications.corpus.LoopResults
 
NO_GDT - Static variable in class meshi.util.Rms
 
noCommandHasThisKeyInItsSecondPosition(String, String) - Method in class meshi.util.CommandsException
 
noCommandsStartWith(String, String) - Method in class meshi.util.CommandsException
 
noCommandStartsWith(String, String) - Method in class meshi.util.CommandsException
 
NoConvergenceException - Exception in meshi.optimizers
 
NoConvergenceException(int) - Constructor for exception meshi.optimizers.NoConvergenceException
 
NON_FROZEN_BOND_DEPTH - Static variable in interface meshi.util.KeyWords
 
NON_FROZEN_RADIUS - Static variable in interface meshi.util.KeyWords
 
NonBondedEnergyElement - Class in meshi.energy.pairwiseNonBondedTerms
 
NonBondedEnergyElement() - Constructor for class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
 
NonBondedEnergyTerm - Class in meshi.energy.pairwiseNonBondedTerms
 
NonBondedEnergyTerm() - Constructor for class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
 
NonBondedEnergyTerm(Updateable[], double, DistanceMatrix) - Constructor for class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
Creates a new NonBondedEnergyTerm instance.
nonBondedFlag - Variable in class meshi.geometry.DistanceMatrix
 
nonBondedFlag - Variable in class meshi.geometry.OldDistanceMatrix
 
nonBondedList - Variable in class meshi.geometry.DistanceMatrix
Atom pairs with inter-atomic distances below rMax (and some of the pairs below rMax+buffer).
nonBondedList() - Method in class meshi.geometry.DistanceMatrix
Returns the non-bonded-list.
nonBondedList - Variable in class meshi.geometry.OldDistanceMatrix
Atom pairs with inter-atomic distances below rMax (and some of the pairs below rMax+buffer).
nonBondedList() - Method in class meshi.geometry.OldDistanceMatrix
Returns the non-bonded-list.
nonBondedListSize() - Method in class meshi.geometry.DistanceMatrix
Returns the bonded list
nonBondedListSize() - Method in class meshi.geometry.OldDistanceMatrix
Returns the bonded list
NONE - Static variable in interface meshi.util.KeyWords
 
nonExsisting - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
NonFrozenRangeDialog - Class in meshi.applications.prediction.homology.gui
 
NonFrozenRangeDialog() - Constructor for class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
NonFrozenRangeDialogLayout - Class in meshi.applications.prediction.homology.gui
 
NonFrozenRangeDialogLayout() - Constructor for class meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout
 
nonFrozens - Variable in class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
NonFrozensRadiusFilter - Class in meshi.applications.prediction.homology
 
NonFrozensRadiusFilter(AtomList, double, int) - Constructor for class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
noOXTFilter() - Method in class meshi.molecularElements.atoms.AtomList
 
norm1() - Method in class meshi.util.mathTools.Jama.Matrix
One norm
norm2() - Method in class meshi.util.mathTools.Jama.Matrix
Two norm
norm2() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Two norm
normal() - Method in class meshi.molecularElements.atoms.Atom
 
normalize(double[]) - Static method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
normCross123squared - Variable in class meshi.geometry.Torsion
 
normCross234squared - Variable in class meshi.geometry.Torsion
 
normF() - Method in class meshi.util.mathTools.Jama.Matrix
Frobenius norm
normInf() - Method in class meshi.util.mathTools.Jama.Matrix
Infinity norm
NOT_A_DESCENT_DIRECTION - Static variable in exception meshi.optimizers.LineSearchException
 
NotEnoughBoundAtomsException - Exception in meshi.geometry.putH
 
NotEnoughBoundAtomsException(String) - Constructor for exception meshi.geometry.putH.NotEnoughBoundAtomsException
 
notInEdge(int) - Method in class meshi.util.dssp.DSSP
 
nowhere - Variable in class meshi.geometry.Coordinates
 
nowhere() - Method in class meshi.geometry.Coordinates
 
nowhere() - Method in class meshi.molecularElements.atoms.Atom
 
nowhere() - Method in enum meshi.molecularElements.atoms.AtomStatus
 
NOWHERE_CONST - Static variable in class meshi.geometry.Coordinates
 
nowhereAtoms() - Method in class meshi.molecularElements.Chain
 
nowhereAtoms() - Method in class meshi.molecularElements.Protein
 
np - Variable in class meshi.optimizers.BFGS
 
npt - Static variable in class meshi.util.overlap.Overlap
 
Nres - Variable in class meshi.applications.corpus.Corpus
 
nSteepestDecent - Variable in class meshi.optimizers.ConjugateGradient
 
nSteps - Static variable in class HeliumClusterMinimization
Maximal number of minimization steps.
nTerm - Static variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
nTraysLabel - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
nTraysText - Variable in class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
nTries - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
nTrys - Variable in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
NTsai - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
NTsai - Variable in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
nType - Variable in enum meshi.parameters.ResidueType
 
nType() - Method in enum meshi.parameters.ResidueType
 
NUM_DIMENSIONS - Static variable in class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
 
num_of_loops - Static variable in class meshi.util.GDTcalculator
 
NUM_SIDECHAIN_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
numAlphaEvaluations - Variable in class meshi.optimizers.WolfConditionLineSearch
 
number - Variable in class meshi.geometry.MatrixRow
 
number() - Method in class meshi.molecularElements.atoms.Atom
A unique identifier of the atom in the molecular system.
number - Variable in class meshi.molecularElements.atoms.AtomCore
 
number() - Method in class meshi.molecularElements.Residue
 
number - Variable in class meshi.molecularElements.ResidueIdentifier
 
number() - Method in class meshi.molecularElements.ResidueIdentifier
 
number - Variable in class meshi.PDB.PdbLine
 
number() - Method in class meshi.PDB.PdbLine
 
number - Variable in class meshi.sequences.AlignmentCell
 
number() - Method in class meshi.sequences.AlignmentCell
 
number - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
number() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
NUMBER - Static variable in interface meshi.util.KeyWords
 
number1 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
number1 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
number2 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
number2 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
number3 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
NUMBER_OF_CA_ITERATIONS - Static variable in interface meshi.util.KeyWords
 
NUMBER_OF_CHAINS - Static variable in interface meshi.util.KeyWords
 
NUMBER_OF_ITERATIONS - Static variable in class meshi.geometry.ArcCos
 
NUMBER_OF_MODELS - Static variable in interface meshi.util.KeyWords
 
NUMBER_OF_RUNS - Static variable in interface meshi.util.KeyWords
 
numberOfAtoms - Static variable in class meshi.molecularElements.atoms.Atom
Number of atoms in all the molecular systems.
numberOfAtoms() - Static method in class meshi.molecularElements.atoms.Atom
 
numberOfAtoms - Variable in class meshi.molecularElements.atoms.MolecularSystem
 
numberOfAtomsWithCoordinates(Protein) - Static method in class meshi.util.Utils
 
numberOfAtomTypes - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
numberOfChainCrosses(AtomList, String, String) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
numberOfChains - Static variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
numberOfChains - Static variable in class meshi.symmetryComplex.topologyMap.BoundariesMap
 
numberOfEachAtomType - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
numberOfEachAtomType() - Static method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
numberOfEnergyTerms - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
numberOfEvaluations - Variable in class meshi.energy.TotalEnergy
Number of times the energy function was evaluated.
numberOfEvaluations() - Method in class meshi.energy.TotalEnergy
 
numberOfKickStrarts - Variable in class meshi.optimizers.Minimizer
 
numberOflegandsOfHeavy - Variable in class meshi.geometry.putH.PutHposLog
 
numberOfLegandsWithCoordinatesOfHeavy - Variable in class meshi.geometry.putH.PutHposLog
 
numberOfModelsLabel - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
numberOfModelsText - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
numberOfMolecularSystems - Static variable in class meshi.molecularElements.atoms.MolecularSystem
 
numberOfNonDummyResidues() - Method in class meshi.molecularElements.Chain
 
numberOfNonDummyResidues(Protein) - Static method in class meshi.util.Utils
 
numberOfOccurrences - Variable in class meshi.util.histogram.HistogramBin
 
numberOfOccurrences() - Method in class meshi.util.histogram.HistogramBin
 
numberOfRenumberings - Variable in class meshi.molecularElements.atoms.AtomPair
 
numberOfReports - Variable in class meshi.energy.TotalEnergy
 
numberOfResiduesPerType - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
numberOfResiduesPerType() - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
numberOfResiduesPerType - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
numberOfResiduesPerType() - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
numberOfResidueTypes - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
numberOfResidueTypes - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
numberOfTwists(AtomList, int) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
numberOfTypes - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
numberOfUpdates - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElementsList
 
numberOfUpdates - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElementsList
 
numberOfUpdates - Variable in class meshi.energy.hydrogenBond.HBondList
 
numberOfUpdates - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
numberOfUpdates - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
numberOfUpdates - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
 
numberOfUpdates - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
numberOfUpdates - Variable in class meshi.energy.templateEnergy.TemplateEnergyElementsList
 
numberOfUpdates - Static variable in class meshi.energy.TotalEnergy
 
numberOfUpdates() - Method in class meshi.energy.TotalEnergy
 
numberOfUpdates - Variable in class meshi.geometry.Angle
 
numberOfUpdates - Variable in class meshi.geometry.AngleList
 
numberOfUpdates - Variable in class meshi.geometry.DistanceMatrix
 
numberOfUpdates - Variable in class meshi.geometry.DistanceMatrixBondedOnly
 
numberOfUpdates - Variable in class meshi.geometry.OldDistanceMatrix
 
numberOfUpdates - Variable in class meshi.geometry.Torsion
 
numberOfUpdates - Variable in class meshi.geometry.TorsionList
 
numberOfUpdates - Variable in class meshi.geometry.TorsionPair
 
numberOfUpdates - Variable in class meshi.geometry.TorsionPairList
 
numberOfUpdates - Variable in class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
numberOfUpdates - Variable in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
numberOfUpdates - Variable in class meshi.util.RgCalculator
 
numbers - Variable in class meshi.applications.hubbard.HubbardPosition
 
numKickStarts - Variable in class meshi.optimizers.BFGS
 
numKickStarts - Variable in class meshi.optimizers.LBFGS
 
numOfClosestPairOfAtoms(Atom, Atom, Atom[], int, boolean) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
numSimilar - Variable in class meshi.applications.corpus.LoopResults
 
numStepsSteepestDecent - Variable in class meshi.optimizers.BFGS
 
numStepsSteepestDecent - Static variable in class meshi.optimizers.ConjugateGradient
 
numStepsSteepestDecent - Variable in class meshi.optimizers.LBFGS
 
numVariables - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
NZ - Variable in class meshi.molecularElements.extendedAtoms.Lys
 

O

O - Variable in class meshi.geometry.fragments.DresserFullFrag
 
O - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
o() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
o1h2SeqGap - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
Key values: firstHBSeqGap = the gap between the two atoms in the first HB (O1-H1) secondHBSeqGap = the gap between the two atoms in the second HB (O2-H2) h1h2SeqGap = the gap between the two Hydrogens o1o2SeqGap = the gap between the two Oxygens h1o2SeqGap = the gap between the H of the first HB and the O of the second HB o1h2SeqGap = the gap between the O of the first HB and the H of the second HB value is proportionaly to the friquency of such pair of HBs in the data base
o1o2SeqGap - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
Key values: firstHBSeqGap = the gap between the two atoms in the first HB (O1-H1) secondHBSeqGap = the gap between the two atoms in the second HB (O2-H2) h1h2SeqGap = the gap between the two Hydrogens o1o2SeqGap = the gap between the two Oxygens h1o2SeqGap = the gap between the H of the first HB and the O of the second HB o1h2SeqGap = the gap between the O of the first HB and the H of the second HB value is proportionaly to the friquency of such pair of HBs in the data base
oAtom - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
oAtom - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
oAtom() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
oAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
oAtom(Distance) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
oAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
oAtom1() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
oAtom1 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
oAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
oAtom2 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
obj - Variable in class meshi.sequences.AlignmentCell
 
object() - Method in class meshi.sequences.AlignmentCell
 
occupancy() - Method in class meshi.molecularElements.atoms.Atom
 
occupancy - Variable in class meshi.PDB.PdbLine
 
occupancy() - Method in class meshi.PDB.PdbLine
 
OD1 - Variable in class meshi.molecularElements.extendedAtoms.Asn
 
OD1 - Variable in class meshi.molecularElements.extendedAtoms.Asp
 
OD2 - Variable in class meshi.molecularElements.extendedAtoms.Asp
 
OE1 - Variable in class meshi.molecularElements.extendedAtoms.Gln
 
OE1 - Variable in class meshi.molecularElements.extendedAtoms.Glu
 
OE2 - Variable in class meshi.molecularElements.extendedAtoms.Glu
 
oFactor - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
oFactor - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
off() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
off() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
off() - Method in class meshi.energy.AbstractEnergy
Turnes the energyTerm OFF.
off() - Method in class meshi.energy.templateEnergy.TemplateEnergyElement
 
off() - Method in class meshi.energy.TotalEnergy
 
OFF - Static variable in interface meshi.util.KeyWords
 
offIfUnhappy(double) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
offIfUnhappy(double) - Method in class meshi.energy.templateEnergy.TemplateEnergyElement
 
OG - Variable in class meshi.molecularElements.extendedAtoms.Ser
 
OG1 - Variable in class meshi.molecularElements.extendedAtoms.Thr
 
OH - Variable in class meshi.molecularElements.extendedAtoms.Tyr
 
ohSeqDistance - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
ohSeqDistance() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
old_e - Variable in class meshi.optimizers.SimpleStepLength
 
OldDistanceMatrix - Class in meshi.geometry
Where all the headache of distances is handled.
OldDistanceMatrix(AtomList, double, double, double, int) - Constructor for class meshi.geometry.OldDistanceMatrix
 
OldDistanceMatrix.Indicator - Class in meshi.geometry
 
OldDistanceMatrix.Indicator() - Constructor for class meshi.geometry.OldDistanceMatrix.Indicator
 
OldDistanceMatrix.RowIterator - Class in meshi.geometry
 
OldDistanceMatrix.RowIterator() - Constructor for class meshi.geometry.OldDistanceMatrix.RowIterator
 
oldE - Variable in class meshi.optimizers.WolfConditionLineSearch
 
OldGrid - Class in meshi.geometry
 
OldGrid(Atom[], double, double) - Constructor for class meshi.geometry.OldGrid
 
oldRelax(AtomList, Protein, EnergyCreator[], CommandList) - Static method in class meshi.util.Utils
 
oldRelax(AtomList, Protein, EnergyCreator[], CommandList, Key) - Static method in class meshi.util.Utils
 
oldSize - Variable in class meshi.energy.hydrogenBond.HBondList
to find easily the last element that was in this list before the new update
OMG - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
OMNI - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
omniPolynomial - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters
the omni polynomial
omniPolynomial - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters
the omni polynomial
on - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
on - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
on - Variable in class meshi.energy.AbstractEnergy
The energy term is evaluated only if it is on.
on() - Method in class meshi.energy.AbstractEnergy
Turnes the energyTerm ON.
on - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
on - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
on - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
on() - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
on - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
on() - Method in class meshi.energy.TotalEnergy
 
ON - Static variable in interface meshi.util.KeyWords
 
ONE_ANGLE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
ONE_DIV_SIX - Static variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
oneBetta - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
oneHelix - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
OneOfTwenty - Class in meshi.PDB
 
OneOfTwenty() - Constructor for class meshi.PDB.OneOfTwenty
 
oneOverSTDs - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
oneOverSTDs - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
ooDistance - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
ooSeqDistance - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
ooSeqDistance() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
openFile(String) - Static method in class Pdb2Fasta
 
optimalNumberOfClashes - Variable in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
Optimize - Class in <Unnamed>
 
Optimize() - Constructor for class Optimize
 
Optimize.OptimizeLogger - Class in <Unnamed>
 
Optimize.OptimizeLogger(Protein, CommandList, String, String) - Constructor for class Optimize.OptimizeLogger
 
Optimizer - Class in meshi.optimizers
Minimize energy according to a given set of coordinates and an energy function
Optimizer(TotalEnergy, int, int) - Constructor for class meshi.optimizers.Optimizer
 
OPTIMIZER - Static variable in interface meshi.util.KeyWords
 
Optimizer.OptimizerStatus - Enum in meshi.optimizers
 
Optimizer.OptimizerStatus() - Constructor for enum meshi.optimizers.Optimizer.OptimizerStatus
 
OptimizerException - Exception in meshi.optimizers
 
OptimizerException(String) - Constructor for exception meshi.optimizers.OptimizerException
 
optimizerTerminator - Static variable in class meshi.optimizers.Optimizer
 
OptionDialog - Class in meshi.applications.prediction.homology.gui
 
OptionDialog() - Constructor for class meshi.applications.prediction.homology.gui.OptionDialog
 
OptionDialog3Layout - Class in meshi.applications.prediction.homology.gui
 
OptionDialog3Layout() - Constructor for class meshi.applications.prediction.homology.gui.OptionDialog3Layout
 
order - Variable in class meshi.applications.hubbard.HubbardPosition
 
order - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
ORIGINAL_ATOM - Static variable in interface meshi.util.MeshiAttribute
 
OriginalAtom - Class in meshi.applications.prediction
 
OriginalAtom() - Constructor for class meshi.applications.prediction.OriginalAtom
 
OriginalAtom.OriginalAtomFilter - Class in meshi.applications.prediction
 
OriginalAtom.OriginalAtomFilter() - Constructor for class meshi.applications.prediction.OriginalAtom.OriginalAtomFilter
 
originalAtoms - Variable in class Beautify.BeautifyLogger
 
OriginalAtoms - Class in meshi.util.filters
 
OriginalAtoms(AtomList) - Constructor for class meshi.util.filters.OriginalAtoms
 
OriginalAtoms(ResidueAlignment, int) - Constructor for class meshi.util.filters.OriginalAtoms
 
ort - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Working storage for nonsymmetric algorithm.
orthes() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
os - Variable in class aligner.FWriter
 
oType - Variable in enum meshi.parameters.ResidueType
 
oType() - Method in enum meshi.parameters.ResidueType
 
OUT_OF_PLANE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
OUT_OFPLANE_ENERGY - Static variable in interface meshi.util.KeyWords
 
outerBarrelFilter - Static variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
outerBarrelHeight - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
outerBarrelInnerR - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
outerBarrelOuterR - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
outerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderCreator
 
outerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
The cylinder's dimensions.
outerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderParameters
 
outerR - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
outFileName - Variable in class AbInitio.AbInitioLogger
 
outFileName - Variable in class Optimize.OptimizeLogger
 
outOfPlaneCreator - Static variable in class Beautify
 
OutOfPlaneCreator - Class in meshi.energy.simpleEnergyTerms.outOfPlane
 
OutOfPlaneCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneCreator
 
OutOfPlaneCreator() - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneCreator
 
OutOfPlaneEnergy - Class in meshi.energy.simpleEnergyTerms.outOfPlane
OutOfPlane energy term.
OutOfPlaneEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
OutOfPlaneEnergy(DistanceMatrix, TorsionList, OutOfPlaneParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
 
OutOfPlaneEnergyElement - Class in meshi.energy.simpleEnergyTerms.outOfPlane
 
OutOfPlaneEnergyElement(Torsion, Parameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
OutOfPlaneParameters - Class in meshi.energy.simpleEnergyTerms.outOfPlane
 
OutOfPlaneParameters() - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
OutOfPlaneParameters(AtomType, AtomType, AtomType, AtomType) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
OutOfPlaneParameters(String) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
OutOfPlaneParameters(StringTokenizer) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
OutOfPlaneParameters(AtomType, AtomType, AtomType, AtomType, double, double) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
OutOfPlaneParameters.isA - Class in meshi.energy.simpleEnergyTerms.outOfPlane
 
OutOfPlaneParameters.isA() - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters.isA
 
OutOfPlaneParametersList - Class in meshi.energy.simpleEnergyTerms.outOfPlane
 
OutOfPlaneParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParametersList
 
outOfTheWay(Protein, int, double) - Static method in class meshi.util.alignmentTools.AlignmentTools
 
output - Variable in class AbInitio.AbInitioLogger
 
output - Variable in class Beautify.BeautifyLogger
 
output - Variable in class HomologyModeling.HomologyLogger
 
output - Variable in class Optimize.OptimizeLogger
 
output - Variable in class Refine.RefineLogger
 
OUTPUT_FILE_NAME - Static variable in interface meshi.util.KeyWords
 
OUTPUT_FILE_PATH - Static variable in interface meshi.util.KeyWords
 
outputDirectoryButton - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
outputFile - Static variable in class HeliumClusterMinimization
for the final coordinates.
outputFileMask - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
outputFileName - Static variable in class ChooseTemplate
 
outputFileName - Static variable in class ModelRanker
 
outputFilePathText - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
overlap - Variable in class meshi.applications.corpus.LocalFragmentLib
 
Overlap - Class in meshi.util.overlap
Kabsch algorithm for optimal superposition.
Overlap(double[][], double[][], int, String, String) - Constructor for class meshi.util.overlap.Overlap
 
overlapRMSsimilarity - Variable in class meshi.applications.corpus.LocalFragmentLib
 
OXT - Variable in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 

P

P - Variable in class meshi.optimizers.BFGS
 
P - Variable in class meshi.optimizers.ConjugateGradient
 
p1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
p1 - Variable in class meshi.energy.solvate.SigmaParameters
 
p2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
p2 - Variable in class meshi.energy.solvate.SigmaParameters
 
Pair - Class in meshi.util
 
Pair(String, Object) - Constructor for class meshi.util.Pair
 
Pair(String, double) - Constructor for class meshi.util.Pair
 
pairFactor - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
PairOfHydrogenBondsElements - Class in meshi.energy.hydrogenBondsPairs
 
PairOfHydrogenBondsElements() - Constructor for class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
PairOfHydrogenBondsElements(PairOfHydrogenBondsElements) - Constructor for class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
PairOfHydrogenBondsElements(Distance, Distance) - Constructor for class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
pairsOfHBEElementsList - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
PairsOfHBEElementsList - Class in meshi.energy.hydrogenBondsPairs
 
PairsOfHBEElementsList() - Constructor for class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
PairsOfHBEElementsList(HydrogenBondsEnergy) - Constructor for class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
PairsOfHBEElementsList.IsWithInRmax - Class in meshi.energy.hydrogenBondsPairs
 
PairsOfHBEElementsList.IsWithInRmax() - Constructor for class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.IsWithInRmax
 
PairsOfHBEElementsList.WithinRmaxPairsIterator - Class in meshi.energy.hydrogenBondsPairs
 
PairsOfHBEElementsList.WithinRmaxPairsIterator(ArrayList) - Constructor for class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
pairValue - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
parallel(HydrogenBondsPairsParameters) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
parallelPrecentage - Variable in class meshi.util.dssp.DSSP
 
parallelshift(int, int) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
parameters - Variable in class meshi.energy.CooperativeEnergyTerm
 
parameters - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
parameters(Object) - Method in class meshi.energy.hydrogenBond.HydrogenBondsParametersList
 
parameters(Object) - Method in class meshi.energy.hydrogenBond.LennardJonesParametersList
 
parameters(Object) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
parameters - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaCreator
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaCreator
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaCreator
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSummaCreator
 
parameters - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
parameters(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameterList
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
parameters - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
parameters(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParametersList
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
parameters - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
parameters - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreatorCa
 
parameters - Static variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
Parameters - Interface in meshi.energy
The parameters needed for the evaluation of an energy elements.
parameters - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
parameters(Object) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParametersList
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParametersList
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParametersList
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.bond.BondParametersList
Returns BondParameters object (which specify target-distance and force-constant) for a pair of atoms).
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList
Returns parameters for ResidueTorsions object according to residue type.
parameters - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityCreator
 
parameters - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityCreator
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList
Returns parameters for ResidueTorsions object according to residue type.
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList
Returns parameters for ResidueTorsions object according to residue type.
parameters - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranCreator
 
parameters - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranCreator
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList
Returns parameters for ResidueTorsions object according to residue type.
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList
Returns parameters for ResidueTorsions object according to residue type.
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.inflate.InflateParametersList
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParametersList
 
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.ParametersList
Energy term specific method to fetch parameters for the interactions between a st of atoms.
parameters(Object) - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParametersList
 
parameters - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
Since currently the hydrogen bond list is only used by the solvate energy, we use the parameters for the hydrogen bond from this class.
parameters - Variable in class meshi.energy.solvate.SolvateEnergy
The instance of the parameter list object.
parameters(Object) - Method in class meshi.energy.solvate.SolvateParametersList
 
parameters - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
parameters(Object) - Method in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
parameters(Object) - Method in class meshi.symmetryComplex.energy.cylinder.CylinderParametersList
 
parameters(Object) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParametersList
the only relevant "parameters" are the splined polynomial, so always return it through a dummy Parameters class.
PARAMETERS_DIRECTORY - Static variable in interface meshi.util.KeyWords
 
parametersDirectory - Static variable in class meshi.energy.EnergyCreator
 
parametersDirectory(CommandList) - Static method in class meshi.energy.EnergyCreator
Extract the path of the parameters directory from the commands list.
parametersDirectory - Static variable in class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
 
parametersExplanationLabel - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
parametersFileName - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator
 
parametersFileName - Variable in class meshi.geometry.rotamers.DunbrackLib
 
ParametersForChainCompletion - Class in meshi.applications.prediction.homology.gui
 
ParametersForChainCompletion() - Constructor for class meshi.applications.prediction.homology.gui.ParametersForChainCompletion
 
ParametersForChainCompletionLayout - Class in meshi.applications.prediction.homology.gui
 
ParametersForChainCompletionLayout() - Constructor for class meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout
 
parametersList - Variable in class meshi.energy.hydrogenBond.HBondList
 
parametersList - Variable in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
parametersList - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergy
 
parametersList - Static variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
parametersList - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
parametersList - Static variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
parametersList - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DCreator
 
parametersList - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranCreator
 
ParametersList - Class in meshi.energy.simpleEnergyTerms
A list of parameters for an energy term.
ParametersList() - Constructor for class meshi.energy.simpleEnergyTerms.ParametersList
 
ParametersList(String, boolean) - Constructor for class meshi.energy.simpleEnergyTerms.ParametersList
Construct a ParametersList object from parameters file.
ParametersList(String[], boolean) - Constructor for class meshi.energy.simpleEnergyTerms.ParametersList
Construct a ParametersList object from multiple files.
parametersList - Variable in class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator.HaveParametersFilter
 
parametersList - Variable in class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
A list of the parameters needed for this energy term.
parametersList() - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
get method for parametersList.
parametersList - Variable in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
A list of all the parameters needed by the energy term.
parametersList - Static variable in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
parametersList - Static variable in class meshi.energy.solvate.SolvateCreatorLongHB
 
parametersList - Static variable in class meshi.energy.solvate.SolvateCreatorRegularHB
 
parametersList - Static variable in class meshi.energy.solvateRot1.SolvateRot1Creator
 
parametersLoaded - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
parentFile - Static variable in class ChooseTemplate
 
parentOutputFileName - Static variable in class ChooseTemplate
 
path - Variable in class meshi.util.file.MeshiLineReader
 
path() - Method in class meshi.util.file.MeshiLineReader
 
path - Variable in class meshi.util.file.MeshiWriter
 
Pdb2Fasta - Class in <Unnamed>
 
Pdb2Fasta() - Constructor for class Pdb2Fasta
 
Pdb2Fasta.MyAtom - Class in <Unnamed>
 
Pdb2Fasta.MyAtom(Atom, String) - Constructor for class Pdb2Fasta.MyAtom
 
Pdb2Fasta.MyChain - Class in <Unnamed>
 
Pdb2Fasta.MyChain(AtomList, String, MeshiLog) - Constructor for class Pdb2Fasta.MyChain
 
Pdb2Fasta.MyFilter - Class in <Unnamed>
 
Pdb2Fasta.MyFilter(String) - Constructor for class Pdb2Fasta.MyFilter
 
Pdb2Fasta.MyResidue - Class in <Unnamed>
 
Pdb2Fasta.MyResidue(AtomList, String) - Constructor for class Pdb2Fasta.MyResidue
 
PDB_FILE - Static variable in interface meshi.util.KeyWords
 
pdbLine - Variable in class meshi.molecularElements.atoms.Atom
 
pdbLine() - Method in class meshi.molecularElements.atoms.Atom
 
PdbLine - Class in meshi.PDB
from http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number.
PdbLine(String) - Constructor for class meshi.PDB.PdbLine
 
PdbLine(int, String, String, String, String, int, double, double, double, double, double) - Constructor for class meshi.PDB.PdbLine
 
PdbLine() - Constructor for class meshi.PDB.PdbLine
 
PdbLineATOM - Class in meshi.PDB
 
PdbLineATOM() - Constructor for class meshi.PDB.PdbLineATOM
 
PdbLineATOM(List<String>) - Constructor for class meshi.PDB.PdbLineATOM
 
PdbLineATOMorHETATOM - Class in meshi.PDB
 
PdbLineATOMorHETATOM() - Constructor for class meshi.PDB.PdbLineATOMorHETATOM
 
PdbLineFilter - Class in meshi.PDB
 
PdbLineFilter() - Constructor for class meshi.PDB.PdbLineFilter
 
PdbLineSEQRES - Class in meshi.PDB
 
PdbLineSEQRES() - Constructor for class meshi.PDB.PdbLineSEQRES
 
PdbReader - Class in meshi.PDB
 
PdbReader(File) - Constructor for class meshi.PDB.PdbReader
 
PdbReader(String) - Constructor for class meshi.PDB.PdbReader
 
PdbReader(String, String) - Constructor for class meshi.PDB.PdbReader
 
perturb() - Method in class meshi.optimizers.Perturbation
 
perturbation - Variable in class meshi.optimizers.MCM
 
Perturbation - Class in meshi.optimizers
 
Perturbation(TotalEnergy, CommandList, AbstractEnergy, Protein, double) - Constructor for class meshi.optimizers.Perturbation
 
Phe - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - CD1 - CE1 | | CD2- CE2 - CZ
Phe(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Phe
 
PHI - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
phi_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.ResidueTorsionsPropensityAttribute
 
phi_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
phipsi(Protein, DistanceMatrix) - Static method in class meshi.util.rotamericTools.RotamericTools
 
piv - Variable in class meshi.util.mathTools.Jama.LUDecomposition
Internal storage of pivot vector.
pivot - Variable in class meshi.util.filters.Differs
 
pivot - Variable in class meshi.util.filters.Equals
 
pivsign - Variable in class meshi.util.mathTools.Jama.LUDecomposition
Row and column dimensions, and pivot sign.
PLANE_ENERGY - Static variable in interface meshi.util.KeyWords
 
PLANE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
planeCreator - Static variable in class Beautify
 
PlaneCreator - Class in meshi.energy.simpleEnergyTerms.plane
 
PlaneCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneCreator
 
PlaneCreator() - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneCreator
 
PlaneEnergy - Class in meshi.energy.simpleEnergyTerms.plane
Plane energy term.
PlaneEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneEnergy
 
PlaneEnergy(TorsionList, DistanceMatrix, PlaneParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneEnergy
 
PlaneEnergyElement - Class in meshi.energy.simpleEnergyTerms.plane
 
PlaneEnergyElement(Torsion, Parameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
PlaneParameters - Class in meshi.energy.simpleEnergyTerms.plane
 
PlaneParameters() - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
PlaneParameters(AtomType, AtomType, AtomType, AtomType) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
PlaneParameters(String) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
PlaneParameters(StringTokenizer) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
PlaneParameters(AtomType, AtomType, AtomType, AtomType, double, int) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
PlaneParameters.isA - Class in meshi.energy.simpleEnergyTerms.plane
 
PlaneParameters.isA() - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParameters.isA
 
PlaneParametersList - Class in meshi.energy.simpleEnergyTerms.plane
 
PlaneParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.plane.PlaneParametersList
 
plus(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
C = A + B
plusEquals(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
A = A + B
plusLinear(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
 
pointOfCrossing(double, double, double, double, double, double, double, double) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
POLYNOMIAL_CHI_1 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_CHI_2 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_CHI_2_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_CHI_3 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_CHI_3_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_CHI_4 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_CHI_4_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_CHI_1_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_PHI_PSI - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_PHI_PSI_CHI_1 - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_PHI_PSI_CHI_1_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
POLYNOMIAL_PHI_PSI_TORSIONS - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
polynomials - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
polynomials used
polynomials - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
polynomials used
Popo - Static variable in class meshi.util.GDTcalculator
 
pos(Atom, BondParametersList, AngleParametersList) - Static method in class meshi.geometry.putH.PutHpos
 
pos(double) - Method in class meshi.util.histogram.Histogram
 
position() - Method in class meshi.molecularElements.Residue
residue number - 1.
position - Variable in class meshi.util.histogram.HistogramBin
 
position() - Method in class meshi.util.histogram.HistogramBin
 
positionAndFreezeCas(Protein, Protein) - Static method in class meshi.symmetryComplex.utils.GJUtils
Coordinates of transmembranal C-Alphas from Sar-el's work were deposited in the PDB under the entry 1txh.
positionTMCas(Protein, Protein) - Static method in class meshi.symmetryComplex.utils.GJUtils
Coordinates of transmembranal C-Alphas from Sar-el's work were deposited in the PDB under the entry 1txh.
pp - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBCreator
 
pp - Variable in class meshi.energy.solvateRot1.SolvateRot1Creator
 
PRECISION - Variable in class meshi.util.formats.Fdouble
 
predictedMap() - Method in class meshi.symmetryComplex.topologyMap.Topology
 
PredictionSequenceAlignment - Class in meshi.applications.prediction
 
PredictionSequenceAlignment(CommandList, Key, Sequence) - Constructor for class meshi.applications.prediction.PredictionSequenceAlignment
 
PredictionSequenceAlignment(Sequence, Protein, SequenceList) - Constructor for class meshi.applications.prediction.PredictionSequenceAlignment
 
PredictionSequenceAlignment.TemplateAlignmentException - Exception in meshi.applications.prediction
 
PredictionSequenceAlignment.TemplateAlignmentException(Protein, SequenceList, SequenceAlignment) - Constructor for exception meshi.applications.prediction.PredictionSequenceAlignment.TemplateAlignmentException
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.HomologyFrame11Layout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.InflateParametersLayout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.OptionDialog3Layout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout
 
preferredLayoutSize(Container) - Method in class meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout
 
prepareRMS(int) - Method in class meshi.geometry.fragments.DresserFullFrag
 
prePro - Variable in class meshi.applications.corpus.Corpus
 
PREPRO - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
prevAtom - Variable in class meshi.molecularElements.Residue
 
prevAtom() - Method in class meshi.molecularElements.Residue
 
prevCoor - Variable in class meshi.geometry.Grid
 
prevCoor - Variable in class meshi.geometry.OldGrid
 
previousCoordinates - Variable in class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
previousResidue - Variable in class Pdb2Fasta.MyChain
 
print() - Method in class aligner.AminoAcidSubstitutionMatrix
 
print() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
print() - Method in class meshi.molecularElements.atoms.AtomList
 
print(MeshiWriter) - Method in class meshi.molecularElements.atoms.AtomList
 
print() - Method in class meshi.molecularElements.ResidueList
 
print() - Method in class meshi.sequences.SequenceAlignment
 
print() - Method in class meshi.sequences.SequenceList
 
print() - Method in class meshi.util.histogram.Histogram
 
print(int, int) - Method in class meshi.util.mathTools.Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class meshi.util.mathTools.Jama.Matrix
Print the matrix to the output stream.
print(NumberFormat, int) - Method in class meshi.util.mathTools.Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class meshi.util.mathTools.Jama.Matrix
Print the matrix to the output stream.
print() - Method in class meshi.util.MeshiProgram.GlobalElementList
 
print(MeshiWriter) - Method in class meshi.util.string.StringList
 
print(Iterable) - Static method in class meshi.util.Utils
 
print(ArrayList, int, String) - Static method in class meshi.util.Utils
Print the list elements in raws.
printAllCoefficients() - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
Print all coefficients to screen.
printAtomsToFile(String) - Method in class meshi.molecularElements.Protein
 
printCaspFormat(ModelData, CommandList, int) - Static method in class meshi.util.Utils
 
printChainsNames() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
printCommandsLines(MeshiWriter) - Method in class meshi.util.CommandList
 
printGlobalTable() - Static method in class meshi.util.MeshiProgram
Print the keyword - value table.
printLaconic(String) - Method in class meshi.molecularElements.atoms.AtomPairList
 
printLib() - Method in class meshi.applications.corpus.LocalFragmentLib
 
printLib(int) - Method in class meshi.applications.corpus.LocalFragmentLib
 
printLine(int, String, String, String, String, int, double, double, double, double, double) - Method in class meshi.PDB.PdbLine
 
printLine(String) - Method in class meshi.util.Command
 
printPresentage() - Method in class meshi.util.dssp.DSSP
 
printResidueFeatures(MeshiWriter, ArrayList<AbstractEnergy>, Protein, String) - Static method in class CalculateEnergyFromStructuresListAverages
 
printResidueFeaturesHeader(MeshiWriter, ArrayList<AbstractEnergy>) - Static method in class CalculateEnergyFromStructuresListAverages
 
printSS() - Method in class meshi.util.dssp.DSSP
 
Pro - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | CD CB \ / CG
Pro(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Pro
 
prob - Variable in class meshi.geometry.rotamers.DunbrackLib
 
probabilityOfScmod - Variable in class meshi.optimizers.Perturbation
 
problematic(Residue) - Static method in class Beautify
 
problematic(ResidueAlignment, int) - Static method in class Beautify
 
problematic - Variable in class meshi.applications.prediction.beautify.BeautifyAttribute
 
problematicComment - Variable in class meshi.applications.prediction.beautify.BeautifyAttribute
 
problematicComment() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
problematicComment(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
problematicNeighbor - Variable in class meshi.applications.prediction.beautify.BeautifyAttribute
 
problematicNeighbor() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
problematicNeighbor(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
processModels(List<ModelData>, MeshiWriter) - Static method in class InitialEvaluation
 
processProtein(Protein, MeshiWriter, CommandList, boolean) - Static method in class CalculateEnergyFromStructuresListAverages
 
processProtein(Protein, CommandList) - Static method in class ColorByEnergy
 
processProtein(Protein, Protein, CommandList, EnergyCreator[]) - Static method in class meshi.applications.prediction.ModelData
 
processProtein(Protein, Protein, CommandList, EnergyCreator[], String) - Static method in class SelectForCASP
 
processProtein(Protein, MeshiWriter, CommandList) - Static method in class TestElectrostatics
 
propEnergy - Variable in class meshi.applications.corpus.LoopResults
 
PROPENSITY_ANGLE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
PROPENSITY_TORSION_ENERGY - Static variable in interface meshi.util.KeyWords
 
PROPENSITY_TORSION_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
propensityCreator - Static variable in class EnergyStatistics
 
propensityCreator - Static variable in class EnergyStatisticsForAtom
 
propensityEnergy - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
propensityEnergy - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
proper(Angle) - Method in class meshi.geometry.Angle
 
proper() - Method in class meshi.geometry.Torsion
 
propPolynomial - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters
propensity polynomial for this residue
propPolynomial - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters
propensity polynomial for this residue
propPolynomial - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParameters
polynomial for this residue
prot - Variable in class meshi.applications.corpus.LocalFragmentLib
 
protCoors - Variable in class meshi.applications.corpus.LocalFragmentLib
 
protein - Variable in class meshi.molecularElements.Chain
 
protein - Variable in class meshi.molecularElements.ChainList
 
Protein - Class in meshi.molecularElements
A protein chain.
Protein(String) - Constructor for class meshi.molecularElements.Protein
 
Protein(Sequence, String, ResidueCreator) - Constructor for class meshi.molecularElements.Protein
Builds a protein from AA sequence.
Protein(Sequence, String, String, ResidueCreator) - Constructor for class meshi.molecularElements.Protein
 
Protein(AtomList, ResidueCreator) - Constructor for class meshi.molecularElements.Protein
Builds a protein from a PDB formatted file and a line filter.
Protein(String, Filter, ResidueCreator) - Constructor for class meshi.molecularElements.Protein
Builds a protein from a PDB formatted file and a line filter.
Protein(Residue) - Constructor for class meshi.molecularElements.Protein
 
Protein(AtomList) - Constructor for class meshi.molecularElements.Protein
Builds a protein from a list of atoms.
protein - Variable in class meshi.optimizers.Perturbation
 
protein - Static variable in class SimplestMinimizeProtein
 
Protein.BackboneFilter - Class in meshi.molecularElements
Sets the chain of this protein, after asserting that it is comprised of residues belonging to a single polypeptide chain.
Protein.BackboneFilter() - Constructor for class meshi.molecularElements.Protein.BackboneFilter
 
proteinNames - Variable in class meshi.applications.corpus.Corpus
 
proteinsFile - Static variable in class ChooseTemplate
 
proteinsFile - Static variable in class ModelRanker
 
protInd - Variable in class meshi.applications.corpus.Corpus
 
PSI - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
psi_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.ResidueTorsionsPropensityAttribute
 
psi_deriv - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
punish - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
purtubrationTerm - Variable in class meshi.optimizers.Perturbation
 
PutHpos - Class in meshi.geometry.putH
This procedure is was copied and manually translated to java, from Ron Elber's puth program available in the MOIL package.
PutHpos() - Constructor for class meshi.geometry.putH.PutHpos
 
PutHposLog - Class in meshi.geometry.putH
 
PutHposLog(Atom, Atom, int, int) - Constructor for class meshi.geometry.putH.PutHposLog
 
putIntoRot1(Protein, DistanceMatrix, DunbrackLib) - Static method in class meshi.util.rotamericTools.RotamericTools
 

Q

Q - Variable in class meshi.optimizers.LBFGS
 
q1 - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
q2 - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
qr() - Method in class meshi.util.mathTools.Jama.Matrix
QR Decomposition
QR - Variable in class meshi.util.mathTools.Jama.QRDecomposition
Array for internal storage of decomposition.
QRDecomposition - Class in meshi.util.mathTools.Jama
QR Decomposition.
QRDecomposition(Matrix) - Constructor for class meshi.util.mathTools.Jama.QRDecomposition
QR Decomposition, computed by Householder reflections.
QuickAndDirtyAngle - Class in meshi.geometry
Allows the use of approximated arc-cos function.
QuickAndDirtyAngle(AtomPair, AtomPair, DistanceMatrix) - Constructor for class meshi.geometry.QuickAndDirtyAngle
 
QuickAndDirtyAngle(Atom, Atom, Atom, DistanceMatrix) - Constructor for class meshi.geometry.QuickAndDirtyAngle
 
QuickAndDirtyAngleList - Class in meshi.geometry
A list of quick and dirty angles.
QuickAndDirtyAngleList() - Constructor for class meshi.geometry.QuickAndDirtyAngleList
 
QuickAndDirtyAngleList(AtomPairList, DistanceMatrix) - Constructor for class meshi.geometry.QuickAndDirtyAngleList
 
QuickAndDirtyTorsion - Class in meshi.geometry
Allows the use of approximated arc-cos function.
QuickAndDirtyTorsion(Angle, Angle, DistanceMatrix) - Constructor for class meshi.geometry.QuickAndDirtyTorsion
 
QuickAndDirtyTorsionList - Class in meshi.geometry
A list of quick and dirty torsion angles.
QuickAndDirtyTorsionList(AngleList, DistanceMatrix) - Constructor for class meshi.geometry.QuickAndDirtyTorsionList
 
quickDistanceFrom(double, double, double, double, double, double) - Static method in class meshi.symmetryComplex.utils.GJUtils
 
quickDistanceFrom(Coordinates, Coordinates) - Static method in class meshi.symmetryComplex.utils.GJUtils
 
quickPower(double, int) - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
Raises a double by the power, with 0 <= power <= 3.
quickPower(double, int) - Static method in class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
Raises a double by the power, with 0 <= power <= 3.
quickPowerMatrix - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 

R

R - Variable in class meshi.optimizers.LBFGS
 
r - Static variable in class meshi.util.mathTools.Ramp
 
R_MAX - Static variable in interface meshi.util.KeyWords
 
r_tag - Static variable in class meshi.util.mathTools.Ramp
 
rad2deg(double) - Static method in class meshi.geometry.Angle
 
radius - Variable in class meshi.applications.prediction.homology.NonFrozensRadiusFilter
 
radius() - Method in class meshi.geometry.DistanceMatrix
 
radius() - Method in class meshi.geometry.OldDistanceMatrix
 
radius() - Method in class meshi.molecularElements.atoms.AtomList
of gyration of the list atoms.
radius(MolecularSystem) - Static method in class meshi.util.Utils
 
radius2() - Method in class meshi.molecularElements.atoms.AtomList
 
RAMACHANDRAN_SIDECHAIN_ENERGY - Static variable in interface meshi.util.KeyWords
 
RamachandranCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
The Ramachandran energy calculates the probability of each amino acid to be in a specific position at the (phi,psi) torsion space.
RamachandranCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranCreator
 
RamachandranCreator() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranCreator
 
RamachandranEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
 
RamachandranEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergy
 
RamachandranEnergy(ResidueTorsionsList, DistanceMatrix, RamachandranParametersList, double, String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergy
 
RamachandranEnergyElement - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
 
RamachandranEnergyElement(ResidueTorsions, RamachandranParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement
 
RamachandranParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
 
RamachandranParameters(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParameters
 
RamachandranParametersList - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran
 
RamachandranParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList
 
ramachandranSidechainEnergy - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
ramachandranSidechainEnergy - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
RamachandranSidechainEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
A Ramachandran plot and sidechain torsions optimization energy term.
RamachandranSidechainEnergy(ResidueTorsionsList, DistanceMatrix, RamachandranSidechainParametersList, double, String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
ramachandranSidechainEnergyCreator - Static variable in class Beautify
 
ramachandranSidechainEnergyCreator - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranCreator
 
ramachandranSidechainEnergyCreator - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranCreator
 
RamachandranSidechainEnergyCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
RamachandranSidechainEnergyCreator() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyCreator
 
RamachandranSidechainEnergyElement - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Encapsulation of RamachandranSidechain energy value for a single residue.
RamachandranSidechainEnergyElement(ResidueTorsions, RamachandranSidechainParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
 
RamachandranSidechainEnergyElementChi0 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain energy element for amino acids with no sidechain torsion angles: ALA, GLY.
RamachandranSidechainEnergyElementChi0(ResidueTorsions, RamachandranSidechainParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi0
 
RamachandranSidechainEnergyElementChi1 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain energy element for amino acids with one sidechain torsion angle: CYS, SER, THR, VAL.
RamachandranSidechainEnergyElementChi1(ResidueTorsions, RamachandranSidechainParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi1
 
RamachandranSidechainEnergyElementChi2 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain energy element for amino acids with no sidechain torsion angles: ASP, PHE, HIS, ILE, LEU, ASN, PRO, TRP, TYR.
RamachandranSidechainEnergyElementChi2(ResidueTorsions, RamachandranSidechainParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi2
 
RamachandranSidechainEnergyElementChi3 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain energy element for amino acids with three sidechain torsion angles: GLU, MET, GLN.
RamachandranSidechainEnergyElementChi3(ResidueTorsions, RamachandranSidechainParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi3
 
RamachandranSidechainEnergyElementChi4 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain parameters for amino acids with four sidechain torsion angles: LYS, ARG.
RamachandranSidechainEnergyElementChi4(ResidueTorsions, RamachandranSidechainParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi4
 
RamachandranSidechainParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Parameters used with the RamachandranSidechainEnergy term.
RamachandranSidechainParameters(int) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
Updates residue type of parameters.
RamachandranSidechainParametersChi0 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain parameters for amino acids with no sidechain torsion angles: ALA, GLY.
RamachandranSidechainParametersChi0(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi0
 
RamachandranSidechainParametersChi1 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain parameters for amino acids with one sidechain torsion angle: CYS, SER, THR, VAL.
RamachandranSidechainParametersChi1(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi1
 
RamachandranSidechainParametersChi2 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain parameters for amino acids with two sidechain torsion angles: ASP, PHE, HIS, ILE, LEU, ASN, PRO, TRP, TYR.
RamachandranSidechainParametersChi2(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi2
 
RamachandranSidechainParametersChi3 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain parameters for amino acids with three sidechain torsion angles: GLU, MET, GLN.
RamachandranSidechainParametersChi3(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi3
 
RamachandranSidechainParametersChi4 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Ramachandran/Sidechain parameters for amino acids with four sidechain torsion angles: LYS, ARG.
RamachandranSidechainParametersChi4(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi4
 
RamachandranSidechainParametersList - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
RamachandranSidechainParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList
Create a new parameters file from the polynomials parameters data file.
ramachCreator - Static variable in class EnergyStatistics
 
ramachCreator - Static variable in class EnergyStatisticsForAtom
 
Ramp - Class in meshi.util.mathTools
This class host the static method "ramp" which gives a derivable ramp function of the following form: x<0 - not defined 0Ramp() - Constructor for class meshi.util.mathTools.Ramp
 
ramp(double, double, double) - Static method in class meshi.util.mathTools.Ramp
 
random - Static variable in class meshi.applications.prediction.AbitSmarterLoopBuilder
 
random - Variable in class meshi.geometry.Coordinates
 
random() - Method in class meshi.geometry.Coordinates
 
random(int, int) - Static method in class meshi.util.mathTools.Jama.Matrix
Generate matrix with random elements
randomize(double, double, double, double) - Method in class meshi.molecularElements.atoms.Atom
Move the atom to a random position within radius from (centerx,centery,centerz).
randomize(double, Atom) - Method in class meshi.molecularElements.atoms.Atom
 
randomNumberGenerator - Static variable in class meshi.geometry.putH.PutHpos
 
randomNumberGenerator - Variable in class meshi.optimizers.Perturbation
 
randomNumberGenerator - Static variable in class meshi.util.MeshiProgram
The single random number generator used by the program.
randomNumberGenerator() - Static method in class meshi.util.MeshiProgram
Gets the program's random number generator.
ranges - Variable in class meshi.symmetryComplex.utils.GJFilters.ResidueRangeFilter
 
rank - Variable in class HomologyModeling.Loop
 
rank() - Method in class HomologyModeling.Loop
 
rank - Variable in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
rank() - Method in class meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
 
rank() - Method in class meshi.util.mathTools.Jama.Matrix
Matrix rank
rank() - Method in class meshi.util.mathTools.Jama.SingularValueDecomposition
Effective numerical matrix rank
Rdiag - Variable in class meshi.util.mathTools.Jama.QRDecomposition
Array for internal storage of diagonal of R.
read(BufferedReader) - Static method in class meshi.util.mathTools.Jama.Matrix
Read a matrix from a stream.
readDSSP() - Method in class meshi.util.dssp.DSSP
 
readLine(Filter) - Method in class meshi.util.file.MeshiLineReader
 
readLine(String) - Method in class meshi.util.file.MeshiLineReader
 
readPdbLine() - Method in class meshi.PDB.PdbReader
 
readPdbLine(Filter) - Method in class meshi.PDB.PdbReader
 
readSigmoidValueFile(double[][], String) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
 
readSigmoidValueFile(double[][], String) - Method in class meshi.energy.solvate.SolvateParametersList
 
readSigmoidValueFile(double[][], String) - Method in class meshi.energy.solvateRot1.SolvateRot1ParametersList
 
readSpecialDistance(int[], Protein, DistanceMatrix, boolean) - Method in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
reference - Variable in class AbInitio.AbInitioLogger
 
reference - Static variable in class AbInitio
 
reference - Variable in class Beautify.BeautifyLogger
 
reference - Variable in class HomologyModeling.HomologyLogger
 
reference - Static variable in class HydrogenTest
 
REFERENCE - Static variable in interface meshi.util.KeyWords
 
reference - Variable in class Optimize.OptimizeLogger
 
reference - Variable in class Refine.RefineLogger
 
referenceExists - Variable in class AbInitio.AbInitioLogger
 
referenceExists - Variable in class Beautify.BeautifyLogger
 
referenceExists - Variable in class HomologyModeling.HomologyLogger
 
referenceExists - Variable in class Optimize.OptimizeLogger
 
referenceExists - Variable in class Refine.RefineLogger
 
referenceFileName - Static variable in class CalcGDT
 
Refine - Class in <Unnamed>
 
Refine() - Constructor for class Refine
 
Refine.RefineLogger - Class in <Unnamed>
 
Refine.RefineLogger(Protein, CommandList) - Constructor for class Refine.RefineLogger
 
refinedModelFileName - Static variable in class CalcGDT
 
refresh() - Method in class meshi.geometry.DistanceMatrixCaOnly
 
refreshVectorEvery - Variable in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
relACCofRes(int) - Method in class meshi.util.dssp.DSSP
 
RELATIVE_ORIENTATION - Static variable in class meshi.symmetryComplex.utils.GJUtils
 
relativeDiffTolerance - Variable in class meshi.energy.CooperativeEnergyTerm
 
relativeDiffTolerance - Static variable in class meshi.energy.EnergyElement
 
relax(Protein, CommandList, Protein, Beautify.BeautifyLogger) - Static method in class Beautify
 
relax(Protein, CommandList, EnergyCreator[]) - Static method in class Beautify
 
RELAX - Static variable in interface meshi.util.KeyWords
 
relax(AtomList, Protein, EnergyCreator[], CommandList) - Static method in class meshi.util.Utils
 
relax(AtomList, Protein, EnergyCreator[], CommandList, Key) - Static method in class meshi.util.Utils
 
relaxCaModel(Protein, Protein, CommandList) - Static method in class Beautify
 
relaxMaxStepsLabel - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
relaxMaxStepsText - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
relaxReportEveryLabel - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
relaxReportEveryText - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
relaxToleranceLabel - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
relaxToleranceText - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
 
relevantRows - Variable in class meshi.energy.hydrogenBond.HBondList
 
reliability - Variable in class meshi.molecularElements.atoms.Atom
 
reliability() - Method in class meshi.molecularElements.atoms.Atom
 
reliability - Variable in class meshi.molecularElements.Residue
 
reliability() - Method in class meshi.molecularElements.Residue
 
remove() - Method in class meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator
 
remove() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator
 
remove() - Method in class meshi.geometry.DistanceList.DistanceIterator
 
remove() - Method in class meshi.geometry.DistanceMatrix.RowIterator
 
remove() - Method in class meshi.geometry.OldDistanceMatrix.RowIterator
 
remove() - Method in class meshi.util.histogram.Histogram.RepresentativesIterator
 
removeBadBonds(double) - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
 
removeBadBonds(double) - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
removeBadBonds(double) - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergy
 
removeBrokenHB() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
This method remove from the vector Hydrogen Bond objects, whose distance between polars is so large, they no longer appears in the non-bonded list of the distance matrix.
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.HomologyFrame11Layout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.InflateParametersLayout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.OptionDialog3Layout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout
 
removeLayoutComponent(Component) - Method in class meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout
 
removeSpaces(String) - Static method in class meshi.sequences.FastaList
 
renumber(Sequence) - Method in class meshi.sequences.Sequence
 
renumber(SequenceAlignment) - Method in class meshi.sequences.Sequence
 
report(int) - Method in class meshi.energy.TotalEnergy
 
REPORT_EVERY - Static variable in interface meshi.util.KeyWords
 
reportEvery - Variable in class meshi.optimizers.Optimizer
 
reportEvery - Variable in class meshi.optimizers.SteepestDecent
 
reportHeader() - Method in class meshi.energy.TotalEnergy
 
reportPolynomialsList() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
Reports contents of all polynomials.
reportPolynomialsList() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
Reports contents of all polynomials.
reportPolynomialsList() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
report list of polynomials
representative(double) - Method in class meshi.util.histogram.Histogram
 
representativesIterator(double) - Method in class meshi.util.histogram.Histogram
 
res - Variable in class meshi.geometry.rotamers.DunbrackLib
 
reset() - Method in class meshi.energy.TotalEnergy
 
reset() - Method in class meshi.geometry.Coordinates
 
reset() - Method in class meshi.geometry.DistanceMatrix
 
reset() - Method in class meshi.geometry.DistanceMatrixBondedOnly
 
reset() - Method in class meshi.geometry.DistanceMatrixCaOnly
 
reset() - Method in class meshi.geometry.OldDistanceMatrix
 
Reset() - Method in class meshi.optimizers.WolfConditionLineSearch
 
Reset(double) - Method in class meshi.optimizers.WolfConditionLineSearch
 
reset() - Method in class meshi.symmetryComplex.geometryImage.DistanceMatrixNoImageAtoms
 
reset() - Method in class meshi.util.Terminator
 
resetAllSigmVals() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
resetAllSigmVals() - Method in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
resetAtomEnergies() - Method in class meshi.energy.TotalEnergy
 
resetAuxilaryArrays() - Method in class meshi.energy.solvate.SolvateEnergy
 
resetCoordinates() - Method in class meshi.molecularElements.atoms.Atom
 
resetEnergy() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
resetEnergy() - Method in class meshi.molecularElements.atoms.Atom
 
resetForces(double[][]) - Static method in class meshi.energy.TotalEnergy
Sets all forces to zero.
resetForces() - Static method in class meshi.energy.TotalEnergy
 
resetForces() - Method in class meshi.geometry.Coordinates
 
resetForces() - Method in class meshi.geometry.FrozenCoordinates
 
resetHBSigmVals() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
resetNumberOfUpdates() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
resetSigmVals() - Method in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
resetSigmVals() - Method in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
resetSigmVals() - Method in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
resHasAllEne - Variable in class meshi.applications.corpus.Corpus
 
residue() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
residue - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
residue - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
residue - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
residue() - Method in class meshi.energy.templateEnergy.TemplateEnergyElement
 
residue - Variable in class meshi.molecularElements.atoms.Atom
Atom's Residue.
residue() - Method in class meshi.molecularElements.atoms.Atom
Returns the atom's residue.
residue(ResidueIdentifier) - Method in class meshi.molecularElements.Chain
Fetches a residue by its residue identifier.
residue(ResidueIdentifier) - Method in class meshi.molecularElements.Protein
Returns the residue.
residue(int) - Method in class meshi.molecularElements.Protein
Returns the residue.
Residue - Class in meshi.molecularElements
A generic residue.
Residue(String) - Constructor for class meshi.molecularElements.Residue
Use this constructor to instantiate a creator object..
Residue(String, ResidueType, ResidueIdentifier, AtomList, ResidueMode) - Constructor for class meshi.molecularElements.Residue
 
Residue(ResidueIdentifier) - Constructor for class meshi.molecularElements.Residue
 
Residue(ResidueIdentifier, String) - Constructor for class meshi.molecularElements.Residue
 
residue(ResidueIdentifier) - Method in class meshi.molecularElements.ResidueList
Fetches a residue by its residue identifier.
residue() - Method in class meshi.sequences.ResidueAlignmentCell
 
residue0() - Method in class meshi.sequences.ResidueAlignmentColumn
 
residue1() - Method in class meshi.sequences.ResidueAlignmentColumn
 
RESIDUE_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
RESIDUE_TORSIONS_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
residueAlignment - Variable in class meshi.energy.templateEnergy.TemplateEnergyCreator
 
ResidueAlignment - Class in meshi.sequences
 
ResidueAlignment() - Constructor for class meshi.sequences.ResidueAlignment
Empty alignment.
ResidueAlignment(Chain, String, Chain, String) - Constructor for class meshi.sequences.ResidueAlignment
A trevial alignment of two protein objects which are assumed to be two models of the same protein.
ResidueAlignment(ResidueSequence, ResidueSequence) - Constructor for class meshi.sequences.ResidueAlignment
 
ResidueAlignment(Chain, Chain, SequenceList) - Constructor for class meshi.sequences.ResidueAlignment
 
ResidueAlignment(SequenceAlignment) - Constructor for class meshi.sequences.ResidueAlignment
 
ResidueAlignmentCell - Class in meshi.sequences
 
ResidueAlignmentCell(Residue) - Constructor for class meshi.sequences.ResidueAlignmentCell
 
ResidueAlignmentColumn - Class in meshi.sequences
A pair of residues each from a different Protein object and a string indicating which atoms in these residues should be aligned.
ResidueAlignmentColumn(int) - Constructor for class meshi.sequences.ResidueAlignmentColumn
 
ResidueAlignmentColumn(Residue, Residue) - Constructor for class meshi.sequences.ResidueAlignmentColumn
 
ResidueAlignmentColumn(ResidueAlignmentCell, ResidueAlignmentCell) - Constructor for class meshi.sequences.ResidueAlignmentColumn
 
ResidueAlignmentOfModels - Class in meshi.sequences
Residue alignment of multiple protein objects, all representing the same protein.
ResidueAlignmentOfModels(Protein[]) - Constructor for class meshi.sequences.ResidueAlignmentOfModels
 
residueAt(int) - Method in class meshi.molecularElements.Chain
Fetch a residue by its position in the list.
residueAt(int) - Method in class meshi.molecularElements.Protein
 
ResidueBuilder - Class in meshi.geometry
 
ResidueBuilder() - Constructor for class meshi.geometry.ResidueBuilder
 
residueCharFilter - Static variable in class meshi.sequences.ResidueSequence
 
ResidueCreator - Interface in meshi.molecularElements
 
residueEnergies - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
ResidueExtendedAtoms - Class in meshi.molecularElements.extendedAtoms
 
ResidueExtendedAtoms(String) - Constructor for class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
ResidueExtendedAtoms(ResidueType, AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
Do not use this constructor to instantiate a creator object.
ResidueExtendedAtomsCreator - Class in meshi.molecularElements.extendedAtoms
 
ResidueExtendedAtomsCreator() - Constructor for class meshi.molecularElements.extendedAtoms.ResidueExtendedAtomsCreator
 
residueFragStart - Variable in class meshi.applications.corpus.LocalFragmentLib
 
residueFragStart() - Method in class meshi.applications.corpus.LocalFragmentLib
 
ResidueIdentifier - Class in meshi.molecularElements
A unique identifier for residues.
ResidueIdentifier(int) - Constructor for class meshi.molecularElements.ResidueIdentifier
 
ResidueIdentifier(String, int) - Constructor for class meshi.molecularElements.ResidueIdentifier
Main constructor of this class.
ResidueList - Class in meshi.molecularElements
A list of residues.
ResidueList() - Constructor for class meshi.molecularElements.ResidueList
 
ResidueList(ChainList) - Constructor for class meshi.molecularElements.ResidueList
 
residueList - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
ResidueList.NonDummyFilter - Class in meshi.molecularElements
 
ResidueList.NonDummyFilter() - Constructor for class meshi.molecularElements.ResidueList.NonDummyFilter
 
ResidueMode - Enum in meshi.parameters
 
ResidueMode() - Constructor for enum meshi.parameters.ResidueMode
 
residueName() - Method in class meshi.molecularElements.atoms.Atom
 
residueName - Variable in class meshi.PDB.PdbLine
 
residueName() - Method in class meshi.PDB.PdbLine
 
ResidueNameConvertor - Class in meshi.util
Converts Residue names from three letter to one letter format.
ResidueNameConvertor() - Constructor for class meshi.util.ResidueNameConvertor
 
residueNumber() - Method in class meshi.molecularElements.atoms.Atom
 
residueNumber - Variable in class meshi.PDB.PdbLine
 
residueNumber() - Method in class meshi.PDB.PdbLine
 
residues - Variable in class meshi.molecularElements.Protein
A list of the protein's residues.
residues() - Method in class meshi.molecularElements.Protein
A list of the protein's residues.
ResidueSequence - Class in meshi.sequences
 
ResidueSequence() - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence(String) - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence(String, String) - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence(Sequence) - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence(FastaList) - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence(FastaList, int) - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence(ResidueList, String) - Constructor for class meshi.sequences.ResidueSequence
 
ResidueSequence.ResidueSequenceCharFilter - Class in meshi.sequences
 
ResidueSequence.ResidueSequenceCharFilter() - Constructor for class meshi.sequences.ResidueSequence.ResidueSequenceCharFilter
 
residuesOfLoopNumber(ResidueList, int) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
residuesOfLoops(ResidueList) - Static method in class meshi.symmetryComplex.utils.LoopUtils
 
residueTorsions - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
residueTorsions - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement
 
residueTorsions - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement
 
residueTorsions - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
 
ResidueTorsions - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
Allows easy access to all of a given residue's torsions.
ResidueTorsions(Residue, TorsionList) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
stores all of the residue's torsion angles.
residueTorsions - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
 
ResidueTorsionsAttribute - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
 
ResidueTorsionsAttribute() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute
 
residueTorsionsList - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
residueTorsionsList() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
residueTorsionsList - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
residueTorsionsList - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
residueTorsionsList - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
residueTorsionsList - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
residueTorsionsList - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
residueTorsionsList() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
ResidueTorsionsList - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
An updateable list of ResidueTorsions.
ResidueTorsionsList() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
 
ResidueTorsionsList(Protein, DistanceMatrix) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
Creates ResidueTorsionsList from protein.
ResidueTorsionsList.CompleteResidueFilter - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
 
ResidueTorsionsList.CompleteResidueFilter() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.CompleteResidueFilter
 
ResidueTorsionsList.IncompleteResidueFilter - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
 
ResidueTorsionsList.IncompleteResidueFilter() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.IncompleteResidueFilter
 
ResidueTorsionsList.PhiPsiResidueFilter - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
 
ResidueTorsionsList.PhiPsiResidueFilter() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.PhiPsiResidueFilter
 
ResidueTorsionsPropensityAttribute - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity
 
ResidueTorsionsPropensityAttribute() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.ResidueTorsionsPropensityAttribute
 
residueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters
residue type
residueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters
residue type
residueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParameters
residue type
residueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
residue type
residueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
residue type
ResidueType - Enum in meshi.parameters
 
ResidueType(String, String, AtomType, AtomType, AtomType, AtomType, AtomType, AtomType, boolean) - Constructor for enum meshi.parameters.ResidueType
 
ResidueTypeException - Exception in meshi.sequences
 
ResidueTypeException(Character, Sequence) - Constructor for exception meshi.sequences.ResidueTypeException
 
ResidueTypeException(Character) - Constructor for exception meshi.sequences.ResidueTypeException
 
residueTypeIndex - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
residueTypeIndex - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
 
residueVals - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
These are fields for temporary array results that are needed in the evaluation stage.
residueVals - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
These are fields for temporary array results that are needed in the evaluation stage.
resNum - Variable in class meshi.applications.corpus.Corpus
 
resNum - Variable in class meshi.util.dssp.DSSP
 
RESTART_EVERY - Static variable in interface meshi.util.KeyWords
 
restartEvery - Variable in class meshi.optimizers.ConjugateGradient
 
restoreAll(ResidueCreator) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
resType - Variable in class meshi.applications.corpus.Corpus
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolOLD
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator
 
Rfac - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
rg - Variable in class meshi.util.RgCalculator
 
rg() - Method in class meshi.util.RgCalculator
 
rgCalculator - Static variable in class AbInitio
 
rgCalculator - Variable in class meshi.energy.linearRG.LinearRgEnergy
 
RgCalculator - Class in meshi.util
 
RgCalculator(AtomList) - Constructor for class meshi.util.RgCalculator
 
RgCreator - Class in meshi.energy.RG
An implicit solvation energy term for all-atom models, modeling a 4.0 angs solvation shell around each atom.
RgCreator(double) - Constructor for class meshi.energy.RG.RgCreator
 
RgCreator() - Constructor for class meshi.energy.RG.RgCreator
 
RgEnergy - Class in meshi.energy.RG
 
RgEnergy() - Constructor for class meshi.energy.RG.RgEnergy
 
RgEnergy(AtomList, DistanceMatrix, double) - Constructor for class meshi.energy.RG.RgEnergy
 
rMax - Variable in class meshi.energy.hydrogenBond.HBondList.IsWithInRmax
 
rMax - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
rMax - Variable in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.IsWithInRmax
 
rMax - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
rMax - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
rMax - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
rMax - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
rMax - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
rMax - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
rMax - Static variable in class meshi.geometry.DistanceMatrix
Maximal distance for nonzero interactions.
rMax() - Static method in class meshi.geometry.DistanceMatrix
 
rMax - Static variable in class meshi.geometry.OldDistanceMatrix
Maximal distance for nonzero interactions.
rMax() - Static method in class meshi.geometry.OldDistanceMatrix
 
rMax2 - Static variable in class meshi.geometry.DistanceMatrix
 
rMax2() - Static method in class meshi.geometry.DistanceMatrix
 
rMax2 - Variable in class meshi.geometry.MatrixRow
 
rMax2 - Static variable in class meshi.geometry.OldDistanceMatrix
 
rMax2() - Static method in class meshi.geometry.OldDistanceMatrix
 
rMaxPlusBuffer - Static variable in class meshi.geometry.DistanceMatrix
rMax+buffer
rMaxPlusBuffer() - Static method in class meshi.geometry.DistanceMatrix
 
rMaxPlusBuffer - Static variable in class meshi.geometry.OldDistanceMatrix
rMax+buffer
rMaxPlusBuffer() - Static method in class meshi.geometry.OldDistanceMatrix
 
rMaxPlusBuffer2 - Static variable in class meshi.geometry.DistanceMatrix
(rMax+buffer)^2
rMaxPlusBuffer2() - Static method in class meshi.geometry.DistanceMatrix
 
rMaxPlusBuffer2 - Variable in class meshi.geometry.MatrixRow
 
rMaxPlusBuffer2 - Static variable in class meshi.geometry.OldDistanceMatrix
(rMax+buffer)^2
rMaxPlusBuffer2() - Static method in class meshi.geometry.OldDistanceMatrix
 
RMS - Variable in class meshi.applications.corpus.LoopResults
 
rms(AtomList) - Method in class meshi.molecularElements.atoms.AtomList
RMS deviation between this list of atom and some other list.
rms() - Method in class meshi.sequences.AtomAlignment
 
rms - Static variable in class meshi.util.overlap.Overlap
 
rms() - Method in class meshi.util.overlap.Overlap
 
Rms - Class in meshi.util
A (hopefully) comfortable handle to the complexity of the Kabsch structural overlap algorithm[1,2].
Rms(ResidueAlignment) - Constructor for class meshi.util.Rms
 
Rms(AtomAlignment) - Constructor for class meshi.util.Rms
 
rms - Variable in class meshi.util.Rms
 
rms(Protein, CommandList) - Static method in class meshi.util.Rms
 
rms(Protein, CommandList, Filter) - Static method in class meshi.util.Rms
 
rms(Protein, Protein) - Static method in class meshi.util.Rms
 
rms(ResidueAlignment) - Static method in class meshi.util.Rms
 
RMS_CUTOFF_IN_OVERLAP - Variable in class meshi.applications.corpus.CorrectRottenRamachandrans
 
RMS_INDEX - Static variable in class meshi.applications.prediction.ModelData
 
RMS_TARGET - Static variable in interface meshi.util.KeyWords
 
rmsCutOff - Variable in class meshi.applications.corpus.LocalFragmentLib
 
RmsException - Exception in meshi.util.overlap
RmsException.java extends Exception
RmsException() - Constructor for exception meshi.util.overlap.RmsException
 
RmsException(String) - Constructor for exception meshi.util.overlap.RmsException
 
RmsGdtEnergy(Object, ResidueSequence, ResidueSequence, TotalEnergy, String) - Static method in class meshi.util.Utils
 
RmsGdtEnergy(Object, Protein, Protein, TotalEnergy, String) - Static method in class meshi.util.Utils
 
RmsGdtEnergy(MeshiWriter, ResidueAlignment, TotalEnergy, String, int) - Static method in class meshi.util.Utils
 
RmsGdtEnergy(StringList, ResidueAlignment, TotalEnergy, String, int) - Static method in class meshi.util.Utils
 
RMSind1 - Static variable in class meshi.applications.corpus.RunThreadingExperiment
 
RMSind2 - Static variable in class meshi.applications.corpus.RunThreadingExperiment
 
rmsPartial(double[][], double[][], int[]) - Static method in class meshi.util.overlap.Overlap
Finds the RMS according to a small subset of the two proteins.
rmsPartialAltRMS(double[][], double[][], int[]) - Static method in class meshi.util.overlap.Overlap
This is exactly the same as 'rmsPartial' except that the rms is calculated on the subset only.
rmsTarget - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
RoisFirstMeshiProgram - Class in <Unnamed>
 
RoisFirstMeshiProgram() - Constructor for class RoisFirstMeshiProgram
 
rot - Variable in class meshi.geometry.rotamers.DunbrackLib
 
Rot1Arrays - Interface in meshi.util.rotamericTools
 
ROTAMER_LIBRARY - Static variable in interface meshi.util.KeyWords
 
RotamericTools - Class in meshi.util.rotamericTools
 
RotamericTools() - Constructor for class meshi.util.rotamericTools.RotamericTools
 
rotateMatrix - Variable in class meshi.util.Rms
 
rotationMatrix() - Method in class meshi.util.overlap.Overlap
 
round(double) - Static method in class meshi.geometry.Grid
 
round(double) - Static method in class meshi.geometry.OldGrid
 
rowChar(int) - Method in class meshi.sequences.aligner.DpMatrix
 
rowIterator() - Method in class meshi.geometry.DistanceMatrix
 
rowIterator() - Method in class meshi.geometry.OldDistanceMatrix
 
rowNumber(int) - Method in class meshi.geometry.DistanceMatrix
 
rowNumber(int) - Method in class meshi.geometry.OldDistanceMatrix
 
rowNumber - Variable in class meshi.sequences.aligner.Cell
 
rows - Variable in class meshi.symmetryComplex.transformations.Matrix1D
 
rsp - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
 
run(Logger) - Method in class meshi.optimizers.MCM
 
run() - Method in class meshi.optimizers.MCM
 
run() - Method in class meshi.optimizers.Minimizer
 
run(boolean) - Method in class meshi.optimizers.Minimizer
 
run() - Method in class meshi.optimizers.Optimizer
 
RunBackboneCompleterAndMinimizer - Class in meshi.symmetryComplex.proteinsGJ
 
RunBackboneCompleterAndMinimizer() - Constructor for class meshi.symmetryComplex.proteinsGJ.RunBackboneCompleterAndMinimizer
 
RunBackboneMCM - Class in meshi.symmetryComplex.proteinsGJ
Created by IntelliJ IDEA.
RunBackboneMCM() - Constructor for class meshi.symmetryComplex.proteinsGJ.RunBackboneMCM
 
RunFullModeller - Class in meshi.symmetryComplex.proteinsGJ
 
RunFullModeller() - Constructor for class meshi.symmetryComplex.proteinsGJ.RunFullModeller
 
RunThreadingExperiment - Class in meshi.applications.corpus
 
RunThreadingExperiment() - Constructor for class meshi.applications.corpus.RunThreadingExperiment
 

S

S - Variable in class meshi.optimizers.BFGS
 
S - Variable in class meshi.optimizers.LBFGS.Element
 
s - Variable in class meshi.util.mathTools.Jama.SingularValueDecomposition
Array for internal storage of singular values.
s - Static variable in class meshi.util.mathTools.Sigma
 
s - Variable in class meshi.util.mathTools.Spline1D
 
s - Variable in class meshi.util.mathTools.Spline2D
 
s_tag - Static variable in class meshi.util.mathTools.Sigma
 
s_tag - Variable in class meshi.util.mathTools.Spline1D
 
s_tag_x - Variable in class meshi.util.mathTools.Spline2D
 
s_tag_y - Variable in class meshi.util.mathTools.Spline2D
 
safeRadius - Static variable in class meshi.util.Scmod
 
SALT_BRIDGE_STRENGTH_ARG_NH - Static variable in class meshi.energy.solvate.SolvateEnergy
 
SALT_BRIDGE_STRENGTH_ASP_OD - Static variable in class meshi.energy.solvate.SolvateEnergy
 
SALT_BRIDGE_STRENGTH_GENERAL - Static variable in class meshi.energy.solvate.SolvateEnergy
The following parameter allow for a different weighting of SALT BRIDGES compared with regular HYDROGEN BONDS for the Ehb energy, that is also claculated.
SALT_BRIDGE_STRENGTH_GLU_OE - Static variable in class meshi.energy.solvate.SolvateEnergy
 
SALT_BRIDGE_STRENGTH_LYS_NZ - Static variable in class meshi.energy.solvate.SolvateEnergy
 
SALT_BRIDGE_STRENGTH_TRN - Static variable in class meshi.energy.solvate.SolvateEnergy
 
SALT_BRIDGE_STRENGTH_TRO - Static variable in class meshi.energy.solvate.SolvateEnergy
 
saltBridgeFactorA1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
saltBridgeFactorA2 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
saltBridgeFactorForHBenergyA1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
saltBridgeFactorForHBenergyA2 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
sameAtoms(AtomList) - Method in class meshi.molecularElements.atoms.AtomList
Returns true if the parameter has the same length and the same composition in terms of atom names.
SATURATION - Static variable in interface meshi.util.KeyWords
 
saveCaCbCoordinates(Protein, int, int) - Method in class meshi.applications.corpus.CorrectRottenRamachandrans
 
scaleWeight(double) - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
scCarbonSplines - Variable in class meshi.energy.solvate.SolvateParametersList
 
Scmod - Class in meshi.util
eThis class perform conccurent sidechain modeling as describe in Kalisman and Keasar (2006).
Scmod() - Constructor for class meshi.util.Scmod
 
scmod(CommandList, Protein, int) - Static method in class meshi.util.Scmod
 
scmod(CommandList, Protein, int, double) - Static method in class meshi.util.Scmod
 
scmod(CommandList, Protein, int, double, TotalEnergy) - Static method in class meshi.util.Scmod
 
SCMOD - Class in <Unnamed>
 
SCMOD() - Constructor for class SCMOD
 
score - Variable in class meshi.applications.corpus.BasicLoopResult
 
score - Variable in class meshi.sequences.aligner.Cell
 
score - Variable in class meshi.sequences.SequenceAlignment
 
score() - Method in class meshi.sequences.SequenceAlignment
 
scores - Variable in class meshi.sequences.aligner.StructureBasedMatrix
 
scoringMatrix - Variable in class aligner.AminoAcidSubstitutionMatrix
 
scPolarSplines - Variable in class meshi.energy.solvate.SolvateParametersList
 
SD - Variable in class meshi.molecularElements.extendedAtoms.Met
 
search(int) - Method in class meshi.geometry.MatrixRow
 
searchCounter - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
 
searchStart - Variable in class meshi.geometry.MatrixRow
 
second - Variable in class HomologyModeling.Three
 
second - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
SECOND - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
SECOND - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
SECONDARY_STRUCTURE - Static variable in interface meshi.util.KeyWords
 
SECONDARY_STRUCTURE_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
secondaryStructure - Variable in class meshi.molecularElements.Residue
HELIX, SHEET ect.
secondaryStructure() - Method in class meshi.molecularElements.Residue
 
SecondaryStructure - Enum in meshi.parameters
 
SecondaryStructure(String) - Constructor for enum meshi.parameters.SecondaryStructure
 
secondaryStructure(char) - Static method in enum meshi.parameters.SecondaryStructure
 
secondaryStructureCharFilter - Static variable in class meshi.sequences.SecondaryStructureSequence
 
SecondaryStructureSequence - Class in meshi.sequences
 
SecondaryStructureSequence(String, String) - Constructor for class meshi.sequences.SecondaryStructureSequence
 
SecondaryStructureSequence.SecondaryStructureSequenceCharFilter - Class in meshi.sequences
 
SecondaryStructureSequence.SecondaryStructureSequenceCharFilter() - Constructor for class meshi.sequences.SecondaryStructureSequence.SecondaryStructureSequenceCharFilter
 
secondHBSeqGap - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
Key values: firstHBSeqGap = the gap between the two atoms in the first HB (O1-H1) secondHBSeqGap = the gap between the two atoms in the second HB (O2-H2) h1h2SeqGap = the gap between the two Hydrogens o1o2SeqGap = the gap between the two Oxygens h1o2SeqGap = the gap between the H of the first HB and the O of the second HB o1h2SeqGap = the gap between the O of the first HB and the H of the second HB value is proportionaly to the friquency of such pair of HBs in the data base
secondPassOverTheNonBondedList() - Method in class meshi.energy.solvate.SolvateEnergy
 
secondWord() - Method in class meshi.util.Command
 
secondWord(Key) - Method in class meshi.util.CommandList
Returns the first command that whose second word is the given keyword.
secondWord(String) - Method in class meshi.util.CommandList
Returns the first command that whose second word is the given keyword.
secondWordDouble() - Method in class meshi.util.Command
 
secondWordExists() - Method in class meshi.util.Command
 
secondWordInt() - Method in class meshi.util.Command
 
secondWordOn() - Method in class meshi.util.Command
 
seder - Static variable in class meshi.util.Scmod
 
SEED - Static variable in interface meshi.util.KeyWords
 
seed - Static variable in class meshi.util.MeshiProgram
The seed of the random number generator.
seed() - Static method in class meshi.util.MeshiProgram
 
SEGMENT - Variable in class meshi.geometry.fragments.DresserFullFrag
 
SelectForCASP - Class in <Unnamed>
 
SelectForCASP() - Constructor for class SelectForCASP
 
selectModels(List<ModelData>) - Static method in class SelectForCASP
 
SelectModels - Class in <Unnamed>
 
SelectModels() - Constructor for class SelectModels
 
SelectModels.ModelComparator - Class in <Unnamed>
 
SelectModels.ModelComparator(String) - Constructor for class SelectModels.ModelComparator
 
seq - Variable in class meshi.applications.corpus.LocalFragmentLib
 
seqDistance1 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
seqDistance1() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
seqDistance2 - Variable in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
seqDistance2() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
sequence() - Method in class meshi.molecularElements.Chain
 
sequence() - Method in class meshi.molecularElements.Protein
 
Sequence - Class in meshi.sequences
Sequence is a single row alignment.
Sequence(String) - Constructor for class meshi.sequences.Sequence
 
Sequence(SequenceCharFilter) - Constructor for class meshi.sequences.Sequence
 
Sequence(String, SequenceCharFilter) - Constructor for class meshi.sequences.Sequence
 
Sequence(Chain, String) - Constructor for class meshi.sequences.Sequence
 
Sequence(String, String) - Constructor for class meshi.sequences.Sequence
 
Sequence(String, String, SequenceCharFilter) - Constructor for class meshi.sequences.Sequence
 
Sequence(Sequence, SequenceCharFilter) - Constructor for class meshi.sequences.Sequence
 
sequence - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
SEQUENCE - Static variable in interface meshi.util.KeyWords
 
Sequence.kolDichfin - Class in meshi.sequences
 
Sequence.kolDichfin() - Constructor for class meshi.sequences.Sequence.kolDichfin
 
sequence1 - Variable in class meshi.sequences.aligner.DpMatrix
 
sequence2 - Variable in class meshi.sequences.aligner.DpMatrix
 
SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
SequenceAlignment - Class in meshi.sequences
 
SequenceAlignment() - Constructor for class meshi.sequences.SequenceAlignment
 
SequenceAlignment(ResidueAlignment) - Constructor for class meshi.sequences.SequenceAlignment
 
SequenceAlignment(Sequence, Sequence) - Constructor for class meshi.sequences.SequenceAlignment
 
SequenceAlignment(SequenceList) - Constructor for class meshi.sequences.SequenceAlignment
 
SequenceAlignmentCell - Class in meshi.sequences
 
SequenceAlignmentCell(char, int) - Constructor for class meshi.sequences.SequenceAlignmentCell
 
SequenceAlignmentCell(int) - Constructor for class meshi.sequences.SequenceAlignmentCell
 
SequenceAlignmentCell() - Constructor for class meshi.sequences.SequenceAlignmentCell
 
SequenceAlignmentColumn - Class in meshi.sequences
 
SequenceAlignmentColumn(ResidueAlignmentColumn) - Constructor for class meshi.sequences.SequenceAlignmentColumn
 
SequenceAlignmentColumn(int) - Constructor for class meshi.sequences.SequenceAlignmentColumn
 
SequenceAlignmentColumn(SequenceAlignmentCell) - Constructor for class meshi.sequences.SequenceAlignmentColumn
 
SequenceAlignmentColumn(SequenceAlignmentCell, SequenceAlignmentCell) - Constructor for class meshi.sequences.SequenceAlignmentColumn
 
SequenceAlignmentColumn(char, int, char, int) - Constructor for class meshi.sequences.SequenceAlignmentColumn
 
SequenceCharFilter - Class in meshi.sequences
 
SequenceCharFilter() - Constructor for class meshi.sequences.SequenceCharFilter
 
SequenceList - Class in meshi.sequences
 
SequenceList() - Constructor for class meshi.sequences.SequenceList
 
SequenceList(String) - Constructor for class meshi.sequences.SequenceList
 
SequenceList(SequenceAlignment) - Constructor for class meshi.sequences.SequenceList
 
sequenceList() - Method in class meshi.util.dssp.DSSP
 
SequenceList.AcceptAll - Class in meshi.sequences
 
SequenceList.AcceptAll() - Constructor for class meshi.sequences.SequenceList.AcceptAll
 
SequenceList.IsSequenceFilter - Class in meshi.sequences
 
SequenceList.IsSequenceFilter() - Constructor for class meshi.sequences.SequenceList.IsSequenceFilter
 
Ser - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | CB / OG
Ser(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Ser
 
serialVersionUID - Static variable in class meshi.applications.corpus.LoopResultVector
 
set(double, double, double, double, double, double, double, Atom, Atom) - Method in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
set(double, double, double, double, double, double, double) - Method in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
set(Atom, Atom) - Method in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
set(Object) - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
set(Object) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
set(Object) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
set(Distance, Distance) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
Sets the relevant charge values for each atom in an atom pair.
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
set(Object) - Method in class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
 
set(Coordinates) - Method in class meshi.geometry.Coordinates
 
set(Coordinates, double) - Method in class meshi.geometry.Coordinates
 
set(int, int, double) - Method in class meshi.util.mathTools.Jama.Matrix
Set a single element.
set(String, Object) - Method in class meshi.util.MeshiProgram.GlobalElementList
 
setAccessibility(String) - Method in class meshi.molecularElements.Residue
 
setAccessibility(char) - Method in class meshi.molecularElements.Residue
 
setAngle() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
setAngle() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
setAngle() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
setAtoms() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
setAtoms() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
setAtoms() - Method in class meshi.energy.EnergyElement
 
setAtoms() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
setAtoms() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
setAtoms() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
setAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
setAtoms
setAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
setAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
setAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
setAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
setAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
setAtoms() - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
setAtoms() - Method in class meshi.energy.templateEnergy.TemplateEnergyElement
 
setAtoms() - Method in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
 
setAtoms() - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
 
setAtoms() - Method in class meshi.symmetryComplex.energy.SymmetryEnergyElement
 
setBack(Cell) - Method in class meshi.sequences.aligner.Cell
 
setBaseAtom() - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
For any polar atom (O,N or S in Cys) we calculate the base atom that participate in the definition of the hydrogen bond angle.
setBBcoors(double[][]) - Method in class meshi.applications.corpus.LoopResults
 
setCAsQD(Protein, HomologyModeling.Loop, CommandList, double, int) - Static method in class HomologyModeling
 
setCell(int, int, Cell) - Method in class meshi.sequences.aligner.DpMatrix
 
setComment() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
set the comment to be the relavent comment according to the instance
setComment() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
set the comment to be the relavent comment according to the instance
setComment() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
set the comment to be the relavent comment according to the instance
setComment(String) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
 
setComment(String) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
setComment(String) - Method in class meshi.energy.solvateRot1.SolvateRot1Energy
 
setComment(String) - Method in class meshi.molecularElements.atoms.AtomList
 
setComment(String) - Method in class meshi.util.string.StringList
 
setConsecutiveChainLetters(int) - Static method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
setCoordinates(AtomList) - Method in class meshi.energy.TotalEnergy
 
setCoordinates(CaResidue) - Method in class meshi.molecularElements.ca.CaResidue
 
setCoordinates(Atom) - Method in class meshi.molecularElements.ca.CaResidue
 
setCoordinates(TotalEnergy, double[][]) - Static method in class meshi.optimizers.MCM
 
setCurrentMolecularSystem(MolecularSystem) - Static method in class meshi.molecularElements.atoms.MolecularSystem
 
setDAngleEnergyDatoms() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
setDAngleEnergyDatoms() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
setDAngleEnergyDatoms() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
setEnergy(double) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
setEnergyElement() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement(double) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement(double, double) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement(double) - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement(double, double) - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
set the energyElement to point on the relavent instance
setEnergyElement(double) - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
 
setEnergyElement(double, double) - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
 
setExcludedProteinsFromUngapped(String[]) - Method in class meshi.applications.corpus.Corpus
 
setFx(double) - Method in class meshi.geometry.Coordinates
 
setFx(double) - Method in class meshi.geometry.FrozenCoordinates
 
setFx(double) - Method in class meshi.molecularElements.atoms.Atom
Sets the force operating on the atom in the X direction.
setFy(double) - Method in class meshi.geometry.Coordinates
 
setFy(double) - Method in class meshi.geometry.FrozenCoordinates
 
setFy(double) - Method in class meshi.molecularElements.atoms.Atom
Sets the force operating on the atom in the Y direction.
setFz(double) - Method in class meshi.geometry.Coordinates
 
setFz(double) - Method in class meshi.geometry.FrozenCoordinates
 
setFz(double) - Method in class meshi.molecularElements.atoms.Atom
Sets the force operating on the atom in the Z direction.
setGJ(String) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
setHOsQD(Protein, HomologyModeling.Loop, CommandList) - Static method in class HomologyModeling
 
setImortal() - Method in class meshi.molecularElements.atoms.AtomPair
 
setLine(Coordinates, Coordinates) - Method in class meshi.symmetryComplex.utils.LoopUtils.Line
 
setLine(double, double, double, double) - Method in class meshi.symmetryComplex.utils.LoopUtils.Line
 
setLoop(boolean) - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setLoop(Residue, boolean) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setMatrix(int, int, int, int, Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Set a submatrix.
setMcmModel(Protein) - Method in class Beautify.BeautifyLogger
 
setMember(int, int, double) - Method in interface meshi.symmetryComplex.transformations.Matrix
 
setMember(int, int, double) - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
setMode(DistanceMode) - Method in class meshi.geometry.Distance
 
setMolecularSystem(MolecularSystem) - Method in class meshi.molecularElements.atoms.Atom
 
setMolecularSystem(MolecularSystem) - Method in class meshi.molecularElements.atoms.AtomList
 
setName(String) - Method in class meshi.molecularElements.Protein
 
setNCCBsQD(Protein, HomologyModeling.Loop, CommandList) - Static method in class HomologyModeling
 
setNextAtom(Atom) - Method in class meshi.molecularElements.Residue
 
setPairFactor(double) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
setPairValue(double) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
setParameters(HydrogenBondsParameters) - Method in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
setPath(String) - Method in class meshi.util.file.MeshiLineReader
 
setPrevAtom(Atom) - Method in class meshi.molecularElements.Residue
 
setPrevNextAtomsToNull() - Method in class meshi.molecularElements.Residue
 
setProblematic(boolean, String) - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setProblematic(Residue, boolean, String) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setProblematicNeighbor(Residue) - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setProblematicNeighbor(Residue, Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setReliability(double) - Method in class meshi.molecularElements.atoms.Atom
 
setReliability(double) - Method in class meshi.molecularElements.Residue
 
setResidue(Residue) - Method in class meshi.molecularElements.atoms.Atom
Set the atom residue.
setResidue(Residue) - Method in class meshi.molecularElements.atoms.AtomList
Sets the parameter to be the residue of this atom.
setResidueInAtoms(AtomList) - Method in class meshi.molecularElements.Residue
 
setResidueNumber(int) - Method in class meshi.molecularElements.atoms.Atom
 
setScore(double) - Method in class meshi.sequences.SequenceAlignment
 
setSecondaryStructure(SecondaryStructure) - Method in class meshi.molecularElements.Residue
 
setSecondaryStructure(char) - Method in class meshi.molecularElements.Residue
 
setSimpleHBweight(double) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
setSS(String) - Method in class meshi.molecularElements.Protein
A method to set the secondary structure of a protein.
setSS(SequenceAlignment) - Method in class meshi.molecularElements.Protein
 
setSS(ResidueList, SequenceAlignment) - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
setStatus(AtomStatus) - Method in class meshi.molecularElements.atoms.Atom
 
setTemperatureFactor(Double) - Method in class meshi.molecularElements.atoms.Atom
 
setTheirdAtom() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
setTheirdAtom() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
setTheirdAtom() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
setToPP() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
setType(AtomType) - Method in class meshi.molecularElements.atoms.Atom
 
setValue(Object) - Method in class meshi.util.MeshiProgram.GlobalElement
 
setValue(Object) - Method in class meshi.util.Pair
 
setValue(double) - Method in class meshi.util.Pair
 
setVisible(Residue) - Static method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
setXRotation(double) - Method in class meshi.symmetryComplex.transformations.SingleAxisRotationTransformation
 
setXYZ(double, double, double) - Method in class meshi.geometry.Coordinates
 
setXYZ(double, double, double) - Method in class meshi.molecularElements.atoms.Atom
Sets the X,Y,Z coordinate of the atom.
setXYZ(double, double, double, AtomStatus) - Method in class meshi.molecularElements.atoms.Atom
 
setXYZ(Coordinates) - Method in class meshi.molecularElements.atoms.Atom
 
setYRotation(double) - Method in class meshi.symmetryComplex.transformations.SingleAxisRotationTransformation
 
setZRotation(double) - Method in class meshi.symmetryComplex.transformations.SingleAxisRotationTransformation
 
sformat - Variable in class meshi.energy.TotalEnergy
 
SG - Variable in class meshi.molecularElements.extendedAtoms.Cys
 
sharedAtom(AtomPair) - Method in class meshi.molecularElements.atoms.AtomPair
 
sharedAtomPair(Angle) - Method in class meshi.geometry.Angle
 
SHEET - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
SHEET - Static variable in interface meshi.parameters.MeshiPotential
 
SHEET_OR_COIL - Static variable in interface meshi.parameters.MeshiPotential
 
sheetPair(Distance) - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
SHORT - Static variable in class meshi.util.formats.Fdouble
 
SHORT - Static variable in class meshi.util.formats.Fint
 
SHORT - Static variable in class meshi.util.formats.Format
 
SHORTER - Static variable in class meshi.util.formats.Fdouble
 
SHORTER - Static variable in class meshi.util.formats.Fint
 
SHORTER - Static variable in class meshi.util.formats.Format
 
shotgun - Variable in class Beautify.BeautifyLogger
 
SHOTGUN_MODEL - Static variable in interface meshi.util.KeyWords
 
SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
SideChainSolvateCreator - Class in meshi.energy.sideChainModelingSolvate
This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package.
SideChainSolvateCreator(double, double, double, double, double, double) - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
SideChainSolvateCreator(double, double) - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
SideChainSolvateCreator(double) - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
SideChainSolvateCreator() - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
SideChainSolvateDistanceAttribute - Class in meshi.energy.sideChainModelingSolvate
This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package.
SideChainSolvateDistanceAttribute() - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
SideChainSolvateEnergy - Class in meshi.energy.sideChainModelingSolvate
This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package.
SideChainSolvateEnergy() - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
SideChainSolvateEnergy(AtomList, DistanceMatrix, SideChainSolvateParametersList, double, double, double, double, double, double) - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
The constructor parameters: atomList,dm,weight - standard CooperativeEnergyTerm inputs.
SideChainSolvateHBAngle - Class in meshi.energy.sideChainModelingSolvate
This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package.
SideChainSolvateHBAngle(DistanceMatrix, double, double, double, double) - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
The constructor parameters: dm - The distance matrix used in this object.
SideChainSolvateParametersList - Class in meshi.energy.sideChainModelingSolvate
This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package.
SideChainSolvateParametersList(String[]) - Constructor for class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
The parameter to the constructor is an array of 12 Strings, giving the 12 files required as parameters.
sigma - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
sigma - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
sigma - Variable in class meshi.energy.hydrogenBond.LennardJonesParameters
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
sigma - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
Sigma - Class in meshi.util.mathTools
This class host the static method "sigma" which gives a derivable sigmoid function of the following form: x<0 - not defined 0Sigma() - Constructor for class meshi.util.mathTools.Sigma
 
sigma(double, double, double, double, double, double) - Static method in class meshi.util.mathTools.Sigma
 
sigma6 - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
sigma6 - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
sigma6 - Variable in class meshi.energy.hydrogenBond.LennardJonesParameters
 
sigma6 - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
sigma6EpsilonFour - Variable in class meshi.energy.hydrogenBond.HB_DistanceAttribute
 
sigma6EpsilonFour - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
sigma6EpsilonFour - Variable in class meshi.energy.hydrogenBond.LennardJonesParameters
 
sigma6EpsilonFour - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
SigmaParameters - Class in meshi.energy.solvate
All the atom type specific parameters of a solvation sigma function
SigmaParameters(double, double, double, double, double) - Constructor for class meshi.energy.solvate.SigmaParameters
 
sigmaParameters - Static variable in class meshi.energy.solvate.SolvateParametersList
 
sigmaParameters_12 - Variable in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
sigmaParameters_12 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
sigmaParameters_21 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
sigmaParameters_21 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
sigmCa1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
sigmCa1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
sigmCa1 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
sigmCa1 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
sigmCa2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
sigmCa2 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
sigmCa2 - Variable in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
sigmCa2 - Variable in class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
sigmCosAng1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmCosAng1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
sigmCosAng2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmCosAng2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
sigmHB - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
sigmHBa1 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
sigmHBa2 - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute
 
sigmoidBegins - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmoidBeginsNoH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
sigmoidBeginsNoH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmoidBeginsNoH - Static variable in interface meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants
 
sigmoidBeginsWithH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
sigmoidBeginsWithH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmoidBeginsWithH - Static variable in interface meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants
 
sigmoidEnds - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmoidEndsNoH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
sigmoidEndsNoH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmoidEndsNoH - Static variable in interface meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants
 
sigmoidEndsWithH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
sigmoidEndsWithH - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
sigmoidEndsWithH - Static variable in interface meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants
 
similarToLib - Variable in class meshi.applications.corpus.LocalFragmentLib
 
SimpleEnergyCreator - Class in meshi.energy.simpleEnergyTerms
Factory classes that generate energy terms.
SimpleEnergyCreator(Key) - Constructor for class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
Constructs an energy creator object.
SimpleEnergyCreator(Key, CommandList) - Constructor for class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
Constructs an energy creator object.
SimpleEnergyCreator(double) - Constructor for class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
Construct a somewhat degenerate creator object that cannot read commands from the commands list.
SimpleEnergyCreator.HaveParametersFilter - Class in meshi.energy.simpleEnergyTerms
Picking the relevant objects.
SimpleEnergyCreator.HaveParametersFilter(ParametersList) - Constructor for class meshi.energy.simpleEnergyTerms.SimpleEnergyCreator.HaveParametersFilter
 
SimpleEnergyTerm - Class in meshi.energy.simpleEnergyTerms
A super class for those energy terms that operate on a fixed list of elements.
SimpleEnergyTerm() - Constructor for class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
 
SimpleEnergyTerm(Updateable[], ParametersList, double) - Constructor for class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
 
simpleHBweight - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator
 
simpleHBweight - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
SimpleInflate - Class in meshi.energy.simpleEnergyTerms.inflate.simpleInflate
 
SimpleInflate() - Constructor for class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
SimpleInflate(DistanceMatrix, double, double) - Constructor for class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
SimpleInflate.TargetFilter - Class in meshi.energy.simpleEnergyTerms.inflate.simpleInflate
 
SimpleInflate.TargetFilter(double) - Constructor for class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate.TargetFilter
 
SimpleInflateCreator - Class in meshi.energy.simpleEnergyTerms.inflate.simpleInflate
 
SimpleInflateCreator() - Constructor for class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateCreator
 
SimpleInflateEnergyElement - Class in meshi.energy.simpleEnergyTerms.inflate.simpleInflate
 
SimpleInflateEnergyElement(Distance, DistanceMatrix, double) - Constructor for class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
SimpleStepLength - Class in meshi.optimizers
This class provide a simple way to find the step length.
SimpleStepLength(TotalEnergy, double, double, double) - Constructor for class meshi.optimizers.SimpleStepLength
 
SimplestMinimizeProtein - Class in <Unnamed>
 
SimplestMinimizeProtein() - Constructor for class SimplestMinimizeProtein
 
sinAngle - Variable in class meshi.geometry.Angle
 
sinAngle() - Method in class meshi.geometry.Angle
 
SingleAxisRotationTransformation - Class in meshi.symmetryComplex.transformations
Source: Rotation matrix (Wikipedia).
SingleAxisRotationTransformation(String, double) - Constructor for class meshi.symmetryComplex.transformations.SingleAxisRotationTransformation
 
SingularValueDecomposition - Class in meshi.util.mathTools.Jama
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class meshi.util.mathTools.Jama.SingularValueDecomposition
Construct the singular value decomposition
sinSign - Variable in class meshi.geometry.Torsion
 
size - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttributes
 
size - Variable in class ColorByEnergy.GaussianAttributes
 
size - Variable in class meshi.geometry.DistanceList.DistanceIterator
 
size - Variable in class meshi.geometry.DistanceList
 
size() - Method in class meshi.geometry.DistanceList
 
size - Variable in class meshi.geometry.DistanceMatrix.RowIterator
 
size - Variable in class meshi.geometry.OldDistanceMatrix.RowIterator
 
size() - Method in class meshi.sequences.AlignmentColumn
 
size - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
size - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
size() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
size - Variable in class meshi.util.filters.OriginalAtoms
 
sizeMinusOne - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
sizeMinusTwo - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
sm2PerAtomType - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
sm2PerAtomType() - Static method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
sm2PerResidueType - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
sm2PerResidueType() - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
sm2PerResidueType - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
sm2PerResidueType() - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
small - Static variable in class meshi.geometry.ArcCos
 
smallNumber - Variable in class meshi.molecularElements.atoms.AtomPair
 
smallNumber() - Method in class meshi.molecularElements.atoms.AtomPair
 
smallType - Variable in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
smallType - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
smallType - Variable in class meshi.geometry.Distance
 
smallType - Variable in class meshi.molecularElements.atoms.AtomPair
 
smallType() - Method in class meshi.molecularElements.atoms.AtomPair
 
SMOOTH_ROTAMER_LIBRARY_ENERGY - Static variable in interface meshi.util.KeyWords
 
SmoothRotamerLibraryEnergy - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library energy term.
SmoothRotamerLibraryEnergy(ResidueTorsionsList, DistanceMatrix, SmoothRotamerLibraryParametersList, double, String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergy
 
SmoothRotamerLibraryEnergyCreator - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
 
SmoothRotamerLibraryEnergyCreator() - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyCreator
 
SmoothRotamerLibraryEnergyElement - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Encapsulation of SmoothRotamer energy value for a single residue.
SmoothRotamerLibraryEnergyElement(ResidueTorsions, SmoothRotamerLibraryParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
 
SmoothRotamerLibraryEnergyElementChi0 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library energy element for amino acids with no sidechain torsion angles: ALA, GLY.
SmoothRotamerLibraryEnergyElementChi0(ResidueTorsions, SmoothRotamerLibraryParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi0
 
SmoothRotamerLibraryEnergyElementChi1 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library energy element for amino acids with one sidechain torsion angle: CYS, SER, THR, VAL.
SmoothRotamerLibraryEnergyElementChi1(ResidueTorsions, SmoothRotamerLibraryParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi1
 
SmoothRotamerLibraryEnergyElementChi2 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library energy element for amino acids with two sidechain torsion angles: ASP, PHE, HIS, ILE, LEU, ASN, PRO, TRP, TYR.
SmoothRotamerLibraryEnergyElementChi2(ResidueTorsions, SmoothRotamerLibraryParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi2
 
SmoothRotamerLibraryEnergyElementChi3 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library energy element for amino acids with three sidechain torsion angles: GLU, MET, GLN.
SmoothRotamerLibraryEnergyElementChi3(ResidueTorsions, SmoothRotamerLibraryParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi3
 
SmoothRotamerLibraryEnergyElementChi4 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library parameters for amino acids with four sidechain torsion angles: LYS, ARG.
SmoothRotamerLibraryEnergyElementChi4(ResidueTorsions, SmoothRotamerLibraryParameters, double) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi4
 
SmoothRotamerLibraryParameters - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Parameters used with the SmoothRotamerLibraryEnergy term.
SmoothRotamerLibraryParameters(int) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
Updates residue type of parameters.
SmoothRotamerLibraryParametersChi0 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library parameters for amino acids with no sidechain torsion angles: ALA, GLY.
SmoothRotamerLibraryParametersChi0(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi0
 
SmoothRotamerLibraryParametersChi1 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library parameters for amino acids with one sidechain torsion angle: CYS, SER, THR, VAL.
SmoothRotamerLibraryParametersChi1(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi1
 
SmoothRotamerLibraryParametersChi2 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library parameters for amino acids with two sidechain torsion angles: ASP, PHE, HIS, ILE, LEU, ASN, PRO, TRP, TYR.
SmoothRotamerLibraryParametersChi2(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi2
 
SmoothRotamerLibraryParametersChi3 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library parameters for amino acids with three sidechain torsion angles: GLU, MET, GLN.
SmoothRotamerLibraryParametersChi3(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi3
 
SmoothRotamerLibraryParametersChi4 - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
Smooth rotamer library parameters for amino acids with four sidechain torsion angles: LYS, ARG.
SmoothRotamerLibraryParametersChi4(int, SplinedPolynomialsLoader) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi4
 
SmoothRotamerLibraryParametersList - Class in meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary
 
SmoothRotamerLibraryParametersList(String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList
Create a new parameters file from the polynomials parameters data file.
solvACC - Variable in class meshi.util.dssp.DSSP
 
SOLVATE_ALL_ATOM_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
SOLVATE_CA_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
SOLVATE_ENERGY - Static variable in interface meshi.util.KeyWords
 
SOLVATE_LONG_HB_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
SOLVATE_MINIMIZE_HB_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
SOLVATE_NOHB_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
SOLVATE_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
SOLVATE_ROT1_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
SOLVATE_SC_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
SolvateCreatorHBforMinimization - Class in meshi.energy.solvate
The different between this creator and the "SolvateCreatorRegularHB" (see the latter main comment for a lot of details), is in the way the hydrogen-bond distance sigmoid is set.
SolvateCreatorHBforMinimization(double, double, double, double, CommandList) - Constructor for class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
SolvateCreatorHBforMinimization(double, double, double, double, CommandList, String) - Constructor for class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
SolvateCreatorHBforMinimization(double) - Constructor for class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
SolvateCreatorHBforMinimization() - Constructor for class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
SolvateCreatorLongHB - Class in meshi.energy.solvate
The different between this creator and the "SolvateCreatorRegularHB" (see the latter main comment for a lot of details), is in the way the hydrogen-bond distance sigmoid is set.
SolvateCreatorLongHB(double, double, double, double) - Constructor for class meshi.energy.solvate.SolvateCreatorLongHB
 
SolvateCreatorLongHB(double) - Constructor for class meshi.energy.solvate.SolvateCreatorLongHB
 
SolvateCreatorLongHB() - Constructor for class meshi.energy.solvate.SolvateCreatorLongHB
 
SolvateCreatorRegularHB - Class in meshi.energy.solvate
The Creator class for setting up an instance of SolvateEnergy as described in Kalisman & Keasar (2008).
SolvateCreatorRegularHB(double, double, double, double) - Constructor for class meshi.energy.solvate.SolvateCreatorRegularHB
 
SolvateCreatorRegularHB(double) - Constructor for class meshi.energy.solvate.SolvateCreatorRegularHB
 
SolvateCreatorRegularHB() - Constructor for class meshi.energy.solvate.SolvateCreatorRegularHB
 
SolvateDistanceAttribute - Class in meshi.energy.solvate
In the SolvateEnergy evaluation function these fields are to be recalculated for EVERY distance in the non-bonded list.
SolvateDistanceAttribute() - Constructor for class meshi.energy.solvate.SolvateDistanceAttribute
 
SolvateDistanceAttributeBetweenPolars - Class in meshi.energy.solvate
 
SolvateDistanceAttributeBetweenPolars(Distance, AbstractHydrogenBondList, double, double, double, double) - Constructor for class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
SolvateDistanceAttributeCreator - Class in meshi.energy.solvate
 
SolvateDistanceAttributeCreator() - Constructor for class meshi.energy.solvate.SolvateDistanceAttributeCreator
 
SolvateDistanceAttributeNonPolarPolar - Class in meshi.energy.solvate
 
SolvateDistanceAttributeNonPolarPolar(Distance, SigmaParameters) - Constructor for class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
SolvateDistanceAttributePolarNonPolar - Class in meshi.energy.solvate
 
SolvateDistanceAttributePolarNonPolar(Distance, SigmaParameters) - Constructor for class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
SolvateDistanceAttributeWithAhydrogen - Class in meshi.energy.solvate
 
SolvateDistanceAttributeWithAhydrogen() - Constructor for class meshi.energy.solvate.SolvateDistanceAttributeWithAhydrogen
 
SolvateDistanceAttributeWithNonPolar - Class in meshi.energy.solvate
 
SolvateDistanceAttributeWithNonPolar(Distance, SigmaParameters, SigmaParameters) - Constructor for class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
SolvateDistanceType - Enum in meshi.energy.solvate
Distances are treated differently by Solvate Energy.
SolvateDistanceType() - Constructor for enum meshi.energy.solvate.SolvateDistanceType
 
SolvateEnergy - Class in meshi.energy.solvate
The implementation of the cooperative solvation term for proteins as described in Kalisman & Keasar (2008).
SolvateEnergy() - Constructor for class meshi.energy.solvate.SolvateEnergy
 
SolvateEnergy(AtomList, DistanceMatrix, SolvateParametersList, double, double, double, double) - Constructor for class meshi.energy.solvate.SolvateEnergy
See the comment at the top of the class for descriptions on the weights.
SolvateEnergy(AtomList, DistanceMatrix, SolvateParametersList, double, double, double, double, String) - Constructor for class meshi.energy.solvate.SolvateEnergy
 
SolvateEnergy.SuperType - Enum in meshi.energy.solvate
Setting the general type for each atom in the atom list: (0) Carbon (1) Backbone polar, (2) Sidechain polar (3) Hydrogens This is done to save time on type checking.
SolvateEnergy.SuperType() - Constructor for enum meshi.energy.solvate.SolvateEnergy.SuperType
 
solvateHB - Variable in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
solvateHB - Variable in class meshi.energy.solvate.SolvateEnergy
The only hydrogen bond list class in the term.
solvateHBAngle - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
SolvateParametersList - Class in meshi.energy.solvate
The parameter class required for the SolvateEnergy class.
SolvateParametersList(String[]) - Constructor for class meshi.energy.solvate.SolvateParametersList
The parameter to the constructor is an array of 14 Strings, giving the 14 files required as parameters.
SolvateRot1Creator - Class in meshi.energy.solvateRot1
 
SolvateRot1Creator(double, double[][], double) - Constructor for class meshi.energy.solvateRot1.SolvateRot1Creator
 
SolvateRot1Creator(double[][], double) - Constructor for class meshi.energy.solvateRot1.SolvateRot1Creator
 
SolvateRot1DistanceAttribute - Class in meshi.energy.solvateRot1
In the SolvateRot1Energy evaluation function these fields are to be recalculated for EVERY distance in the non-bonded list.
SolvateRot1DistanceAttribute() - Constructor for class meshi.energy.solvateRot1.SolvateRot1DistanceAttribute
 
SolvateRot1Energy - Class in meshi.energy.solvateRot1
 
SolvateRot1Energy() - Constructor for class meshi.energy.solvateRot1.SolvateRot1Energy
 
SolvateRot1Energy(AtomList, DistanceMatrix, SolvateRot1ParametersList, double[][], double, double) - Constructor for class meshi.energy.solvateRot1.SolvateRot1Energy
 
SolvateRot1ParametersList - Class in meshi.energy.solvateRot1
 
SolvateRot1ParametersList(String[]) - Constructor for class meshi.energy.solvateRot1.SolvateRot1ParametersList
The parameter to the constructor is an array of 7 Strings, giving the 7 files required as parameters.
solve(Matrix) - Method in class meshi.util.mathTools.Jama.CholeskyDecomposition
Solve A*X = B
solve(Matrix) - Method in class meshi.util.mathTools.Jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class meshi.util.mathTools.Jama.QRDecomposition
Least squares solution of A*X = B
solvEnergy - Variable in class meshi.applications.corpus.LoopResults
 
solveTranspose(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Solve X*A = B, which is also A'*X' = B'
somewhere() - Method in class meshi.geometry.Coordinates
 
somewhere() - Method in class meshi.molecularElements.atoms.AtomList
 
sort() - Method in class meshi.applications.hubbard.HubbardPosition
 
sort() - Method in class meshi.energy.simpleEnergyTerms.ParametersList
Sort the list.
sort() - Method in class meshi.geometry.DistanceList
 
sort() - Method in class meshi.molecularElements.atoms.AtomPairList
 
sort() - Method in class meshi.molecularElements.ResidueList
 
sortable - Variable in class meshi.energy.simpleEnergyTerms.ParametersList
True if the list is sortable.
sortable() - Method in class meshi.geometry.TorsionPairList
 
sortable() - Method in class meshi.molecularElements.atoms.AtomList
 
sortable() - Method in class meshi.util.histogram.Histogram
 
sortBest(double[], String[], String[]) - Static method in class ChooseTemplate
 
sortBest(double[], String[]) - Static method in class ModelRanker
 
sorted - Variable in class meshi.energy.simpleEnergyTerms.ParametersList
True if the list is sorted.
sortEigenval(double[]) - Static method in class meshi.util.overlap.Overlap
this function sorts the eigenvalues in descending order, according to Kabsch(1978) so we obtain the proper rotation matrix
source - Variable in class meshi.geometry.DistanceMirror
 
source - Variable in class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
source() - Method in class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
source - Variable in class meshi.symmetryComplex.molecularImageElements.ImageChain
 
source() - Method in class meshi.symmetryComplex.molecularImageElements.ImageChain
 
source - Variable in class meshi.symmetryComplex.molecularImageElements.ImageResidue
 
source() - Method in class meshi.symmetryComplex.molecularImageElements.ImageResidue
 
sourceFile - Variable in class meshi.molecularElements.atoms.AtomList
 
sourceFile() - Method in class meshi.molecularElements.atoms.AtomList
 
specialDis - Variable in class meshi.energy.hydrogenBond.GoodResiduesForHB
 
specialDis - Variable in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
specialDisArray - Variable in class meshi.energy.hydrogenBond.HydrogenBondsCreator
 
specialDisArray - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
specialMutate(Protein, int, int, double[][], DunbrackLib) - Method in class meshi.applications.corpus.Corpus
 
SPHERE_COND - Variable in class meshi.geometry.Grid
 
SPHERE_COND - Variable in class meshi.geometry.OldGrid
 
spl - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList
 
spl - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList
 
spl - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList
 
spl - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList
Loader contains all of the polynomials in the data file.
spl - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList
Loader contains all of the polynomials in the data file.
Spline1D - Class in meshi.util.mathTools
The class creates a 1D cubic spline object from given parameters, and allows for the calculation of the spline value and derivative at any given point inside the spline intervals.
Spline1D(String) - Constructor for class meshi.util.mathTools.Spline1D
The constructor can create a specific spline object from a string with the format: {break 1} {interval 1 X^3 coefficient} {interval 1 X^2 coef} {interval 1 X coef} {interval 1 constant coef} {break 2} {interval 2 X^3 coefficient} ...
Spline1D(StringTokenizer) - Constructor for class meshi.util.mathTools.Spline1D
 
Spline2D - Class in meshi.util.mathTools
The class creates a 2D cubic spline object from given parameters, and allows for the calculation of the spline value and derivative at any given point inside the spline intervals.
Spline2D(String) - Constructor for class meshi.util.mathTools.Spline2D
The constructor can create a specific spline object from a string with the format (Note that following 6 lines should appear in the SAME line, but I broke it for clarity).
Spline2D(StringTokenizer) - Constructor for class meshi.util.mathTools.Spline2D
 
SplinedPolynomial - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
Polynomial for calculating energy values for a given amino acid, and given torsion angles.
SplinedPolynomial(int, int, int[], int, double[][], double[]) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
Creates a new splined polynomial.
splinedPolynomials - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
 
SplinedPolynomialsLoader - Class in meshi.energy.simpleEnergyTerms.compositeTorsions
Manages the list of splined polynomials.
SplinedPolynomialsLoader(String) - Constructor for class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
Loads polynomials from given file.
splineForAtomPair(AtomType, AtomType) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
Retrieve spline for atom pair.
splineForAtomPair(int, int) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
 
splines - Variable in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
 
splines - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
splinesBB - Variable in class meshi.energy.solvate.SolvateEnergy
The 2D spline array (i.e.
splinesSCCarbon - Variable in class meshi.energy.solvate.SolvateEnergy
The 1D spline array (i.e.
splinesSCPolar - Variable in class meshi.energy.solvate.SolvateEnergy
The 2D spline array (i.e.
splineVals - Variable in class meshi.energy.solvateRot1.SolvateRot1Energy
 
splitToChains() - Method in class meshi.molecularElements.atoms.AtomList
 
SQR_SIX_OF_TWO - Static variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
sqrSixOfTwoSigma - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
srlp - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
 
ss - Variable in class meshi.util.dssp.DSSP
 
SS_NAME - Static variable in interface meshi.util.KeyWords
 
SS_SEQUENCE - Static variable in interface meshi.util.KeyWords
 
SSofRes(int) - Method in class meshi.util.dssp.DSSP
 
ssType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
stage - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
standard - Variable in enum meshi.parameters.ResidueType
 
standard() - Method in enum meshi.parameters.ResidueType
 
STANDARD - Static variable in class meshi.util.formats.Fdouble
 
STANDARD - Static variable in class meshi.util.formats.Fint
 
STANDARD - Static variable in class meshi.util.formats.Format
 
standard(String) - Static method in class meshi.util.string.StringParser
 
STANDARD_RESIDUES - Static variable in class Pdb2Fasta
 
standardSeparators() - Static method in class meshi.util.string.StringList
 
startAlphaALL - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
startAlphaCOIL - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
startAlphaHELIX - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
startAlphaHELIX - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
startAlphaSHEET - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
startAlphaSHEET - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
startsIn() - Method in class meshi.sequences.Sequence
 
startsWith(String) - Method in class meshi.util.string.StringList
 
startTime - Variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
Used by Window.
status - Variable in class meshi.molecularElements.atoms.AtomCore
 
status() - Method in class meshi.molecularElements.atoms.AtomCore
 
status(int) - Method in class meshi.optimizers.Minimizer
 
statusLabel - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
std - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
std - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaParameters
 
std - Variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZParameters
 
std - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
std - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
std - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityParameters
 
std - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
std - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranParameters
 
std - Variable in class meshi.energy.TotalEnergy.SortedAtoms
 
std() - Method in class meshi.energy.TotalEnergy.SortedAtoms
 
std - Static variable in interface meshi.util.rotamericTools.Rot1Arrays
 
stdModel(ModelData, ModelData) - Static method in class meshi.applications.prediction.ModelData
 
STEEPEST_DECENT - Static variable in interface meshi.util.KeyWords
 
steepestDecent - Variable in class meshi.optimizers.BFGS
 
steepestDecent - Variable in class meshi.optimizers.LBFGS
 
SteepestDecent - Class in meshi.optimizers
This class implements a simple steepest descent minimizer, using a simple back tracking line search.
SteepestDecent(TotalEnergy, double, int, int, double, double, double) - Constructor for class meshi.optimizers.SteepestDecent
 
SteepestDecent(TotalEnergy, double, int, int) - Constructor for class meshi.optimizers.SteepestDecent
 
SteepestDecent(TotalEnergy) - Constructor for class meshi.optimizers.SteepestDecent
 
step(Iterator, HomologyModeling.Three) - Static method in class HomologyModeling
 
step() - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
STEPS - Static variable in interface meshi.util.KeyWords
 
stepSize - Variable in class meshi.optimizers.SimpleStepLength
 
stepSizeExpansion - Variable in class meshi.optimizers.SimpleStepLength
 
stepSizeExpansion - Variable in class meshi.optimizers.SteepestDecent
 
stepSizeExpansionSteepestDecent - Variable in class meshi.optimizers.BFGS
 
stepSizeExpansionSteepestDecent - Static variable in class meshi.optimizers.ConjugateGradient
 
stepSizeExpansionSteepestDecent - Variable in class meshi.optimizers.LBFGS
 
stepSizeReduction - Variable in class meshi.optimizers.SimpleStepLength
 
stepSizeReduction - Variable in class meshi.optimizers.SteepestDecent
 
stepSizeReductionSteepestDecent - Variable in class meshi.optimizers.BFGS
 
stepSizeReductionSteepestDecent - Static variable in class meshi.optimizers.ConjugateGradient
 
stepSizeReductionSteepestDecent - Variable in class meshi.optimizers.LBFGS
 
stop - Variable in class meshi.optimizers.WolfConditionLineSearch
 
storage - Variable in class meshi.optimizers.LBFGS
 
str - Variable in class aligner.FastaReader
 
str - Variable in class aligner.FileToString
 
STRICT_CLASHES - Static variable in interface meshi.util.KeyWords
 
StringFilter - Class in meshi.util.string
 
StringFilter(String) - Constructor for class meshi.util.string.StringFilter
 
StringFilter(StringList) - Constructor for class meshi.util.string.StringFilter
 
StringFilterEndsWith - Class in meshi.util.string
 
StringFilterEndsWith(String) - Constructor for class meshi.util.string.StringFilterEndsWith
 
StringFilterEndsWith(StringList) - Constructor for class meshi.util.string.StringFilterEndsWith
 
StringFilterEquals - Class in meshi.util.string
 
StringFilterEquals(String) - Constructor for class meshi.util.string.StringFilterEquals
 
StringFilterEquals(StringList) - Constructor for class meshi.util.string.StringFilterEquals
 
StringFilterGrep - Class in meshi.util.string
 
StringFilterGrep(String) - Constructor for class meshi.util.string.StringFilterGrep
 
StringFilterGrep(StringList) - Constructor for class meshi.util.string.StringFilterGrep
 
StringFilterStartsWith - Class in meshi.util.string
 
StringFilterStartsWith(String) - Constructor for class meshi.util.string.StringFilterStartsWith
 
StringFilterStartsWith(StringList) - Constructor for class meshi.util.string.StringFilterStartsWith
 
StringList - Class in meshi.util.string
 
StringList() - Constructor for class meshi.util.string.StringList
 
StringList(String) - Constructor for class meshi.util.string.StringList
 
StringList(StringTokenizer) - Constructor for class meshi.util.string.StringList
 
StringList(MeshiLineReader) - Constructor for class meshi.util.string.StringList
 
StringList(File) - Constructor for class meshi.util.string.StringList
 
StringList(MeshiLineReader, Filter) - Constructor for class meshi.util.string.StringList
 
StringList.IsString - Class in meshi.util.string
 
StringList.IsString() - Constructor for class meshi.util.string.StringList.IsString
 
stringParseAt(int, StringList) - Method in class meshi.util.string.StringList
 
stringParseAt(int, String) - Method in class meshi.util.string.StringList
 
stringParseAt(int) - Method in class meshi.util.string.StringList
 
StringParser - Class in meshi.util.string
 
StringParser() - Constructor for class meshi.util.string.StringParser
 
STRUCTURE_NAMES - Static variable in interface meshi.util.KeyWords
 
StructureBasedMatrix - Class in meshi.sequences.aligner
 
StructureBasedMatrix(double, double[][]) - Constructor for class meshi.sequences.aligner.StructureBasedMatrix
 
SUB - Static variable in class meshi.util.GDTcalculator
 
submit - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
subset - Variable in class meshi.applications.hubbard.HubbardPosition
 
SubstitutionMatrix - Interface in aligner
 
suffix - Variable in class meshi.applications.prediction.homology.gui.HomologyFileFilter
 
sum(double) - Method in class meshi.energy.TotalEnergy.SortedAtoms
 
sum - Variable in class meshi.util.histogram.Histogram
 
sum() - Method in class meshi.util.histogram.Histogram
 
sum0001 - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttribute
 
sum0001 - Variable in class ColorByEnergy.GaussianAttribute
 
sum001 - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttribute
 
sum001 - Variable in class ColorByEnergy.GaussianAttribute
 
sum01 - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttribute
 
sum01 - Variable in class ColorByEnergy.GaussianAttribute
 
sum1 - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttribute
 
sum1 - Variable in class ColorByEnergy.GaussianAttribute
 
sum10 - Variable in class CalculateEnergyFromStructuresListAverages.GaussianAttribute
 
sum10 - Variable in class ColorByEnergy.GaussianAttribute
 
sum2Model(List<ModelData>) - Static method in class meshi.applications.prediction.ModelData
 
SUMMA_ATTRIBUTE - Static variable in interface meshi.util.MeshiAttribute
 
summaAtomNameToParametersAtomIndex(String) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
Translates Summa atom name to parameters file atom index.
summaAttribute - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
summaAttribute - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
summaAttribute - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
summaAttribute - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
SummaAttribute - Class in meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
 
SummaAttribute() - Constructor for class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.SummaAttribute
 
summaCreator - Static variable in class EnergyStatistics
 
summaCreator - Static variable in class EnergyStatisticsForAtom
 
summary(TotalEnergy, int) - Static method in class AbInitio
 
summary(TotalEnergy, int) - Static method in class EnergyStatistics
 
summary(TotalEnergy, int) - Static method in class EnergyStatisticsForAtom
 
summary() - Method in class meshi.energy.TotalEnergy
 
summary(TotalEnergy, int) - Static method in class Optimize
 
summery(TotalEnergy) - Static method in class HydrogenTest
 
sumModel(List<ModelData>) - Static method in class meshi.applications.prediction.ModelData
 
sumPerAtomType - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
sumPerAtomType() - Static method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
sumPerResidueType - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
sumPerResidueType() - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy
 
sumPerResidueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
sumPerResidueType - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
sumPerResidueType - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
sumPerResidueType() - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy
 
SUPERIMPOSE - Static variable in interface meshi.util.KeyWords
 
superimpose(Protein, Protein, ResidueAlignment) - Static method in class meshi.util.Rms
 
superimposeFrag(int, Protein, int, int, int) - Method in class meshi.applications.corpus.LocalFragmentLib
Superimposing fragment 'indInCorpus' in the corpus to a given portion in a protein.
superType - Variable in class meshi.energy.solvate.SolvateEnergy
 
svd() - Method in class meshi.util.mathTools.Jama.Matrix
Singular Value Decomposition
symmetricComplex - Variable in class meshi.symmetryComplex.energy.SymmetryEnergyElement
 
SymmetricComplex - Class in meshi.symmetryComplex.molecularImageElements
Symmetric protein, each chain is a Protein object.
SymmetricComplex(Transformation[], String) - Constructor for class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
SymmetricComplex(AtomList, ResidueCreator, Transformation[]) - Constructor for class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
SymmetricComplex(AtomList, ResidueCreator, SequenceAlignment, Transformation[]) - Constructor for class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
SymmetricComplex(AtomList, ResidueCreator, SequenceAlignment, Transformation[], String) - Constructor for class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
SymmetricComplex(AtomList, ResidueCreator, Transformation[], String, boolean) - Constructor for class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
SymmetricComplexCompleter - Class in meshi.symmetryComplex.molecularImageElements
 
SymmetricComplexCompleter(AtomList, ResidueCreator, Transformation[], CommandList, Topology) - Constructor for class meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter
 
SYMMETRY_ENERGY - Static variable in interface meshi.util.KeyWords
 
SymmetryCreator - Class in meshi.symmetryComplex.energy
 
SymmetryCreator() - Constructor for class meshi.symmetryComplex.energy.SymmetryCreator
 
SymmetryCreator(double) - Constructor for class meshi.symmetryComplex.energy.SymmetryCreator
 
SymmetryEnergy - Class in meshi.symmetryComplex.energy
 
SymmetryEnergy(SymmetricComplex, DistanceMatrix, ParametersList, double) - Constructor for class meshi.symmetryComplex.energy.SymmetryEnergy
 
SymmetryEnergyElement - Class in meshi.symmetryComplex.energy
This energy element always contributes zero to the total energy, but in every iteration it updates image atoms/proteins...
SymmetryEnergyElement(SymmetricComplex, double) - Constructor for class meshi.symmetryComplex.energy.SymmetryEnergyElement
 
SynchronizedUpdateException - Exception in meshi.energy.hydrogenBond
Created by IntelliJ IDEA.
SynchronizedUpdateException(String) - Constructor for exception meshi.energy.hydrogenBond.SynchronizedUpdateException
 

T

tableGet(String) - Static method in class meshi.util.MeshiProgram
Gets the value associated with the keyword key.
tableIncludes(String) - Static method in class meshi.util.MeshiProgram
 
tableSet(String, Object) - Static method in class meshi.util.MeshiProgram
Associate a value to a keyword.
tagPreProline() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
A method to tag as Pre-Proline all the residues that are such.
tail() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
tail - Variable in class meshi.molecularElements.Residue
last atom of the residue (typicaly C).
tail() - Method in class meshi.molecularElements.Residue
 
tail() - Method in class meshi.sequences.Sequence
 
target - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
target - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
target - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
target - Variable in class meshi.energy.simpleEnergyTerms.bond.BondParameters
The target distance for this type of bond.
target - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate.TargetFilter
 
target - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
target - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
target - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
TARGET_FILE_PATH - Static variable in interface meshi.util.KeyWords
 
TARGET_NAME - Static variable in interface meshi.util.KeyWords
 
TARGET_SEQUENCE - Static variable in interface meshi.util.KeyWords
 
targetDistance - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
targetFileButton - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
targetFilePathText - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
targetMinusBUFF - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
targetPlus2PIMinusBUFF - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
targetPlusBUFF - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
targetPlusPI - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
targetPlusPIMinusBUFF - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
targetPlusPIPlusBUFF - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
targetRG - Variable in class meshi.energy.linearRG.LinearRgCreator
 
targetRG - Variable in class meshi.energy.linearRG.LinearRgEnergy
 
targetSigma - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
targetSigma - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
targetSigma - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
temp - Static variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
temp - Static variable in class meshi.util.overlap.Overlap
 
temperatureFactor - Variable in class meshi.molecularElements.atoms.Atom
 
temperatureFactor() - Method in class meshi.molecularElements.atoms.Atom
 
temperatureFactor - Variable in class meshi.PDB.PdbLine
 
temperatureFactor() - Method in class meshi.PDB.PdbLine
 
temperatureGenerator - Variable in class meshi.optimizers.MCM
 
TemperatureGenerator - Class in meshi.optimizers
 
TemperatureGenerator(double, double, int) - Constructor for class meshi.optimizers.TemperatureGenerator
 
template - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyCreator
 
template - Variable in class meshi.energy.templateEnergy.TemplateEnergyCreator
 
TEMPLATE_DISTANCE_CONSTRAINTS - Static variable in interface meshi.util.KeyWords
 
TEMPLATE_DSSP - Static variable in interface meshi.util.KeyWords
 
TEMPLATE_ENERGY - Static variable in interface meshi.util.KeyWords
 
TEMPLATE_FILE_PATH - Static variable in interface meshi.util.KeyWords
 
TEMPLATE_NAME - Static variable in interface meshi.util.KeyWords
 
TEMPLATE_STRUCTURE - Static variable in interface meshi.util.KeyWords
 
TEMPLATE_TARGET_ALIGNMENT - Static variable in interface meshi.util.KeyWords
 
templateDistanceConstrainsInterSegmentFactorLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsInterSegmentFactorText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsInterSegmentToleranceLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsInterSegmentToleranceText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsIntraSegmentFactorLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsIntraSegmentFactorText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsIntraSegmentToleranceLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsIntraSegmentToleranceText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsSaturationLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsSaturationText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsUnsatisfiedCutoffLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsUnsatisfiedCutoffText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsUpToCutoffLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsUpToCutoffText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsWeightLabel - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
templateDistanceConstrainsWeightText - Variable in class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
 
TemplateEnergy - Class in meshi.energy.templateEnergy
 
TemplateEnergy(double) - Constructor for class meshi.energy.templateEnergy.TemplateEnergy
 
TemplateEnergyCreator - Class in meshi.energy.templateEnergy
 
TemplateEnergyCreator(ResidueAlignment, TemplateEnergyCreator.Template, double) - Constructor for class meshi.energy.templateEnergy.TemplateEnergyCreator
 
TemplateEnergyCreator.Template - Enum in meshi.energy.templateEnergy
 
TemplateEnergyCreator.Template() - Constructor for enum meshi.energy.templateEnergy.TemplateEnergyCreator.Template
 
TemplateEnergyElement - Class in meshi.energy.templateEnergy
 
TemplateEnergyElement(Atom, Atom, double) - Constructor for class meshi.energy.templateEnergy.TemplateEnergyElement
 
TemplateEnergyElementsList - Class in meshi.energy.templateEnergy
 
TemplateEnergyElementsList() - Constructor for class meshi.energy.templateEnergy.TemplateEnergyElementsList
 
templateFileButton - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
templateFilePathText - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
templateThreshold - Variable in class meshi.energy.templateEnergy.TemplateEnergyCreator
 
term - Variable in class meshi.energy.EnergyCreator
 
term() - Method in class meshi.energy.EnergyCreator
 
termComparator(String) - Static method in class meshi.applications.prediction.ModelData
 
terminator - Static variable in class meshi.energy.TotalEnergy
 
terminator - Static variable in class meshi.geometry.DistanceMatrix
 
terminator - Static variable in class meshi.geometry.OldDistanceMatrix
 
terminator - Static variable in class meshi.optimizers.Minimizer
 
Terminator - Class in meshi.util
 
Terminator() - Constructor for class meshi.util.Terminator
 
test(Protein) - Static method in class Beautify
 
test(TotalEnergy, Atom) - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
test(TotalEnergy, Atom) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
test(TotalEnergy, Atom) - Method in class meshi.energy.AbstractEnergy
Looking for one "criminal" atom whose derivation is wrong.
test(TotalEnergy, Atom) - Method in class meshi.energy.CooperativeEnergyTerm
Test the accuracy of deriving the energy function by coordinate number "i".
test(TotalEnergy, Atom) - Method in class meshi.energy.EnergyElement
 
test(TotalEnergy, Atom) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
 
test(TotalEnergy, Atom) - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
 
test(TotalEnergy, Atom) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
test(TotalEnergy, Atom) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
test(TotalEnergy, Atom) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
test(TotalEnergy, Atom) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
test(TotalEnergy, Atom) - Method in class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
Testing of one atom in all energy elements
test(TotalEnergy, Atom) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
test(TotalEnergy, Atom) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy
 
test(TotalEnergy, Atom) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
test(TotalEnergy, Atom) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran
 
test(TotalEnergy, Atom) - Method in class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
Testing of one atom in all energy elements
test(TotalEnergy, Atom) - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
test() - Method in class meshi.energy.TotalEnergy
 
test() - Method in class meshi.molecularElements.Residue
 
test(TotalEnergy, Atom) - Method in class meshi.symmetryComplex.energy.SymmetryEnergy
 
test() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter
 
TestElectrostatics - Class in <Unnamed>
This program receives a list of structures, a list of energy terms, and a list of alpha values.
TestElectrostatics() - Constructor for class TestElectrostatics
 
testForEvenBreaks(double[]) - Method in class meshi.util.mathTools.Spline2D
 
testMolecularSystemIntegrity(MolecularSystem, String) - Static method in class meshi.util.Utils
 
testNonBondedList() - Method in class meshi.geometry.DistanceMatrixBondedOnly
 
testNonBondedList() - Method in class meshi.geometry.DistanceMatrixCaOnly
 
testNonBondedList(DistanceList) - Static method in class meshi.util.Utils
 
TETHER_ENERGY - Static variable in interface meshi.util.KeyWords
 
tetherCreator - Static variable in class Beautify
 
TetherCreator - Class in meshi.energy.simpleEnergyTerms.tether
 
TetherCreator() - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherCreator
 
TetherCreator(Key, Filter, CommandList, String) - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherCreator
 
TetherCreator(Key) - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherCreator
 
TetherEnergy - Class in meshi.energy.simpleEnergyTerms.tether
 
TetherEnergy() - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
TetherEnergy(AtomList, double[][], double, String) - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
TetherEnergyElement - Class in meshi.energy.simpleEnergyTerms.tether
 
TetherEnergyElement() - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
TetherEnergyElement(Atom, double, double, double, double) - Constructor for class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
textAlphaAngleEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textAlphaTorsionEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textAngleEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textBondedEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textExcludedVolumeWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textfieldParameters - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
textFlatRamachEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textHydrogenBondsPairsWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textHydrogenBondsWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textInflateEnergyRmsTarget - Variable in class meshi.applications.prediction.homology.gui.InflateParametersDialog
 
textInflateEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.InflateParametersDialog
 
textLennardJonesCaWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textLennardJonesWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textLoopNIterationsAllAtoms - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
textLoopNIterationsBackbone - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
textLoopNIterationsCA - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
textLoosenEdgeLength - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
textMinimizeMaxSteps - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
textMinimizeReportEvery - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
textMinimizeTolerane - Variable in class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
 
textNonFrozenBondDepth - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
textNonFrozenRadius - Variable in class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
 
textOutOfPlaneEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textPlaneEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textPropensityTorsionEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textSecondaryStructure - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
textSeedNumber - Variable in class meshi.applications.prediction.homology.gui.OptionDialog
 
textSolvateCA100EnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textSolventAa40 - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textSolventBb60 - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
textTargetName - Variable in class meshi.applications.prediction.homology.gui.HomologyFrame
 
textTwoTorsionsEnergyWeight - Variable in class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
theirdAtom - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
theOnlyTotalEnergy - Static variable in class meshi.energy.TotalEnergy
 
third - Variable in class HomologyModeling.Three
 
thirdWord() - Method in class meshi.util.Command
 
thirdWordDouble() - Method in class meshi.util.Command
 
thirdWordInt() - Method in class meshi.util.Command
 
thirdWordOn() - Method in class meshi.util.Command
 
thirdWordPositiveInt() - Method in class meshi.util.Command
 
Thr - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | CB / \ OG1 CG2
Thr(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Thr
 
thread(Protein, int, int, int) - Static method in class meshi.util.alignmentTools.AlignmentTools
 
threadingExperiment(int) - Method in class meshi.applications.corpus.Corpus
 
threadingExperiment_withPP(int, double, double) - Method in class meshi.applications.corpus.Corpus
 
threadingExperimentnoPG(int) - Method in class meshi.applications.corpus.Corpus
 
three2one(String) - Static method in class meshi.util.ResidueNameConvertor
 
threshold - Variable in class meshi.util.histogram.Histogram.RepresentativesIterator.ThresholdFilter
 
times(double) - Method in class meshi.util.mathTools.Jama.Matrix
Multiply a matrix by a scalar, C = s*A
times(Matrix) - Method in class meshi.util.mathTools.Jama.Matrix
Linear algebraic matrix multiplication, A * B
timesEquals(double) - Method in class meshi.util.mathTools.Jama.Matrix
Multiply a matrix by a scalar in place, A = s*A
timeStamp() - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
timeToDie - Variable in class HomologyModeling.TimeTerminator
 
timeToDie() - Method in class HomologyModeling.TimeTerminator
 
tmpSQRT - Variable in class meshi.geometry.Torsion
 
toAla() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toArg() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toArray(List<ModelData>) - Static method in class meshi.applications.prediction.ModelData
 
toArray() - Static method in class meshi.energy.AbstractEnergy
Generates an empty array.
toArray(Updateable) - Static method in class meshi.energy.AbstractEnergy
Generates an aray with one element - the parameter.
toArray(Updateable, Updateable) - Static method in class meshi.energy.AbstractEnergy
 
toArray(Updateable, Updateable, Updateable) - Static method in class meshi.energy.AbstractEnergy
 
toArray() - Method in class meshi.geometry.DistanceList
 
toArrayOfAtoms() - Method in class meshi.molecularElements.atoms.AtomList
 
toAsn() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toAsp() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toConstrict - Static variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
toContinue(String) - Method in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
toCys() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toDouble(String) - Static method in class meshi.util.Utils
Converts a string to a double.
toGln() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toGlu() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toHis() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toIle() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toInt(String) - Static method in class meshi.util.Utils
Converts a string to an int.
tolerance - Variable in class meshi.optimizers.Minimizer
 
TOLERANCE - Static variable in interface meshi.util.KeyWords
 
toLeu() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toLys() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toMet() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toNonBonded - Static variable in class meshi.geometry.MatrixRow
 
toNonBonded - Static variable in class meshi.symmetryComplex.geometryImage.MatrixRowNoImageAtoms
 
topology - Variable in class meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter
 
topology - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
topology - Static variable in class meshi.symmetryComplex.proteinsGJ.GJModeller
 
Topology - Class in meshi.symmetryComplex.topologyMap
Created by IntelliJ IDEA.
Topology(CommandList) - Constructor for class meshi.symmetryComplex.topologyMap.Topology
 
TOPOLOGY_MAP - Static variable in interface meshi.util.KeyWords
 
toPrint - Static variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
toPro() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
torsion - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
torsion - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
torsion - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
Torsion - Class in meshi.geometry
--------------------------- Torsion ----------------------------------- Addapted from Ron Elber's MOIL (ephi).
Torsion(Angle, Angle, DistanceMatrix) - Constructor for class meshi.geometry.Torsion
 
Torsion(Atom, Atom, Atom, Atom, Distance, Distance, Distance) - Constructor for class meshi.geometry.Torsion
This constructor should be used only by DisposableAngle.
torsion - Variable in class meshi.geometry.Torsion
 
torsion() - Method in class meshi.geometry.Torsion
 
torsion1 - Variable in class meshi.geometry.TorsionPair
 
torsion1() - Method in class meshi.geometry.TorsionPair
 
torsion2 - Variable in class meshi.geometry.TorsionPair
 
torsion2() - Method in class meshi.geometry.TorsionPair
 
torsionAngles - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
torsionAngles - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
 
torsionAt(int) - Method in class meshi.geometry.TorsionList
 
torsionCode - Variable in class meshi.geometry.Torsion
 
torsionList - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
 
torsionList - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
The constructor associates any outOfPlane with its parameters.
torsionList - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergy
 
TorsionList - Class in meshi.geometry
 
TorsionList() - Constructor for class meshi.geometry.TorsionList
An Torsion list based on a angle list
TorsionList(AngleList, DistanceMatrix) - Constructor for class meshi.geometry.TorsionList
 
TorsionList.FilterChi1 - Class in meshi.geometry
 
TorsionList.FilterChi1() - Constructor for class meshi.geometry.TorsionList.FilterChi1
 
TorsionList.FilterChi2 - Class in meshi.geometry
 
TorsionList.FilterChi2() - Constructor for class meshi.geometry.TorsionList.FilterChi2
 
TorsionList.FilterChi3 - Class in meshi.geometry
 
TorsionList.FilterChi3() - Constructor for class meshi.geometry.TorsionList.FilterChi3
 
TorsionList.FilterChi4 - Class in meshi.geometry
 
TorsionList.FilterChi4() - Constructor for class meshi.geometry.TorsionList.FilterChi4
 
TorsionList.FilterOOP - Class in meshi.geometry
 
TorsionList.FilterOOP() - Constructor for class meshi.geometry.TorsionList.FilterOOP
 
TorsionList.FilterPhi - Class in meshi.geometry
 
TorsionList.FilterPhi() - Constructor for class meshi.geometry.TorsionList.FilterPhi
 
TorsionList.FilterPsi - Class in meshi.geometry
 
TorsionList.FilterPsi() - Constructor for class meshi.geometry.TorsionList.FilterPsi
 
TorsionList.FilterSideChain - Class in meshi.geometry
 
TorsionList.FilterSideChain() - Constructor for class meshi.geometry.TorsionList.FilterSideChain
 
torsionName - Variable in class meshi.geometry.Torsion
 
torsionNeeded - Variable in class meshi.geometry.Torsion
 
torsionNum(Torsion) - Static method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
returns type of given torsion
TorsionPair - Class in meshi.geometry
This class defines a torsion pair for the use of the various two torsion energies.
TorsionPair(Torsion, Torsion) - Constructor for class meshi.geometry.TorsionPair
 
TorsionPairList - Class in meshi.geometry
A list of torsion pairs, used mainly for the various two torsion energies.
TorsionPairList() - Constructor for class meshi.geometry.TorsionPairList
 
TorsionPairList(TorsionList) - Constructor for class meshi.geometry.TorsionPairList
A TorsionPair list based on a Torsion list.
torsionResName - Variable in class meshi.geometry.Torsion
 
torsionResNum - Variable in class meshi.geometry.Torsion
 
torsions - Variable in class meshi.applications.corpus.Corpus
 
torsions - Variable in class meshi.molecularElements.Protein
 
toSer() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toSrtring() - Method in class meshi.applications.prediction.beautify.BeautifyAttribute
 
toString() - Method in class HomologyModeling.Three
 
toString(boolean, boolean, boolean, String) - Method in class meshi.applications.prediction.ModelData
 
toString() - Method in class meshi.applications.prediction.ModelData
 
toString() - Method in class meshi.energy.AbstractEnergy
 
toString() - Method in class meshi.energy.EnergyCreator
 
toString() - Method in class meshi.energy.hydrogenBond.HB_AtomAttribute
 
toString() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
toString() - Method in class meshi.energy.hydrogenBond.LennardJonesParameters
 
toString() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
toString() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
toString() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
toString() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
toString() - Method in class meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
toString
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
toString() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
toString() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
toString() - Method in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
toString() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.bond.BondParameters
 
toString() - Method in class meshi.energy.simpleEnergyTerms.bond.BondParametersList
 
toString() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters
Converts attributes of RamachandranSidechainParameters to string.
toString() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
Converts attributes of ResidueTorsions to string.
toString() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters
Converts attributes of SmoothRotamerLibraryParameters to string.
toString() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
Converts attributes of polynomial to string.
toString() - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
toString() - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
toString() - Method in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
toString() - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
toString() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
 
toString() - Method in class meshi.geometry.Angle
 
toString() - Method in class meshi.geometry.Coordinates
 
toString() - Method in class meshi.geometry.Distance
 
toString() - Method in class meshi.geometry.DistanceMatrix
 
toString() - Method in class meshi.geometry.DistanceMatrixBondedOnly
 
toString() - Method in class meshi.geometry.DistanceMatrixCaOnly
 
toString() - Method in class meshi.geometry.MatrixRow
 
toString() - Method in class meshi.geometry.MatrixRowCaOnly
 
toString() - Method in class meshi.geometry.OldDistanceMatrix
 
toString() - Method in class meshi.geometry.Torsion
 
toString() - Method in class meshi.geometry.TorsionPair
 
toString() - Method in class meshi.molecularElements.atoms.Atom
 
toString() - Method in class meshi.molecularElements.atoms.AtomCore
 
toString() - Method in class meshi.molecularElements.atoms.AtomList
 
toString() - Method in class meshi.molecularElements.atoms.AtomPair
 
toString() - Method in class meshi.molecularElements.atoms.MolecularSystem
 
toString() - Method in class meshi.molecularElements.Chain
 
toString() - Method in class meshi.molecularElements.ChainList
 
toString() - Method in class meshi.molecularElements.Protein
 
toString() - Method in class meshi.molecularElements.Residue
 
toString() - Method in class meshi.molecularElements.ResidueList
 
toString() - Method in class meshi.optimizers.BFGS
 
toString() - Method in class meshi.optimizers.ConjugateGradient
 
toString() - Method in class meshi.optimizers.LBFGS
 
toString() - Method in class meshi.optimizers.SteepestDecent
 
toString() - Method in class meshi.PDB.PdbLine
 
toString() - Method in class meshi.sequences.aligner.Cell
 
toString() - Method in class meshi.sequences.AlignmentColumn
 
toString() - Method in class meshi.sequences.ResidueAlignment
 
toString() - Method in class meshi.sequences.ResidueAlignmentColumn
 
toString() - Method in class meshi.sequences.ResidueAlignmentOfModels
 
toString() - Method in class meshi.sequences.Sequence
 
toString() - Method in class meshi.sequences.SequenceAlignment
 
toString() - Method in class meshi.sequences.SequenceAlignmentCell
 
toString() - Method in class meshi.sequences.SequenceList
 
toString() - Method in class meshi.symmetryComplex.energy.SymmetryEnergyElement
 
toString() - Method in interface meshi.symmetryComplex.transformations.Matrix
 
toString() - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
toString() - Method in class meshi.util.Command
 
toString() - Method in class meshi.util.file.MeshiLineReader
 
toString() - Method in class meshi.util.file.MeshiWriter
 
toString() - Method in class meshi.util.MeshiProgram.GlobalElementList
 
toString() - Method in class meshi.util.MeshiProgram
 
toString() - Method in class meshi.util.Pair
 
toString() - Method in class meshi.util.Rms
 
toStringPhiPsiChi1() - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
Partial conversion to string.
TOTAL_TORSION_ANGLES - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
TotalEnergy - Class in meshi.energy
A generic class for all meshi energy functions.
TotalEnergy(AtomList, DistanceMatrix, AbstractEnergy[]) - Constructor for class meshi.energy.TotalEnergy
 
TotalEnergy(Protein, DistanceMatrix, EnergyCreator[], CommandList) - Constructor for class meshi.energy.TotalEnergy
 
TotalEnergy(AtomList, DistanceMatrix) - Constructor for class meshi.energy.TotalEnergy
 
TotalEnergy(AtomList) - Constructor for class meshi.energy.TotalEnergy
 
TotalEnergy(Protein, DistanceMatrix, EnergyCreator[], CommandList, AtomList) - Constructor for class meshi.energy.TotalEnergy
 
totalEnergy - Variable in class meshi.energy.TotalEnergy
 
totalEnergy() - Method in class meshi.energy.TotalEnergy
 
TotalEnergy.EnergyComparator - Class in meshi.energy
 
TotalEnergy.EnergyComparator() - Constructor for class meshi.energy.TotalEnergy.EnergyComparator
 
TotalEnergy.FreeAtom - Class in meshi.energy
 
TotalEnergy.FreeAtom() - Constructor for class meshi.energy.TotalEnergy.FreeAtom
 
TotalEnergy.IsEnergy - Class in meshi.energy
 
TotalEnergy.IsEnergy() - Constructor for class meshi.energy.TotalEnergy.IsEnergy
 
TotalEnergy.SortedAtoms - Class in meshi.energy
 
TotalEnergy.SortedAtoms() - Constructor for class meshi.energy.TotalEnergy.SortedAtoms
 
toThr() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toTrp() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toTyr() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
toVal() - Method in class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
 
tql2() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
trace() - Method in class meshi.util.mathTools.Jama.Matrix
Matrix trace.
trans - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
TRANS - Static variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
trans - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
transform(double[][]) - Method in class meshi.symmetryComplex.transformations.Transformation
 
transform(double[]) - Method in class meshi.symmetryComplex.transformations.Transformation
 
transformation - Variable in class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
transformation() - Method in class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
transformation - Variable in class meshi.symmetryComplex.molecularImageElements.ImageAtomList
 
transformation - Variable in class meshi.symmetryComplex.molecularImageElements.ImageChain
 
transformation() - Method in class meshi.symmetryComplex.molecularImageElements.ImageChain
 
Transformation - Class in meshi.symmetryComplex.transformations
This class represents a transformation on points in space.
Transformation() - Constructor for class meshi.symmetryComplex.transformations.Transformation
 
Transformation(Matrix) - Constructor for class meshi.symmetryComplex.transformations.Transformation
 
Transformation(double[][]) - Constructor for class meshi.symmetryComplex.transformations.Transformation
Transformation constructor which can handle double[4][4] and double[3][3].
Transformation(double, double, double, double) - Constructor for class meshi.symmetryComplex.transformations.Transformation
Axis-angle constructor.
transformations - Variable in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
transformations() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
transformations - Variable in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
transformToOrigin(double[][], double[][], Atom, Atom, Atom) - Static method in class meshi.geometry.ViewAt
 
transformToOrigin(double[][], double[][], double[], double[], double[]) - Static method in class meshi.geometry.ViewAt
 
transpose() - Method in interface meshi.symmetryComplex.transformations.Matrix
 
transpose() - Method in class meshi.symmetryComplex.transformations.Matrix1D
 
transpose() - Method in class meshi.util.mathTools.Jama.Matrix
Matrix transpose.
tred2() - Method in class meshi.util.mathTools.Jama.EigenvalueDecomposition
 
Trp - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB CE3 - CZ3 - CH2 | | | CG - CD2 - CE2 - CZ2 | | CD1 ------ NE1 - HE1
Trp(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Trp
 
trueFragEnd - Variable in class meshi.applications.corpus.LocalFragmentLib
 
trueFragEnd() - Method in class meshi.applications.corpus.LocalFragmentLib
 
trueFragStart - Variable in class meshi.applications.corpus.LocalFragmentLib
 
trueFragStart() - Method in class meshi.applications.corpus.LocalFragmentLib
 
truncate(Protein, Protein) - Static method in class Beautify
 
tryToGenerateNewAtomLeft(CaResidue) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
tryToGenerateNewAtomRight(CaResidue) - Method in class meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
 
turnOff() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
turnOff() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
turnOff() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
turnOn() - Method in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
turnOn() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
turnOn() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
TWO_ANGLES_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
TWO_TORSIONS_ENERGY - Static variable in interface meshi.util.KeyWords
 
TWO_TORSIONS_PARAMETERS - Static variable in interface meshi.parameters.MeshiPotential
 
type - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator
 
type - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
type - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy
 
type - Static variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran
 
type() - Method in class meshi.energy.solvate.SolvateDistanceAttribute
 
type() - Method in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
type() - Method in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
type() - Method in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
type() - Method in class meshi.energy.solvate.SolvateDistanceAttributeWithAhydrogen
 
type() - Method in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
type() - Method in class meshi.molecularElements.atoms.Atom
The atom type.
type - Variable in class meshi.molecularElements.atoms.AtomCore
 
type() - Method in class meshi.molecularElements.atoms.AtomCore
 
type - Variable in class meshi.molecularElements.Residue
which of the 20 possible it is.
type() - Method in class meshi.molecularElements.Residue
 
type(String, String) - Static method in enum meshi.parameters.AtomType
 
type(String) - Static method in enum meshi.parameters.AtomType
 
type(int) - Static method in enum meshi.parameters.AtomType
 
type(String) - Static method in enum meshi.parameters.ResidueType
 
type(char) - Static method in enum meshi.parameters.ResidueType
 
type(AtomType) - Static method in enum meshi.parameters.ResidueType
 
type() - Method in class meshi.PDB.PdbLine
 
type1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
type1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
type1 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
type1 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
type1 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondParameters
Atom type of the first atom.
type1 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
type1 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
type1() - Method in class meshi.geometry.Torsion
 
type2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
 
type2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
type2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
type2 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
type2 - Variable in class meshi.energy.simpleEnergyTerms.bond.BondParameters
Atom type of the second atom.
type2 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
type2 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
type2() - Method in class meshi.geometry.Torsion
 
type3 - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleParameters
 
type3 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
type3 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
type3() - Method in class meshi.geometry.Torsion
 
type4 - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters
 
type4 - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneParameters
 
Tyr - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB | CG - CD1 - CE1 | | CD2- CE2 - CZ-OH
Tyr(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Tyr
 

U

U - Variable in class meshi.util.mathTools.Jama.SingularValueDecomposition
Arrays for internal storage of U and V.
Umatrix - Static variable in class meshi.util.overlap.Overlap
 
uminus() - Method in class meshi.util.mathTools.Jama.Matrix
Unary minus
UN_WARP_ENERGY - Static variable in interface meshi.util.KeyWords
 
ungapped - Variable in class meshi.applications.corpus.Corpus
 
UNIDENTIFIED_TORSION_TYPE - Static variable in interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
 
UNKNOWN - Static variable in class meshi.sequences.Sequence
 
UnknownAtomTypeException - Exception in meshi.PDB
 
UnknownAtomTypeException(String) - Constructor for exception meshi.PDB.UnknownAtomTypeException
 
UNSATISFIED_CUTTOF - Static variable in interface meshi.util.KeyWords
 
UnWarpEnergy - Class in meshi.applications.prediction.beautify.unWarpEnergy
 
UnWarpEnergy(double, Protein) - Constructor for class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
UnWarpEnergyCreator - Class in meshi.applications.prediction.beautify.unWarpEnergy
 
UnWarpEnergyCreator() - Constructor for class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyCreator
 
UnWarpEnergyElement - Class in meshi.applications.prediction.beautify.unWarpEnergy
 
UnWarpEnergyElement(Atom, Atom, double, double) - Constructor for class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
UnWarpEnergyElementsList - Class in meshi.applications.prediction.beautify.unWarpEnergy
 
UnWarpEnergyElementsList(Protein, double) - Constructor for class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElementsList
 
UP_TO_CUTOFF - Static variable in interface meshi.util.KeyWords
 
upCell - Variable in class meshi.sequences.aligner.Cell
 
update(CalculateEnergyFromStructuresListAverages.GaussianAttribute, int) - Method in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
update() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
update(int) - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy
 
update() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
update(int) - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElementsList
Updates the distances.
update() - Method in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElementsList
 
update() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
update(int) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
update() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
update(int) - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElementsList
Updates the distances.
update() - Method in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElementsList
 
update(int) - Method in class meshi.energy.AbstractEnergy
Updates the updatable resources.
update(int) - Method in class meshi.energy.AbstractEnergy.UpdateableList
Iterates over the list updates each of its elements.
update(int) - Method in class meshi.energy.hydrogenBond.HBondList
 
update() - Method in class meshi.energy.hydrogenBond.HBondList
 
update(int) - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
update() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
update(int) - Method in class meshi.energy.RG.RgEnergy
 
update(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions
 
update(int) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList
 
update() - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
update(int) - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergy
 
update() - Method in class meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
 
update(int) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
 
update(boolean, int) - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList
The 'toRefreshVector' parameter determines if broken H-bonds are removed from the vector.
update() - Method in class meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
 
update() - Method in class meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
 
update() - Method in class meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
 
update() - Method in class meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
 
update() - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
update(int) - Method in class meshi.energy.templateEnergy.TemplateEnergy
 
update() - Method in class meshi.energy.templateEnergy.TemplateEnergyElement
 
update(int) - Method in class meshi.energy.templateEnergy.TemplateEnergyElementsList
Updates the distances.
update() - Method in class meshi.energy.templateEnergy.TemplateEnergyElementsList
 
update() - Method in class meshi.energy.TotalEnergy
Updates all factors related to the energy function (for example the distance matrix).
update(int) - Method in class meshi.geometry.Angle
 
update() - Method in class meshi.geometry.Angle
 
update(int) - Method in class meshi.geometry.AngleList
 
update() - Method in class meshi.geometry.BondedDistance
 
update(double) - Method in class meshi.geometry.Distance
 
update(int) - Method in class meshi.geometry.DistanceMatrix
Updates the distance matrix.
update() - Method in class meshi.geometry.DistanceMatrix
 
update(int) - Method in class meshi.geometry.DistanceMatrixBondedOnly
Updates the distance matrix.
update() - Method in class meshi.geometry.DistanceMatrixBondedOnly
 
update(int) - Method in class meshi.geometry.DistanceMatrixCaOnly
Updates the distance matrix.
update() - Method in class meshi.geometry.DistanceMatrixCaOnly
 
update() - Method in class meshi.geometry.FreeDistance
 
update(DistanceList, ArrayList<DistanceList>) - Method in class meshi.geometry.MatrixRow
 
update(DistanceList, ArrayList<DistanceList>, int) - Method in class meshi.geometry.MatrixRowCaOnly
 
update(int) - Method in class meshi.geometry.OldDistanceMatrix
Updates the distance matrix.
update() - Method in class meshi.geometry.OldDistanceMatrix
 
update(int) - Method in class meshi.geometry.Torsion
 
update() - Method in class meshi.geometry.Torsion
 
update(int) - Method in class meshi.geometry.TorsionList
 
update(int) - Method in class meshi.geometry.TorsionPair
 
update(int) - Method in class meshi.geometry.TorsionPairList
 
update(int) - Method in class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
update() - Method in class meshi.symmetryComplex.geometryImage.DistanceMatrixNoImageAtoms
 
update(DistanceList, ArrayList<DistanceList>) - Method in class meshi.symmetryComplex.geometryImage.MatrixRowNoImageAtoms
 
update(int) - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
update(int) - Method in class meshi.util.RgCalculator
 
update() - Method in class meshi.util.RgCalculator
 
update(int) - Method in interface meshi.util.Updateable
 
update_dm() - Method in class meshi.energy.hydrogenBond.HBondList
 
UPDATE_EVERY_X_STEPS - Variable in class meshi.energy.hydrogenBond.HBondList
 
Updateable - Interface in meshi.util
 
UpdateableException - Exception in meshi.util
 
UpdateableException() - Constructor for exception meshi.util.UpdateableException
 
updateableResources - Variable in class meshi.energy.AbstractEnergy
 
updateAndEvaluateAtoms123(Atom, Atom, Atom) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
updateAndEvaluateAtoms1234(Atom, Atom, Atom, Atom) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
updateAndEvaluateAtoms234(Atom, Atom, Atom) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
 
updateAng123() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
updateAng234() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
updateAngProduct1234() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
This method update the product: sigmoidAng(angle1)*sigmoidAng(angle2) and all the relevent derivatives.
updateAtoms() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
updateAtoms(double) - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
updateAtoms() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
updateAtoms(double) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
updateAtoms() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
updateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
Updates the atoms position
updateAtoms() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
updateCosine() - Method in class meshi.geometry.Torsion
 
updateCylindricalCoors() - Method in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
Updates the cylindrical coordinates according to the cartesian coordinates.
updateDebug() - Method in class meshi.energy.TotalEnergy
 
updateDis() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
This method update the distance sigmoid and all the relevent derivatives.
updateEnergy() - Method in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
energy and dirivarives calculation.
updateEnergy() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
energy and dirivarives calculation.
updateEnergy() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
updateEnergy() - Method in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
Updates the energy
updateEnergy() - Method in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
updateForces(double, double) - Method in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
Updates the forces on the atom.
updateFrozen() - Method in class meshi.energy.EnergyElement
 
updateFrozen() - Method in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
updateHBvalueAndDerivatives() - Method in class meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
This update method should be used if a change to the atoms coordinates has occured.
updateHBvalueAndDerivatives() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
This method activates all the code for updating the Dahiyat H-bond.
updateLocation() - Method in class meshi.symmetryComplex.molecularImageElements.ImageAtom
 
updateLocations() - Method in class meshi.symmetryComplex.molecularImageElements.SymmetricComplex
 
updateMovingAtoms() - Method in class meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
 
updateNew(DistanceList, int) - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
updateNumbers() - Method in class meshi.applications.hubbard.HubbardPosition
Updateing the numberst
updateSigmVals(Distance) - Method in class meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis.
updateSigmVals(Distance) - Method in class meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis.
updateSigmVals(Distance) - Method in class meshi.energy.solvateRot1.SolvateRot1Energy
Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis.
updateSubset() - Method in class meshi.applications.hubbard.HubbardPosition
Updateing the subset
updateTheirdAtom(double) - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
updateTheirdAtom() - Method in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
updateTheirdAtom() - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
updateTheirdAtom(double) - Method in class meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
 
updateTheirdAtom() - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
updateTheirdAtom(double) - Method in class meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
 
updateTwoLists(HBdistanceList) - Method in class meshi.energy.hydrogenBond.HBondList
 
upLeftCell - Variable in class meshi.sequences.aligner.Cell
 
upperLeft() - Method in class meshi.geometry.OldDistanceMatrix
 
usageMessage() - Method in class meshi.util.CommandsException
 
usageString() - Static method in class HeliumClusterMinimization
 
usageString - Variable in class meshi.util.CommandsException
 
usageString() - Static method in class MinimizeProtein
 
usageString() - Static method in class SimplestMinimizeProtein
 
USE_FAST_ARCCOS - Static variable in class meshi.geometry.ArcCos
 
USE_FAST_ARCCOS - Static variable in interface meshi.util.KeyWords
 
useFastArcCos() - Static method in class meshi.geometry.ArcCos
Set flag for using fast acos and initialize acos lookup table
useGama - Variable in class meshi.optimizers.LBFGS
 
Utils - Class in meshi.util
Where we store useful static methods that do not make sense anywhere else.
Utils() - Constructor for class meshi.util.Utils
 
Utils.DefaultExceptionHandler - Class in meshi.util
 
Utils.DefaultExceptionHandler() - Constructor for class meshi.util.Utils.DefaultExceptionHandler
 
Utils.DoNothingExceptionHandler - Class in meshi.util
 
Utils.DoNothingExceptionHandler() - Constructor for class meshi.util.Utils.DoNothingExceptionHandler
 
uu - Variable in class meshi.geometry.Torsion
 
uu2 - Variable in class meshi.geometry.Torsion
 
uv - Variable in class meshi.geometry.Torsion
 
ux - Variable in class meshi.geometry.Torsion
 
uy - Variable in class meshi.geometry.Torsion
 
uz - Variable in class meshi.geometry.Torsion
 

V

V - Variable in class meshi.util.mathTools.Jama.EigenvalueDecomposition
Array for internal storage of eigenvectors.
V - Variable in class meshi.util.mathTools.Jama.SingularValueDecomposition
Arrays for internal storage of U and V.
Val - Class in meshi.molecularElements.extendedAtoms
O | N - CA - C...n | | H CB - CG1 | CG2
Val(AtomList, ResidueIdentifier, ResidueMode) - Constructor for class meshi.molecularElements.extendedAtoms.Val
 
valAtp1 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
valAtp1 - Variable in class meshi.energy.solvate.SigmaParameters
 
valAtp2 - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
valAtp2 - Variable in class meshi.energy.solvate.SigmaParameters
 
value - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
value() - Method in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters
 
value(int, double...) - Method in class meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial
Calculates polynomial's derivation for given variable with value for list of arguments.
value(int, double...) - Method in class meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
Evaluate value of polynomial or any of its first derivations at given point.
value - Variable in class meshi.util.MeshiProgram.GlobalElement
 
value() - Method in class meshi.util.MeshiProgram.GlobalElement
 
value - Variable in class meshi.util.Pair
 
value() - Method in class meshi.util.Pair
 
VALUE_KEY - Static variable in interface meshi.util.KeyWords
 
valueOf(String) - Static method in enum HomologyModeling.LoopMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.applications.prediction.AbitSmarterLoopBuilder.Loop.End
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.energy.solvate.SolvateDistanceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.energy.solvate.SolvateEnergy.SuperType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.energy.templateEnergy.TemplateEnergyCreator.Template
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.geometry.DistanceMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.molecularElements.atoms.AtomStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.optimizers.Optimizer.OptimizerStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.AddAtomsFlag
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.AtomType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.BBatom
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.Element
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.ResidueMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.ResidueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum meshi.parameters.SecondaryStructure
Returns the enum constant of this type with the specified name.
values() - Static method in enum HomologyModeling.LoopMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.applications.prediction.AbitSmarterLoopBuilder.Loop.End
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.energy.solvate.SolvateDistanceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.energy.solvate.SolvateEnergy.SuperType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.energy.templateEnergy.TemplateEnergyCreator.Template
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.geometry.DistanceMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.molecularElements.atoms.AtomStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.optimizers.Optimizer.OptimizerStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.AddAtomsFlag
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.AtomType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.BBatom
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.Element
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.ResidueMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.ResidueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum meshi.parameters.SecondaryStructure
Returns an array containing the constants of this enum type, in the order they are declared.
variabilityZ - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
verbose(int) - Method in class meshi.molecularElements.atoms.Atom
Returns the atom as a PDB formatted String.
verbose - Variable in class meshi.molecularElements.Protein
 
verbose() - Static method in class meshi.util.MeshiProgram
Gets the boolean value associated with the keyword verbose.
Verbose - Interface in meshi.util
 
verbose(int) - Method in interface meshi.util.Verbose
 
VERY_SHORT - Static variable in class meshi.util.formats.Fdouble
 
VERY_SHORT - Static variable in class meshi.util.formats.Format
 
VERY_SMALL - Static variable in class meshi.energy.EnergyElement
 
verySmall - Variable in class meshi.energy.CooperativeEnergyTerm
 
verySmall - Static variable in class meshi.energy.TotalEnergy
 
verySmall - Static variable in class meshi.geometry.ArcCos
 
verySmall - Variable in class meshi.optimizers.SimpleStepLength
 
ViewAt - Class in meshi.geometry
Title:
ViewAt() - Constructor for class meshi.geometry.ViewAt
 
visible - Variable in class meshi.applications.prediction.beautify.BeautifyAttribute
 
VOLUME_CONSTRAINT - Static variable in interface meshi.util.KeyWords
 
vv - Variable in class meshi.geometry.Torsion
 
vv2 - Variable in class meshi.geometry.Torsion
 
vx - Variable in class meshi.geometry.Torsion
 
vy - Variable in class meshi.geometry.Torsion
 
vz - Variable in class meshi.geometry.Torsion
 

W

w1 - Static variable in class meshi.util.Scmod
 
w2 - Static variable in class meshi.util.Scmod
 
w3 - Static variable in class meshi.util.Scmod
 
w4 - Static variable in class meshi.util.Scmod
 
w5 - Static variable in class meshi.util.Scmod
 
w6 - Static variable in class meshi.util.Scmod
 
warp(Protein, Protein, CommandList) - Static method in class Beautify
 
WARP_ENERGY - Static variable in interface meshi.util.KeyWords
 
WARP_STEP_SIZE - Static variable in interface meshi.util.KeyWords
 
WARP_THRESHOLD - Static variable in interface meshi.util.KeyWords
 
WarpEnergy - Class in meshi.applications.prediction.beautify.warpEnergy
 
WarpEnergy(double) - Constructor for class meshi.applications.prediction.beautify.warpEnergy.WarpEnergy
 
warpEnergyCreator - Static variable in class Beautify
 
WarpEnergyCreator - Class in meshi.applications.prediction.beautify.warpEnergy
 
WarpEnergyCreator() - Constructor for class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyCreator
 
WarpEnergyCreator(Protein, double) - Constructor for class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyCreator
 
WarpEnergyElement - Class in meshi.applications.prediction.beautify.warpEnergy
 
WarpEnergyElement(Atom, Atom, double) - Constructor for class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
WarpEnergyElementsList - Class in meshi.applications.prediction.beautify.warpEnergy
 
WarpEnergyElementsList() - Constructor for class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElementsList
 
warpThreshold - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyCreator
 
WC - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
WCDMinusSig3 - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
WCDMinusSig4 - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
weight - Variable in class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
 
weight - Variable in class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
 
weight - Variable in class meshi.energy.AbstractEnergy
The weight of the energy term within the total energy.
weight - Variable in class meshi.energy.EnergyCreator
The weight of the energy term within the total energy function.
weight() - Method in class meshi.energy.EnergyCreator
The weight of the energy term.
weight - Variable in class meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
 
weight - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
weight - Variable in class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
 
weight - Variable in class meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
 
weight - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
 
weight - Variable in class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
 
weight - Variable in class meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
 
weight - Variable in class meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
 
weight - Variable in class meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
weight() - Method in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
 
weight() - Method in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
 
weight - Variable in class meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
 
weight - Variable in class meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
 
weight - Variable in class meshi.energy.templateEnergy.TemplateEnergyElement
 
weight - Variable in class meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
 
weight - Variable in class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
 
weight - Variable in class meshi.symmetryComplex.energy.SymmetryEnergyElement
 
WEIGHT - Static variable in interface meshi.util.KeyWords
 
weightAA - Variable in class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters
 
weightAA - Variable in class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters
 
weightBBPolarSolvate - Variable in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
weightBBPolarSolvate - Variable in class meshi.energy.solvate.SolvateCreatorLongHB
 
weightBBPolarSolvate - Variable in class meshi.energy.solvate.SolvateCreatorRegularHB
 
weightBBPolarSolvate - Variable in class meshi.energy.solvate.SolvateEnergy
 
WeightForHB - Static variable in class ModelRanker
 
WeightForRot1Solvation - Static variable in class ModelRanker
 
weightHB - Variable in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
weightHB - Variable in class meshi.energy.solvate.SolvateCreatorLongHB
 
weightHB - Variable in class meshi.energy.solvate.SolvateCreatorRegularHB
 
weightHB - Variable in class meshi.energy.solvate.SolvateEnergy
 
weightSCCarbonSolvate - Variable in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
weightSCCarbonSolvate - Variable in class meshi.energy.solvate.SolvateCreatorLongHB
 
weightSCCarbonSolvate - Variable in class meshi.energy.solvate.SolvateCreatorRegularHB
 
weightSCCarbonSolvate - Variable in class meshi.energy.solvate.SolvateEnergy
 
weightSCPolarSolvate - Variable in class meshi.energy.solvate.SolvateCreatorHBforMinimization
 
weightSCPolarSolvate - Variable in class meshi.energy.solvate.SolvateCreatorLongHB
 
weightSCPolarSolvate - Variable in class meshi.energy.solvate.SolvateCreatorRegularHB
 
weightSCPolarSolvate - Variable in class meshi.energy.solvate.SolvateEnergy
 
WeightsForEnergyTerms - Class in meshi.applications.prediction.homology.gui
 
WeightsForEnergyTerms() - Constructor for class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
 
WeightsForEnergyTermsLayout - Class in meshi.applications.prediction.homology.gui
 
WeightsForEnergyTermsLayout() - Constructor for class meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout
 
weightWasSet - Variable in class meshi.energy.EnergyCreator
 
weightWasSet() - Method in class meshi.energy.EnergyCreator
 
WEIRD_INPUT_TO_FIND_STEP_LENGTH - Static variable in exception meshi.optimizers.LineSearchException
 
weirdAtom(Atom) - Static method in class meshi.util.Utils
 
weirdChar(String) - Method in class meshi.sequences.Sequence
 
whereIs(Atom) - Method in class meshi.molecularElements.atoms.AtomList
 
whichChainsInZone(double, AtomList) - Static method in class meshi.symmetryComplex.utils.GJUtils
Calculates the average distance between atoms from loops E1 and E2.
whichChainsInZone(ChainList, double) - Static method in class meshi.symmetryComplex.utils.GJUtils
 
whichLoop(int) - Method in class meshi.symmetryComplex.topologyMap.Topology
Returns '1' if the residue number belongs to loop E1, '2' if it belongs to loop E2 and '0' otherwise.
WIDTH_OF_HAIRPIN - Static variable in interface meshi.util.KeyWords
 
widthOfHairpin - Variable in class meshi.symmetryComplex.topologyMap.Loop
 
widthOfHairpin() - Method in class meshi.symmetryComplex.topologyMap.Loop
 
WILDCARD - Static variable in class meshi.sequences.SequenceAlignmentCell
 
wildcard() - Method in class meshi.sequences.SequenceAlignmentCell
 
WILDCARD_CHAR - Static variable in class meshi.sequences.SequenceAlignmentCell
 
wildcardOrGap(SequenceAlignmentCell) - Static method in class meshi.sequences.SequenceAlignmentCell
 
wildcardOrGap(SequenceAlignmentColumn) - Static method in class meshi.sequences.SequenceAlignmentCell
 
withinRmaxIterator() - Method in class meshi.energy.hydrogenBond.HBondList
 
withinRmaxPairsIterator() - Method in class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList
 
WOLF_CONDITION_NOT_MET - Static variable in exception meshi.optimizers.LineSearchException
 
WolfConditionLineSearch - Class in meshi.optimizers
This class implements a line search that satisfies the Wolf conditions according to the scheme in: Numerical Optimization by J.
WolfConditionLineSearch(TotalEnergy, double, double, double, int) - Constructor for class meshi.optimizers.WolfConditionLineSearch
 
words - Variable in class meshi.util.Command
 
write(String) - Method in class aligner.FWriter
 
write(char) - Method in class aligner.FWriter
 
writeln() - Method in class aligner.FWriter
 
writeln(String) - Method in class aligner.FWriter
 
writer - Variable in class CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
 
writeToDisk(String, boolean[]) - Method in class meshi.applications.corpus.Corpus
Writing all the residues in the corpus that are marked as TRUE in the 'toWrite' input array (its length must be as the corpus's).
writeToDisk(String) - Method in class meshi.applications.corpus.Corpus
This overload writes the entire corpus to disk.
writeToDisk(String, int, int) - Method in class meshi.applications.corpus.Corpus
This overload writes to disk a subset of the corpus, all the residues that have of the previous method, that writes to disk only residues from the fragments whos indices are given in the input array.

X

x - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
x - Variable in class meshi.geometry.Coordinates
 
x() - Method in class meshi.geometry.Coordinates
 
X() - Method in class meshi.geometry.Coordinates
 
x() - Method in class meshi.molecularElements.atoms.Atom
Returns the X coordinate of the atom.
X() - Method in class meshi.molecularElements.atoms.Atom
 
x - Variable in class meshi.molecularElements.atoms.AtomCore
 
x() - Method in class meshi.molecularElements.atoms.AtomCore
 
X - Variable in class meshi.optimizers.BFGS
 
X - Variable in class meshi.optimizers.LBFGS
 
x - Variable in class meshi.PDB.PdbLine
 
x() - Method in class meshi.PDB.PdbLine
 
x - Variable in class meshi.symmetryComplex.utils.LoopUtils.Point
 
x() - Method in class meshi.symmetryComplex.utils.LoopUtils.Point
 
x1 - Static variable in class meshi.geometry.MatrixRow
 
x2 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
x3 - Static variable in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
 
X_ANGLE - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
X_ANGLE2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
X_MAX - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
X_MAX2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
xSize - Variable in class meshi.geometry.Grid
 
xSize - Variable in class meshi.geometry.OldGrid
 
xSizeNew - Variable in class meshi.geometry.Grid
 
xSizeNew - Variable in class meshi.geometry.OldGrid
 
XYZ - Variable in class meshi.energy.CooperativeEnergyTerm
 
XYZ - Static variable in class meshi.energy.EnergyElement
 
XYZ - Static variable in class meshi.energy.TotalEnergy
 
xyza - Static variable in class meshi.geometry.ResidueBuilder
 

Y

y - Variable in class meshi.geometry.Coordinates
 
y() - Method in class meshi.geometry.Coordinates
 
Y() - Method in class meshi.geometry.Coordinates
 
y() - Method in class meshi.molecularElements.atoms.Atom
Returns the Y coordinate of the atom.
Y() - Method in class meshi.molecularElements.atoms.Atom
 
y - Variable in class meshi.molecularElements.atoms.AtomCore
 
y() - Method in class meshi.molecularElements.atoms.AtomCore
 
Y - Variable in class meshi.optimizers.BFGS
 
Y - Variable in class meshi.optimizers.LBFGS.Element
 
y - Variable in class meshi.PDB.PdbLine
 
y() - Method in class meshi.PDB.PdbLine
 
y - Variable in class meshi.symmetryComplex.utils.LoopUtils.Point
 
y() - Method in class meshi.symmetryComplex.utils.LoopUtils.Point
 
y1 - Static variable in class meshi.geometry.MatrixRow
 
y1X_Angle2 - Variable in class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
 
ySize - Variable in class meshi.geometry.Grid
 
ySize - Variable in class meshi.geometry.OldGrid
 
ySizeNew - Variable in class meshi.geometry.Grid
 
ySizeNew - Variable in class meshi.geometry.OldGrid
 

Z

z - Variable in class meshi.geometry.Coordinates
 
z() - Method in class meshi.geometry.Coordinates
 
Z() - Method in class meshi.geometry.Coordinates
 
z() - Method in class meshi.molecularElements.atoms.Atom
Returns the Z coordinate of the atom.
Z() - Method in class meshi.molecularElements.atoms.Atom
 
z - Variable in class meshi.molecularElements.atoms.AtomCore
 
z() - Method in class meshi.molecularElements.atoms.AtomCore
 
z - Variable in class meshi.PDB.PdbLine
 
z() - Method in class meshi.PDB.PdbLine
 
z1 - Static variable in class meshi.geometry.MatrixRow
 
zeroDerivative - Variable in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
zeroDerivative() - Method in class meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat
 
Zoom(double[][], int) - Method in class meshi.optimizers.WolfConditionLineSearch
 
zScore(double, double, double) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
 
zScore(double, double, double) - Method in class meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
 
zScoreOfModels(List<ModelData>) - Static method in class meshi.applications.prediction.ModelData
 
zSize - Variable in class meshi.geometry.Grid
 
zSize - Variable in class meshi.geometry.OldGrid
 
zSizeNew - Variable in class meshi.geometry.Grid
 
zSizeNew - Variable in class meshi.geometry.OldGrid
 
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