A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

P

P1 - Variable in class energy.Bornradii_STILL

P2 - Variable in class energy.Bornradii_STILL

P3 - Variable in class energy.Bornradii_STILL

P4 - Variable in class energy.Bornradii_STILL

P5 - Variable in class energy.Bornradii_STILL

PBC - class core.pbc.PBC.

PBC (Periodic Boundary Condition).

PBC(String) - Constructor for class core.pbc.PBC

Vacuum is he vanilla periodic boundary condition.

PBC.ByMoleculeGatherer - class core.pbc.PBC.ByMoleculeGatherer.

PBC.ByMoleculeGatherer() - Constructor for class core.pbc.PBC.ByMoleculeGatherer

PBC.CoGGatherer - class core.pbc.PBC.CoGGatherer.

PBC.CoGGatherer() - Constructor for class core.pbc.PBC.CoGGatherer

PBC.G96Gatherer - class core.pbc.PBC.G96Gatherer.

PBC.G96Gatherer() - Constructor for class core.pbc.PBC.G96Gatherer

PBC.Gatherer - interface core.pbc.PBC.Gatherer.

PBC.InBoxGatherer - class core.pbc.PBC.InBoxGatherer.

gathers all molecules first individually and moves them afterwards into the central box.

PBC.InBoxGatherer() - Constructor for class core.pbc.PBC.InBoxGatherer

PBC_RectBox - class core.pbc.PBC_RectBox.

Reconstructs systems from PBC that use rectangular box boundary conditions.

PBC_RectBox(String) - Constructor for class core.pbc.PBC_RectBox

PBC_TruncOct - class core.pbc.PBC_TruncOct.

reconstructs systems from PBC that use truncated octahedron boundary conditions.

PBC_TruncOct(String) - Constructor for class core.pbc.PBC_TruncOct

PBboundary - Variable in class energy.FDPoissonBoltzmann

PBcrgGrid - Variable in class energy.FDPoissonBoltzmann

PBeps - Variable in class energy.FDPoissonBoltzmann

PD - Variable in class forcefield.DihedralType

PD - Variable in class forcefield.Dihedrals

Phase shift of dihedral-angle torsion[num].

PDBAtomFormatter - class io.pdb.PDBAtomFormatter.

PDBAtomFormatter() - Constructor for class io.pdb.PDBAtomFormatter

PDBTitleFormatter - class io.pdb.PDBTitleFormatter.

PDBTitleFormatter() - Constructor for class io.pdb.PDBTitleFormatter

PI - Variable in class energy.FDPoissonBoltzmann_Boundary

Particles - class core.Particles.

A flat container of atomic properties.

Particles() - Constructor for class core.Particles

Particles(int) - Constructor for class core.Particles

PfF - Variable in class io.g96.out.OutTopoG96

Pffloat - Variable in class energy.FD_WriteGrid

Pfint - Variable in class energy.FD_WriteGrid

PositionUtils - class energy.PositionUtils.

PositionUtils() - Constructor for class energy.PositionUtils

The PositionsUtils class constructor.

PrintfFormat - class contrib.PrintfFormat.

PrintfFormat allows the formatting of an array of objects embedded within a string.

PrintfFormat(String) - Constructor for class contrib.PrintfFormat

Constructs an array of control specifications possibly preceded, separated, or followed by ordinary strings.

PrintfFormat(Locale, String) - Constructor for class contrib.PrintfFormat

Constructs an array of control specifications possibly preceded, separated, or followed by ordinary strings.

PrintfFormat.ConversionSpecification - class contrib.PrintfFormat.ConversionSpecification.

ConversionSpecification allows the formatting of a single primitive or object embedded within a string.

PrintfFormat.ConversionSpecification() - Constructor for class contrib.PrintfFormat.ConversionSpecification

Constructor.

PrintfFormat.ConversionSpecification(String) - Constructor for class contrib.PrintfFormat.ConversionSpecification

Constructor for a conversion specification.

parallelBetaBridgeT - Static variable in class conformation.Dssp

parallelBetaSheetT - Static variable in class conformation.Dssp

parameters - Variable in class io.g96.in.InTopoG96.Topology

parse(String[]) - Method in class io.args.ArgumentParser

parses an array of strings, doing cross checks against defined arguments and defined argument values.

parseAngleBlock(ArrayList, Hashtable) - Static method in class io.g96.in.InTopoG96

parseArgs(String[]) - Static method in class programs.pb_protligand

parseAtomTypeNameBlock(ArrayList, InteractionParameters) - Static method in class io.g96.in.InTopoG96

parseBondAngleTypeBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseBondBlock(ArrayList, Hashtable) - Static method in class io.g96.in.InTopoG96

parseBondTypeBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseBoxBlock(ArrayList) - Method in class io.g96.in.InCorG96

Parse the (BOX) block and put the stuff into box.

parseDihedralBlock(ArrayList, Hashtable) - Static method in class io.g96.in.InTopoG96

parseDihedralTypeBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseDoubleArray(String[]) - Static method in class io.g96.in.InBlock

parse an array of doubles from an array of strings, one double per string.

parseDoubleArray(String) - Static method in class io.g96.in.InBlock

parse an array of doubles from a string.

parseDoubleArray(String, int) - Static method in class io.g96.in.InBlock

parseDoubleMatrix(String[], int) - Static method in class io.g96.in.InBlock

parse an matrix of doubles from an array of strings, nCols doubles per line.

parseEnergyBlock(ArrayList) - Static method in class io.g96.in.InEnergiesG96

parseExclusionLine(String[], int, ArrayList) - Static method in class io.g96.in.InTopoG96

Parse the remaining exclusions from an array of Strings.

parseGenBoxBlock(ArrayList) - Method in class io.g96.in.InCorG96

Parse the (GENBOX) block and put the stuff into box.

parseImpDihedralTypeBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseImproperBlock(ArrayList, Hashtable) - Static method in class io.g96.in.InTopoG96

parseLJBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseParticles() - Method in class io.mol2.InMol2

Parses atom information from mol2 file into a Particles object, which are then returned.

parsePositionBlock(ArrayList) - Static method in class io.g96.in.InCorG96

parsePositionredBlock(ArrayList) - Static method in class io.g96.in.InCorG96

parseResNameBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseSoluteAtomBlock(ArrayList, ArrayList, SimSystem) - Static method in class io.g96.in.InTopoG96

parseSolventAtomBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseSolventConstraintBlock(ArrayList) - Static method in class io.g96.in.InTopoG96

parseSystem() - Method in class io.mol2.InMol2

Parses system information from mol2 file into a SimSystem object, which are then returned.

parseTimeStepBlock(ArrayList) - Method in class io.g96.in.InCorG96

Parse a Gromos96 TIMESTEP block.

parseTopPhysConBlock(ArrayList, SimSystem) - Static method in class io.g96.in.InTopoG96

parseTopVersionBlock(ArrayList, InteractionParameters) - Static method in class io.g96.in.InTopoG96

particles() - Method in class core.G96SolventTopology

particles - Variable in class io.g96.in.InTopoG96.Topology

pattern - Variable in class io.args.ArgumentValueSpec

pb_protligand - class programs.pb_protligand.

pb_protligand() - Constructor for class programs.pb_protligand

pbc - Variable in class energy.FD_WriteGrid

pbcGatherPattern - Static variable in class io.args.ArgumentChecker

pbcPattern - Static variable in class io.args.ArgumentChecker

pciccg(double[], double[], double[], double[], double[], double[]) - Method in class energy.FDPoissonBoltzmann_ICCG

pciccg(double[], double[], double[], double[], double[], double[]) - Method in class energy.FDPoissonBoltzmann_ICCG_NPBC

perm - Variable in class contrib.CBZip2InputStream

phi - Variable in class energy.Bornradii_STILL

phigrid - Variable in class energy.FDPoissonBoltzmann

phigrid[GPX*GPY*GPZ] will become the solution vector when solving for the electrostatic potential

piHelixT - Static variable in class conformation.Dssp

placeHolderFormat - Static variable in class io.pdb.PDBAtomFormatter

plusAntiClinalType - Static variable in class conformation.AlkaneDihedrals

plusSynClinalType - Static variable in class conformation.AlkaneDihedrals

pos - Variable in class contrib.PrintfFormat.ConversionSpecification

Position within the control string.

pos - Variable in class core.Particles

The atomic positions.

pos - Variable in class io.g96.G96Frame

positionFormatter - Static variable in class io.g96.out.OutPosG96

positionalFieldWidth - Variable in class contrib.PrintfFormat.ConversionSpecification

positionalPrecision - Variable in class contrib.PrintfFormat.ConversionSpecification

positionalSpecification - Variable in class contrib.PrintfFormat.ConversionSpecification

positionredFormatter - Variable in class io.g96.out.OutTrajG96

precision - Variable in class contrib.PrintfFormat.ConversionSpecification

The minimum number of digits to appear for the d, i, o, u, x, or X conversions.

precisionSet - Variable in class contrib.PrintfFormat.ConversionSpecification

Flag indicating whether or not the precision has been set.

printBondBlock(String, Bonds) - Method in class io.g96.out.OutTopoG96

printCFormat(char) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the c conversion character and char argument.

printDFormat(short) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the d conversion specifer and short argument.

printDFormat(long) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the d conversion character and long argument.

printDFormat(int) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the d conversion character and int argument.

printDFormat(String) - Method in class contrib.PrintfFormat.ConversionSpecification

Utility method for formatting using the d conversion character.

printEFormat(double) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the e or E conversion character.

printFFormat(double) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the f conversion character.

printGFormat(double) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the g conversion character.

printOFormat(short) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the o conversion character and short argument.

printOFormat(long) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the o conversion character and long argument.

printOFormat(int) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the o conversion character and int argument.

printOFormat(String) - Method in class contrib.PrintfFormat.ConversionSpecification

Utility method for formatting using the o conversion character.

printSFormat(String) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the s conversion character and String argument.

printStatistics(Particles, HydrogenBonds.HBDefinitions, HydrogenBonds.HBTrajectoryStats, double) - Static method in class io.g96.out.HBondFormatter

Print the hydrogen bonding statistics in Gromos96 block format.

printTsFrame(boolean[], double) - Static method in class io.g96.out.HBondFormatter

Print a frame of the hydrogen bond time series.

printXFormat(short) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the x conversion character and short argument.

printXFormat(long) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the x conversion character and long argument.

printXFormat(int) - Method in class contrib.PrintfFormat.ConversionSpecification

Format method for the x conversion character and int argument.

printXFormat(String) - Method in class contrib.PrintfFormat.ConversionSpecification

Utility method for formatting using the x conversion character.

printangle(String, Angles) - Method in class io.g96.out.OutTopoG96

printdih(String, Dihedrals) - Method in class io.g96.out.OutTopoG96

printimpdih(String, ImproperDihedrals) - Method in class io.g96.out.OutTopoG96

println(String) - Method in class io.g96.out.OutTopoG96

proberadius - Variable in class energy.FDPoissonBoltzmann_Parameters

progname - Variable in class io.args.ArgumentParser

programs - package programs

put(int, int, boolean) - Method in class forcefield.DenseExclusions

set an exclusion

put(int, int, boolean) - Method in class forcefield.LJ14HashMap

put(int, int, LJType) - Method in class forcefield.LJTypeHashMap

put(ArgumentDescription) - Method in class io.args.ArgumentParser

Add another argument description

pw - Variable in class energy.FD_WriteGrid

pw - Variable in class io.g96.out.OutTopoG96