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

I

I - Variable in class forcefield.Angles

Atom i of bond-angle[num].

I - Variable in class forcefield.Bonds

Atom i of bond[num].

I - Variable in class forcefield.Dihedrals

Atom i of dihedral-angle torsion[num].

I - Variable in class forcefield.ImproperDihedrals

Atom i of improper dihedral-angle[num].

I - Variable in class forcefield.LJType

IAC - Variable in class core.G96SolventTopology

IAC - Variable in class core.Particles

Integer Atom Code (IAC) of Particle i in Topology.

ImpDihedralType - class forcefield.ImpDihedralType.

The ImpDihedralType class contains all the improper dihedral information from the topology.

ImpDihedralType() - Constructor for class forcefield.ImpDihedralType

ImpDihedralType - Variable in class forcefield.InteractionParameters

HashTable for ImpDihedralType look-up.

ImproperDihedrals - class forcefield.ImproperDihedrals.

The ImproperDihedrals class contains all the improper dihedral information from the sytem.

ImproperDihedrals(int) - Constructor for class forcefield.ImproperDihedrals

The ImproperDihedrals class contructor.

InBlock - class io.g96.in.InBlock.

InBlock() - Constructor for class io.g96.in.InBlock

InBlock(String) - Constructor for class io.g96.in.InBlock

InCorG96 - class io.g96.in.InCorG96.

Read blocks from a final coordinate (POSITION) or a trajectory (POSITIONRED) file until all requirements are fulfilled.

InCorG96() - Constructor for class io.g96.in.InCorG96

InCorG96(String) - Constructor for class io.g96.in.InCorG96

InEnergiesG96 - class io.g96.in.InEnergiesG96.

InEnergiesG96() - Constructor for class io.g96.in.InEnergiesG96

InEnergiesG96(String) - Constructor for class io.g96.in.InEnergiesG96

InEnergiesG96.G96Energies - class io.g96.in.InEnergiesG96.G96Energies.

InEnergiesG96.G96Energies() - Constructor for class io.g96.in.InEnergiesG96.G96Energies

InMol2 - class io.mol2.InMol2.

Created on Feb 22, 2005 see www.tripos.com/data/support/mol2.pdf for format specification.

InMol2() - Constructor for class io.mol2.InMol2

InMol2(String) - Constructor for class io.mol2.InMol2

InMol2Test - class io.mol2.InMol2Test.

InMol2Test() - Constructor for class io.mol2.InMol2Test

InPDB - class io.pdb.InPDB.

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

InPDB(String) - Constructor for class io.pdb.InPDB

InTopoG96 - class io.g96.in.InTopoG96.

The InTopoG96 class reads in a GROMOS96 topology file.

InTopoG96() - Constructor for class io.g96.in.InTopoG96

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

A collection of stuff to hold data read from the topology file.

InTopoG96.Topology() - Constructor for class io.g96.in.InTopoG96.Topology

InTopoG96Test - class io.g96.in.InTopoG96Test.

InTopoG96Test() - Constructor for class io.g96.in.InTopoG96Test

InTrajG96 - class io.g96.in.InTrajG96.

InTrajG96(ArrayList) - Constructor for class io.g96.in.InTrajG96

InTrajG96() - Constructor for class io.g96.in.InTrajG96

InteractionParameters - class forcefield.InteractionParameters.

Purpose: InteractionParameters class Description: The InteractionParameters class contains the topology interaction parameters, stored as Hashtables for type look-up.

InteractionParameters() - Constructor for class forcefield.InteractionParameters

The InteractionParameters class constructor.

InteractionsEnergy - interface energy.InteractionsEnergy.

i - Variable in class contrib.CBZip2InputStream

i2 - Variable in class contrib.CBZip2InputStream

iccg - Variable in class energy.FDPoissonBoltzmann

idht - Variable in class forcefield.ImproperDihedrals

String of the ImproperDihedralType.

idih - Variable in class core.SimSystem

All ImproperDihedrals involving non-hydrogen atoms.

idih - Variable in class energy.Energy_ImpDihedral

idihh - Variable in class core.SimSystem

All ImproperDihedrals involving hydrogen atoms.

idihh - Variable in class energy.Energy_ImpDihedral

in - Variable in class io.g96.in.InTrajG96

inUse - Variable in class contrib.CBZip2InputStream

index(int, int, int) - Method in class energy.FDPoissonBoltzmann

static final int index converts 3D to 1D array index.

index - Variable in class energy.FDPoissonBoltzmann_ICCG_NPBC

index(int, int, int) - Method in class energy.FD_WriteGrid

static final int index converts 3D to 1D array index.

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

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

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

inertiaTensor(double[][], double[]) - Static method in class esraMath.Geometry

Compute the inertia tensor for a set of 3D-coordinates with masses.

init() - Method in class energy.Bornradii_STILL

initBlock() - Method in class contrib.CBZip2InputStream

initialiseCRC() - Method in class contrib.CRC

initialize() - Method in class contrib.CBZip2InputStream

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

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

inspectFrame(HydrogenBonds.HBDefinitions, double[][], double, double) - Static method in class conformation.HydrogenBonds

Looks for hydrogen bonds in the supplied frame.

integerPattern - Static variable in class io.args.ArgumentChecker

interactionsEnergy - Static variable in class energy.Energy

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

Format an int argument using this conversion specification.

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

Format a long argument using this conversion specification.

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

Format a double argument using this conversion specification.

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

Format a String argument using this conversion specification.

internalsprintf(Object) - Method in class contrib.PrintfFormat.ConversionSpecification

Format an Object argument using this conversion specification.

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

invP5 - Variable in class energy.Bornradii_STILL

invert(double[]) - Static method in class esraMath.BLA

{aa1, aa2, -breakiterator} -> { 1 / aa1, 1 / aa2, ...}

invert(double[][]) - Static method in class esraMath.BLA

Naive and slow (but simple) matrix inversion routine ("Complete Gauss-Jordan").

io - package io

io.args - package io.args

io.g96 - package io.g96

io.g96.in - package io.g96.in

io.g96.out - package io.g96.out

io.mol2 - package io.mol2

io.pdb - package io.pdb

io.vmd - package io.vmd

io.xplor - package io.xplor

ionicstrength - Variable in class energy.FDPoissonBoltzmann_Parameters

is - Variable in class io.pdb.InPDB

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

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

isNameToken(String) - Static method in class core.AtomSpecifier

isNumberToken(String) - Static method in class core.AtomSpecifier

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

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

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

isRangeToken(String) - Static method in class core.AtomSpecifier

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

isValidToken(String) - Static method in class core.AtomSpecifier

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

Check whether the specifier has a variable field width that is going to be set by an argument.

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

Check whether the specifier has a variable precision that is going to be set by an argument.

iterativeRotationalFit(double[][], double[][], double[]) - Static method in class esraMath.Fit

DEPRECATED use rotationalFit() instead.

iupac2math(double) - Static method in class esraMath.Geometry

Transform a IUPAC dihedral angle into a dihedral angle following the mathematical standard conventions: a counterclockwise rotation is positive; default ranges go from [0, 2pi]