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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
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