Overview  Package  Class  Tree  Deprecated  Index  Help 
 PREV   NEXT FRAMES    NO FRAMES    

Constant Field Values

Contents
<Unnamed>.*

AbInitio
public static final java.lang.String NAME "AbInitio"

Beautify
public static final double FAR_AWAY 5.0
public static final int FRAGMENT_LENGTH 20
public static final java.lang.String NAME "Beautify"

CalcGDT
public static final java.lang.String NAME "CalcGDT"

CalculateEnergyFromStructuresListAverages.GaussianAttributes
public final int MAX_FEATURES 100

ColorByEnergy.GaussianAttributes
public final int MAX_FEATURES 100

EnergyStatistics
public static final java.lang.String NAME "EnergyStatistics"

EnergyStatisticsForAtom
public static final java.lang.String NAME "EnergyStatistics"

HeliumClusterMinimization
private static final double MIN_DISTANCE_SQR 4.0

HomologyModeling
public static final double CA_CA_DISTANCE 3.8
public static final java.lang.String NAME "HolologyModeling"

Optimize
public static final java.lang.String NAME "Optimize"

Pdb2Fasta
public static final java.lang.String MONOMERS_TO_IGNORE "HOH HEM GDP TRS LLP CA CS K CAC AMP ALF SO4 AP5 ACE AXT 3PP PO4 D12 CO UNK IHP FBP PGA FAD BME NAG DAC ADP FMN MN FE HEA B12 GTS GOL T5A MG NAP CU DCA CL ZN PER POP CIT AGM CMP GL3 MGN ORO F43 PGC TP7 SHT EGL CYO FS4 COM COB PYR GOA ISP 3PY CBX NH2 NAD TPO SM IPS SPS NDP FUC CAS C20 PLP PHO DCD TAU FE2 POH HEC NMO"
public static final java.lang.String STANDARD_RESIDUES "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR"

Refine
public static final java.lang.String NAME "Refine"

RoisFirstMeshiProgram
public static final java.lang.String NAME "RoisFirstMeshiProgram"

meshi.applications.*

meshi.applications.corpus.CorrectRottenRamachandrans
private final double CUTOFF_GLY 0.9
private final double CUTOFF_NON_GLY 0.8
private final double DIVERSITY_RMS_IN_LIB 0.1
private final double FACTOR_LARGE_CONTIG_RMS_CUTOFF_IN_OVERLAP 0.2
private final int MAX_LIB_SIZE_FOR_EACH_ROTTEN 200
private final double RMS_CUTOFF_IN_OVERLAP 0.8

meshi.applications.corpus.LoopResultVector
private static final long serialVersionUID 314159L

meshi.applications.prediction.AbitSmarterLoopBuilder
public static final double CA_CA_DISTANCE 3.8
public static final double CA_CA_DISTANCE2 14.44
public static final int MAX_CLASHES 100

meshi.applications.prediction.ModelData
private static final int AVG_ENERGY_INDEX 1
private static final int BASE_INDEX 4
private static final int GDT_INDEX 3
private static final int NAME_INDEX 0
private static final int RMS_INDEX 2

meshi.energy.*

meshi.energy.AbstractEnergy
public static final double INFINITY 1d/0d

meshi.energy.CooperativeEnergyTerm
public final double DX 1.0E-7
public final double relativeDiffTolerance 0.01
public final java.lang.String XYZ "XYZ"

meshi.energy.EnergyElement
public static final double DX 1.0E-7
public static final double relativeDiffTolerance 5.0E-4
public static final java.lang.String XYZ "xyz"

meshi.energy.TotalEnergy
static final double DX 1.0E-7
private static final double INFINITY 1d/0d

meshi.energy.hydrogenBond.HB_AtomAttribute
public static final int key 2

meshi.energy.hydrogenBond.HB_DistanceAttribute
public static final int key 2

meshi.energy.hydrogenBond.HBondList
private final int UPDATE_EVERY_X_STEPS 50

meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
public static final double ALPHA 1.0E-5
private static final double ONE_DIV_SIX 0.16666666666666666

meshi.energy.hydrogenBond.LennardJonesParameters
public static final int key 0

meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
private static final double DIFULT_HPUNISHMENT -100.0
private static final double DIFULT_PUNISHMENT -10.0

meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
private static final int HB_PAIR_CAPACITY 4
public final int MAX_INER_SEQ_DISTANCE 10
public final int MAX_SEQ_PAIRS_DISTANCE 5

meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters
private static final java.lang.String LABEL_ATOM_NAMES_BEGIN "ATOM_NAMES_BEGIN"
private static final java.lang.String LABEL_ATOM_NAMES_END "ATOM_NAMES_END"
private static final java.lang.String LABEL_BINS_BEGIN "BINS_BEGIN"
private static final java.lang.String LABEL_BINS_END "BINS_END"
private static final java.lang.String LABEL_PMF_BEGIN "PMF_BEGIN"
private static final java.lang.String LABEL_PMF_END "PMF_END"

meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
public static final double ALPHA 0.5
private final int FIRST 0
public static final double MAX_ENERGY 100.0
private final int SECOND 1

meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy
static final double ALPHA 0.01

meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
public final double ALPHA 0.2
public final double C 624.9999999999998

meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters
public final double ALPHA1 1.0
public final double ALPHA2 0.2

meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
public final double ALPHA 0.2
public final double C 624.9999999999998

meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
public final double ALPHA 0.2
public final double BETA 1000.0
public final double C 624.9999999999998

meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
public static final double ALPHA 0.5
private final int FIRST 0
public static final double MAX_ENERGY 10000.0
private final int SECOND 1

meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList
public final int NTsai 14

meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement
private final double BUFF 0.05
private final double infForce 0.14285714285714285
private final double infForce3 0.0029154518950437313
private final double INV_BUFF 20.0

meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement
private final double BUFF 0.05
private final double INV_BUFF 20.0

meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
protected final double infForce 0.14285714285714285
protected final double infForce3 0.0029154518950437313

meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
public static final int ALL 9
public static final int CHI_1 3
public static final int CHI_2 4
public static final int CHI_3 5
public static final int CHI_4 6
public static final int COIL 3
public static final int HELIX 1
public static final int OMG 0
public static final int OMNI 21
public static final int PHI 1
public static final int POLYNOMIAL_CHI_1 3
public static final int POLYNOMIAL_CHI_1_CHI_2 2
public static final int POLYNOMIAL_CHI_1_CHI_3 4
public static final int POLYNOMIAL_CHI_1_CHI_4 5
public static final int POLYNOMIAL_PHI_PSI 0
public static final int POLYNOMIAL_PHI_PSI_CHI_1 1
public static final int PREPRO 20
public static final int PSI 2
public static final int SHEET 2
public static final int TOTAL_TORSION_ANGLES 7
public static final int UNIDENTIFIED_TORSION_TYPE -1

meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
private static final double BREAKS_PADDING 1.0E-8

meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
public static final double ALPHA 0.1

meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
protected final double BUFF 0.12

meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
public final double BETA 0.05

meshi.energy.simpleEnergyTerms.plane.PlaneParameters
public static final int CIS 2
public static final int CIS_TRANS 3
public static final int TRANS 1

meshi.energy.solvate.SolvateEnergy
public static final double SALT_BRIDGE_STRENGTH_ARG_NH 1.5
public static final double SALT_BRIDGE_STRENGTH_ASP_OD 0.45
public static final double SALT_BRIDGE_STRENGTH_GENERAL 1.0
public static final double SALT_BRIDGE_STRENGTH_GLU_OE 0.45
public static final double SALT_BRIDGE_STRENGTH_LYS_NZ 1.65
public static final double SALT_BRIDGE_STRENGTH_TRN 1.8
public static final double SALT_BRIDGE_STRENGTH_TRO 0.45

meshi.energy.solvate.SolvateParametersList
public static final int N_TSAI 14

meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants
public static final double sigmoidBeginsNoH 80.0
public static final double sigmoidBeginsWithH 90.0
public static final double sigmoidEndsNoH 90.0
public static final double sigmoidEndsWithH 100.0

meshi.energy.solvateRot1.SolvateRot1ParametersList
public final int NTsai 14

meshi.geometry.*

meshi.geometry.ArcCos
private static final boolean debug false

meshi.geometry.Distance
public static final double INFINITE_DISTANCE 1.7976931348623157E308

meshi.geometry.DistanceMatrix
public static final int DEFAULT_BONDED_LIST_DEPTH 5
public static final double DEFAULT_BUFFER 1.0
public static final double DEFAULT_RMAX 5.5

meshi.geometry.FrozenCoordinates
private final double INFINITY 1d/0d

meshi.geometry.Grid
private final long MAX_GRID_SIZE 1000000L
private final double SPHERE_COND 1.3

meshi.geometry.MatrixRow
public static final int CAPACITY 10

meshi.geometry.OldDistanceMatrix
public static final int DEFAULT_BONDED_LIST_DEPTH 5
public static final double DEFAULT_BUFFER 1.0
public static final double DEFAULT_RMAX 5.5

meshi.geometry.OldGrid
private final long MAX_GRID_SIZE 1000000L
private final double SPHERE_COND 1.3

meshi.geometry.rotamers.DunbrackLib
public final double res 0.17453292519943295

meshi.molecularElements.*

meshi.molecularElements.Chain
public static final java.lang.String GENERIC_CHAIN_NAME " "

meshi.molecularElements.ResidueIdentifier
public static final java.lang.String DEFAULT_CHAIN " "

meshi.molecularElements.atoms.Atom
private final int ATOM_BONDED_CAPACITY 4

meshi.molecularElements.atoms.AtomPair
public static final int ATOM_PAIR_CAPACITY 2

meshi.molecularElements.extendedAtoms.Ala
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n CB O\n | |\n N - CA - C...n\n |\n H\n"

meshi.molecularElements.extendedAtoms.Arg
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD - NE - CZ - NH1\n | |\n HE NH2\n"

meshi.molecularElements.extendedAtoms.Asn
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - ND2 - HD21\n | |\n OD1 HD22\n"
public static final java.lang.String NAME "ASN"

meshi.molecularElements.extendedAtoms.Asp
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - OD2\n | \n OD1\n"

meshi.molecularElements.extendedAtoms.BackboneResidue
public static final java.lang.String COMMENT "General backbone residue."

meshi.molecularElements.extendedAtoms.Cys
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n SG \n"

meshi.molecularElements.extendedAtoms.Gln
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD - NE2 - HE21\n | |\n OE1 HE22\n"

meshi.molecularElements.extendedAtoms.Glu
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD - OE2\n |\n OE1\n"

meshi.molecularElements.extendedAtoms.Gly
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n |\n H\n"

meshi.molecularElements.extendedAtoms.His
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD2 - NE2 - HE2\n | |\n HD1 - ND1 ------ CE1\n"

meshi.molecularElements.extendedAtoms.Ile
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB - CG1 - CD1\n |\n CG2\n"

meshi.molecularElements.extendedAtoms.Leu
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB - CG - CD1\n |\n CD2\n"

meshi.molecularElements.extendedAtoms.Lys
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD - CE - NZ\n"

meshi.molecularElements.extendedAtoms.Met
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - SD - CE\n"

meshi.molecularElements.extendedAtoms.Phe
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD1 - CE1\n | |\n CD2- CE2 - CZ\n"

meshi.molecularElements.extendedAtoms.Pro
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n CD CB\n \\ /\n CG\n"

meshi.molecularElements.extendedAtoms.Ser
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n |\n CB\n /\n OG\n"

meshi.molecularElements.extendedAtoms.Thr
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n |\n CB\n / \\\n OG1 CG2\n"

meshi.molecularElements.extendedAtoms.Trp
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB CE3 - CZ3 - CH2\n | | |\n CG - CD2 - CE2 - CZ2\n | |\n CD1 ------ NE1 - HE1\n"

meshi.molecularElements.extendedAtoms.Tyr
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB\n |\n CG - CD1 - CE1\n | |\n CD2- CE2 - CZ-OH\n"

meshi.molecularElements.extendedAtoms.Val
public static final java.lang.String COMMENT "From Levitt, JMB 168:592 (1983) table 2.\n O\n |\n N - CA - C...n\n | |\n H CB - CG1\n |\n CG2\n"

meshi.optimizers.*

meshi.optimizers.BFGS
private static final double DEFAULT_ALLOWED_MAX_H_FACTOR 100.0
private static final double DEFAULT_C1 1.0E-4
private static final double DEFAULT_C2 0.9
private static final double DEFAULT_EXTENDED_ALPHA_FACTOR_WOLF_SEARCH 3.0
private static final double DEFAULT_INIT_STEP_STEEPEST_DECENT 1.0E-4
private static final int DEFAULT_MAX_NUM_EVALUATIONS_WOLF_SEARCH 10
private static final int DEFAULT_MAX_NUM_KICK_STARTS 3
public static final int DEFAULT_NUM_STEP_STEEPEST_DECENT 50
private static final double DEFAULT_STEP_SIZE_EXPENTION_STEEPEST_DECENT 2.0
private static final double DEFAULT_STEP_SIZE_REDUCTION_STEEPEST_DECENT 0.5
private final int MAX_NUM_VARIABLES 3000

meshi.optimizers.ConjugateGradient
private static final double DEFAULT_C1 0.0010
private static final double DEFAULT_C2 0.4
private static final double DEFAULT_EXTENDED_ALPHA_FACTOR_WOLF_SEARCH 3.0
private static final int DEFAULT_MAX_ITERATION 100000
private static final int DEFAULT_MAX_NUM_EVALUATIONS_WOLF_SEARCH 10
private static final int DEFAULT_REPORT_EVERY 10
private static final int DEFAULT_RESTART_EVERY 0
private static final double DEFAULT_TOLERANCE 1.0E-5

meshi.optimizers.LBFGS
private static final int DEFAULT_ALLOWED_MAX_R_FACTOR 100
private static final double DEFAULT_C1 1.0E-4
private static final double DEFAULT_C2 0.9
private static final double DEFAULT_EXTENDED_ALPHA_FACTOR_WOLF_SEARCH 3.0
private static final double DEFAULT_INIT_STEP_STEEPEST_DECENT 1.0E-8
private static final int DEFAULT_M 20
private static final int DEFAULT_MAX_NUM_EVALUATIONS_WOLF_SEARCH 100
private static final int DEFAULT_MAX_NUM_KICK_STARTS 5
public static final int DEFAULT_NUM_STEP_STEEPEST_DECENT 500
private static final double DEFAULT_STEP_SIZE_EXPENTION_STEEPEST_DECENT 1.1
private static final double DEFAULT_STEP_SIZE_REDUCTION_STEEPEST_DECENT 0.5
private static final boolean DEFAULT_USE_GAMA true

meshi.optimizers.LineSearchException
public static final int NOT_A_DESCENT_DIRECTION 1
public static final int WEIRD_INPUT_TO_FIND_STEP_LENGTH 0
public static final int WOLF_CONDITION_NOT_MET 2

meshi.optimizers.Minimizer
public final int MAX_KICKSTARTS 1000

meshi.optimizers.SimpleStepLength
private final double INFINITY 1d/0d

meshi.optimizers.SteepestDecent
private static final double DEFAULT_INITIAL_STEP_LENGTH 1.0E-8
private static final int DEFAULT_MAX_ITERATION 100000
private static final int DEFAULT_REPORT_EVERY 1
private static final double DEFAULT_STEP_SIZE_EXPENTION 1.1
private static final double DEFAULT_STEP_SIZE_REDUCTION 0.5
private static final double DEFAULT_TOLERANCE 1.0E-5

meshi.optimizers.WolfConditionLineSearch
private final double interSafeGuardFactor 20.0

meshi.parameters.*

meshi.parameters.MeshiPotential
public static final java.lang.String ACCESSIBLE "ACCESSIBLE"
public static final java.lang.String ALPHA_ANGLE_PARAMETERS "meshiPotential/alphaRangeParameters.dat"
public static final java.lang.String ALPHA_TORSION_PARAMETERS "meshiPotential/alphaTorsionRangeParameters.dat"
public static final java.lang.String ANGLE_PARAMETERS "meshiPotential/angleEnergyParameters.dat"
public static final java.lang.String ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS "meshiPotential/PairwiseAtomicPMF_summa_5.5.dat"
public static final java.lang.String BOND_PARAMETERS "meshiPotential/bondEnergyParameters.dat"
public static final java.lang.String BURIED "BURIED"
public static final java.lang.String COIL "COIL"
public static final java.lang.String COMPOSITE_PROPENSITY_2D_PARAMETERS "meshiPotential/CompositePropensity2D_withPP.dat"
public static final java.lang.String COMPOSITE_PROPENSITY_2D_WITH_PP_PARAMETERS "meshiPotential/CompositePropensity2D_withPP.dat"
public static final java.lang.String COMPOSITE_PROPENSITY_PARAMETERS "meshiPotential/CompositePropensity2D.dat"
public static final java.lang.String COMPOSITE_TORSIONS_PARAMETERS "meshiPotential/CompositeTorsionsParameters.dat"
public static final java.lang.String CONTACTS_ENVIRONMENT_PARAMETERS "meshiPotential/contactsEnvironment.dat"
public static final java.lang.String CONTACTS_PARAMETERS "meshiPotential/contactsParameters.dat"
public static final java.lang.String COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS "meshiPotential/PairwiseAtomicPMF_summa_5.5.cooperative.dat"
public static final java.lang.String COOPERATIVE_PROPENSITY_PARAMETERS "meshiPotential/cooperativePropensity.dat"
public static final java.lang.String COOPERATIVE_RAMACHANDRAN_PARAMETERS "meshiPotential/CooperativeRamachandran.dat"
public static final java.lang.String ELECTROSTATICS_PARAMETERS "meshiPotential/ElectrostaticParameters.dat"
public static final java.lang.String EXCLUDED_VOL_PARAMETERS "meshiPotential/ExcludedVolumeParameters.dat"
public static final java.lang.String HELIX "HELIX"
public static final java.lang.String HELIX_OR_COIL "HELIX_OR_COIL"
public static final java.lang.String HYDROGEN_BONDS_PAIRS_BETA_PARAMETERS "meshiPotential/HydrogenBondsBetaParameters.dat"
public static final java.lang.String HYDROGEN_BONDS_PAIRS_HELIX_PARAMETERS "meshiPotential/HydrogenBondsHelixParameters.dat"
public static final java.lang.String HYDROGEN_BONDS_PAIRS_PARAMETERS_SURFACE "meshiPotential/HydrogenBondsParameters.surface.dat"
public static final java.lang.String LENNARD_JONES_PARAMETERS "meshiPotential/LennardJonesParameters.dat"
public static final java.lang.String LENNARD_JONES_PARAMETERS_BACKBONE "meshiPotential/LennardJonesParametersBackbone.dat"
public static final java.lang.String LENNARD_JONES_PARAMETERS_CA "meshiPotential/LennardJonesParametersCa.dat"
public static final java.lang.String LJ_ENVIRONMENT_PARAMETERS "meshiPotential/LJEnvironment.dat"
public static final java.lang.String LJ_ENVIRONMENT_PARAMETERS_BACKBONE "meshiPotential/LJEnvironmentBackbone.dat"
public static final java.lang.String LJ_ENVIRONMENT_PARAMETERS_CA "meshiPotential/LJEnvironmentCa.dat"
public static final java.lang.String OUT_OF_PLANE_PARAMETERS "meshiPotential/outOfPlaneEnergyParameters.dat"
public static final java.lang.String PLANE_PARAMETERS "meshiPotential/planeEnergyParameters.dat"
public static final java.lang.String SHEET "SHEET"
public static final java.lang.String SHEET_OR_COIL "SHEET_OR_COIL"

meshi.sequences.*

meshi.sequences.Sequence
public static final char UNKNOWN 95

meshi.sequences.SequenceAlignmentCell
public static final char GAP_CHAR 45
public static final char WILDCARD_CHAR 88

meshi.symmetryComplex.*

meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
private static final int NUM_DIMENSIONS 3

meshi.symmetryComplex.molecularImageElements.SymmetricComplex
private static final java.lang.String CHAIN_LETTERS "ABCDEFGHIJKLMNOPQRSTUVWXYZ"

meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner
public static final double CA_CA_DISTANCE 3.8
public static final double CA_CA_DISTANCE2 14.44
public final int nLoops 2

meshi.symmetryComplex.proteinsGJ.GJModeller
protected static final double DISTANCE_AS_NEIGHBOUR_CHAINS 10.0

meshi.symmetryComplex.proteinsGJ.RunBackboneCompleterAndMinimizer
public static final java.lang.String NAME "RunBackboneCompleterAndMinimizer"

meshi.symmetryComplex.proteinsGJ.RunBackboneMCM
public static final java.lang.String NAME "RunGJBackboneMCM"

meshi.symmetryComplex.proteinsGJ.RunFullModeller
public static final java.lang.String NAME "RunFullGJModeller"

meshi.symmetryComplex.topologyMap.Topology
private final java.lang.String LOOP "loop"

meshi.symmetryComplex.transformations.Matrix1D
private static final double EPSILON 1.0E-4

meshi.symmetryComplex.utils.GJUtils
public static final double RELATIVE_ORIENTATION 43.0

meshi.util.*

meshi.util.AttributesRack
public static final int MAX_ATTRIBUTES 20

meshi.util.GDTcalculator
public static final double maximal_distance 4.9
public static final int num_of_loops 20
public static final int SUB 4

meshi.util.MeshiAttribute
public static final int BEAUTIFY_ATTRIBUTE 12
public static final int CN_ATTRIBUTE 3
public static final int DISTANCE_FROM_CATALYTIC_ATTRIBUTE 11
public static final int EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE 1
public static final int GAUSSIAN_ALPHA 9
public static final int GAUSSIAN_ATTRIBUTE 8
public static final int HYDROGEN_BONDS_ATTRIBUTE 2
public static final int LENNARD_JONES_ELEMENT_ATTRIBUTE 0
public static final int LOOP_RESIDUE 13
public static final int ORIGINAL_ATOM 14
public static final int RESIDUE_ATTRIBUTE 7
public static final int RESIDUE_TORSIONS_ATTRIBUTE 18
public static final int SECONDARY_STRUCTURE_ATTRIBUTE 10
public static final int SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE 4
public static final int SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE 16
public static final int SOLVATE_ALL_ATOM_ATTRIBUTE 5
public static final int SOLVATE_CA_ATTRIBUTE 6
public static final int SOLVATE_ROT1_ATTRIBUTE 15
public static final int SUMMA_ATTRIBUTE 17

Overview  Package  Class  Tree  Deprecated  Index  Help 
 PREV   NEXT FRAMES    NO FRAMES