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

G

G96BoxFormatter - class io.g96.out.G96BoxFormatter.

G96BoxFormatter() - Constructor for class io.g96.out.G96BoxFormatter

G96Frame - class io.g96.G96Frame.

G96Frame() - Constructor for class io.g96.G96Frame

G96GenericFormatter - class io.g96.out.G96GenericFormatter.

A class for writing generic block contents.

G96GenericFormatter() - Constructor for class io.g96.out.G96GenericFormatter

G96PositionFormatter - class io.g96.out.G96PositionFormatter.

G96PositionFormatter() - Constructor for class io.g96.out.G96PositionFormatter

G96PositionredFormatter - class io.g96.out.G96PositionredFormatter.

G96PositionredFormatter() - Constructor for class io.g96.out.G96PositionredFormatter

G96SolventTopology - class core.G96SolventTopology.

a place where to put solvent topology stuff from the g96 topology file.

G96SolventTopology() - Constructor for class core.G96SolventTopology

G96SolventTopology(int) - Constructor for class core.G96SolventTopology

G96TimestepFormatter - class io.g96.out.G96TimestepFormatter.

G96TimestepFormatter() - Constructor for class io.g96.out.G96TimestepFormatter

G96TitleFormatter - class io.g96.out.G96TitleFormatter.

G96TitleFormatter() - Constructor for class io.g96.out.G96TitleFormatter

G96radii(Particles, SimSystem) - Static method in class energy.PositionUtils

GPX - Static variable in class energy.FDPoissonBoltzmann

number of grid points along X.

GPX - Variable in class energy.FDPoissonBoltzmann_ICCG_NPBC

GPX - Variable in class energy.FDPoissonBoltzmann_Parameters

GPX - Variable in class energy.FD_WriteGrid

GPXGPY - Variable in class energy.FDPoissonBoltzmann

GPXGPY - Variable in class energy.FDPoissonBoltzmann_ICCG_NPBC

GPXGPYGPZ - Variable in class energy.FDPoissonBoltzmann

GPXGPYGPZ - Variable in class energy.FDPoissonBoltzmann_ICCG_NPBC

GPY - Static variable in class energy.FDPoissonBoltzmann

number of grid points along Y.

GPY - Variable in class energy.FDPoissonBoltzmann_ICCG_NPBC

GPY - Variable in class energy.FDPoissonBoltzmann_Parameters

GPY - Variable in class energy.FD_WriteGrid

GPZ - Static variable in class energy.FDPoissonBoltzmann

number of grid points along Z.

GPZ - Variable in class energy.FDPoissonBoltzmann_ICCG_NPBC

GPZ - Variable in class energy.FDPoissonBoltzmann_Parameters

GPZ - Variable in class energy.FD_WriteGrid

G_SIZE - Static variable in interface contrib.BZip2Constants

Geometry - class esraMath.Geometry.

Geometry() - Constructor for class esraMath.Geometry

GeometryTest - class esraMath.GeometryTest.

GeometryTest() - Constructor for class esraMath.GeometryTest

g96Comment - Static variable in class io.g96.out.HBondFormatter

gather(double[][], int[], double[]) - Method in class core.pbc.PBC

gatherMethod - Variable in class core.pbc.PBC

Comment for gatherMethod

gatherPattern - Static variable in class io.args.ArgumentChecker

gaucheMinusType - Static variable in class conformation.AlkaneDihedrals

gauchePlusType - Static variable in class conformation.AlkaneDihedrals

get(int, int) - Method in class forcefield.DenseExclusions

get an exclusions

get(int, int) - Method in class forcefield.LJ14HashMap

get(int, int) - Method in class forcefield.LJTypeHashMap

getAndMoveToFrontDecode() - Method in class contrib.CBZip2InputStream

getArgs(String[]) - Method in class io.args.ArgumentGetter

Generate a HashMap from a String[] of arguments.

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

read the argument data from various sources (argument vector, or file).

getArgumentPosition() - Method in class contrib.PrintfFormat.ConversionSpecification

getArgumentPositionForFieldWidth() - Method in class contrib.PrintfFormat.ConversionSpecification

getArgumentPositionForPrecision() - Method in class contrib.PrintfFormat.ConversionSpecification

getAtomNumbers(String[], Particles) - Static method in class core.AtomSpecifier

Same as getAtomNumbers(ArrayList, Particles), but returns int[] rather than an ArrayList of Integer objects.

getAtomNumbers(ArrayList, Particles) - Static method in class core.AtomSpecifier

Same as getAtomNumbers(ArrayList, Particles), but returns int[] rather than an ArrayList of Integer objects.

getAtomNumbers(String, Particles) - Static method in class core.AtomSpecifier

Same as getAtomsNumbers(ArrayList, Particles), but takes a String rather than an ArrayList of Strings.

getAtoms(ArrayList, ArrayList, ArrayList, ArrayList, ArrayList, Particles) - Static method in class core.AtomSpecifier

Go over all atoms in the first molecule and see if they conform to an atomPattern (atomNumbers and atomNames) (if any) and a residuePattern (residueNumbers and residueNames) (if any) and return those that do.

getAtoms(String, Particles) - Static method in class core.AtomSpecifier

Parses an atomSpecifier string, generating an ArrayList of atom numbers (Integer objects).

getAtoms(String[], Particles) - Static method in class core.AtomSpecifier

Parses an ArrayList of atomSpecifier Strings, by iteratively calling getAtoms(String, Particles).

getAtomsByMoleculeNumber(int) - Method in class core.Particles

getAtomsByResidueName(String) - Method in class core.Particles

getAtomsByResidueNumber(int) - Method in class core.Particles

getBackboneCoords(double[][], int[][]) - Static method in class conformation.Dssp

get the coords of the backbone atoms.

getBlocks(ArrayList) - Method in class io.g96.in.InBlock

read blocks until all blocks corresponding to the block names have been read.

getBoundaryAtoms(int[]) - Static method in class io.g96.in.InTopoG96

Find the last atom of each molecule.

getConversionCharacter() - Method in class contrib.PrintfFormat.ConversionSpecification

Get the conversion character that tells what type of control character this instance has.

getDefs(int[], int[], Bonds) - Static method in class conformation.HydrogenBonds

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge and Mathematica's J/Link.

getDefs(int) - Static method in class conformation.HydrogenBonds

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge and Mathematica's J/Link.

getDihedralType(double) - Static method in class conformation.AlkaneDihedrals

getFinalCRC() - Method in class contrib.CRC

getFrame(boolean) - Method in class io.g96.in.InCorG96

Read all the blocks we need to have a valid frame.

getFrameStats(int) - Static method in class conformation.HydrogenBonds

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge.

getGlobalCRC() - Method in class contrib.CRC

getHBDefinitions(HashMap, Particles, Bonds) - Static method in class io.g96.out.HBondFormatter

Get the hydrogen bond definitions from various sources (command line options etc.).

getLiteral() - Method in class contrib.PrintfFormat.ConversionSpecification

Get the String for this instance.

getNextBlock() - Method in class io.g96.in.InBlock

getPbc(String, String) - Static method in class core.pbc.PBC

simple pbc selector.

getTestParticles() - Method in class conformation.DsspTest

getTrajStats(int) - Static method in class conformation.HydrogenBonds

Needed to avoid some uglyness regarding nested classes in the Jython/Java bridge.

getWriter(String, String) - Static method in class io.TrajectoryWriter

Get a trajectory writer for a given output format.

getbornradii() - Method in class energy.Bornradii_STILL

getdG() - Method in class energy.FDPoissonBoltzmann

getgpol() - Method in class energy.Bornradii_STILL

getgridstart() - Method in class energy.FDPoissonBoltzmann

getpotential() - Method in class energy.FDPoissonBoltzmann

globalCrc - Variable in class contrib.CRC

gpol - Variable in class energy.Bornradii_STILL

gpol() - Method in class energy.Energy_GBorn

gpxgpygpz - Variable in class energy.FDPoissonBoltzmann_ChargeGrid

The PoissonBoltzmann class constructor.

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

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

gridDensities3D(double[], double[], int[], double[][], double[]) - Static method in class esraMath.Statistics

gridcenterX - Variable in class energy.FDPoissonBoltzmann_Parameters

gridcenterY - Variable in class energy.FDPoissonBoltzmann_Parameters

gridcenterZ - Variable in class energy.FDPoissonBoltzmann_Parameters

gridcheck() - Method in class energy.FDPoissonBoltzmann

static final void gridcheck checks whether any atom exceeds the grid

gridspacing - Static variable in class energy.FDPoissonBoltzmann

gridspacing @f$ h @f$

gridspacing - Variable in class energy.FDPoissonBoltzmann_Parameters

gridstart - Static variable in class energy.FDPoissonBoltzmann

grid origin