core
Class Particles

java.lang.Object
  core.Particles

public class Particles

extends java.lang.Object

A flat container of atomic properties. lookup tables i.e. for single-center interaction parameters.

Since:

0.1

Version:

0.1, November 2002

Author:

Mika Kastenholz, Vincent Kraeutler

See Also:

SimSystem, InTopoG96.Topology, G96SolventTopology, InteractionParameters

Field Summary

int[]	anum Number of Particle i in Topology.
int[]	boundaryAtoms Last atom[m] i of Molecule m in Topology.
double[]	charge Charge of Particle i.
int[]	chgrp Charge Group of Particle i in Topology.
int[]	IAC Integer Atom Code (IAC) of Particle i in Topology.
double[]	mass Mass of Particle i.
int[]	molecule Molecule number of Particle i in Topology.
java.lang.String[]	name Particle name of Particle i in Topology.
int	number Total Number of solute Particles.
int	numMolecules Number of Molecules in Topology.
int	numResidues Total Number of residues.
double[][]	pos The atomic positions.
double[]	radius The atomic radii.
java.lang.String[]	rname Residue name of Particle i in Topology.
int[]	rnum Residue number of Particle i in Topology.
double[]	SASA The SASA of atoms i.
double[]	SASAweight The SASA weight.

Constructor Summary

Particles()

Particles(int num)

Method Summary

Particles	copy(int numCopies) Generate a (multiple) of the particles.
int[]	getAtomsByMoleculeNumber(int moleculeNumber)
int[]	getAtomsByResidueName(java.lang.String residueName)
int[]	getAtomsByResidueNumber(int residueNumber)
Particles	join(Particles particles) Joins two sets of particles.
Particles	subset(int[] indices) Select a subset of particles.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

number

public int number

Total Number of solute Particles.

numResidues

public int numResidues

Total Number of residues.

anum

public int[] anum

Number of Particle i in Topology. Fortran indexing vs. C/Java indexing, so we just add 1.

rnum

public int[] rnum

Residue number of Particle i in Topology. Watch out, Fortran indexing!.

name

public java.lang.String[] name

Particle name of Particle i in Topology.

rname

public java.lang.String[] rname

Residue name of Particle i in Topology.

IAC

public int[] IAC

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

numMolecules

public int numMolecules

Number of Molecules in Topology.

molecule

public int[] molecule

Molecule number of Particle i in Topology.

boundaryAtoms

public int[] boundaryAtoms

Last atom[m] i of Molecule m in Topology.

mass

public double[] mass

Mass of Particle i.

charge

public double[] charge

Charge of Particle i.

chgrp

public int[] chgrp

Charge Group of Particle i in Topology.

pos

public double[][] pos

The atomic positions.

radius

public double[] radius

The atomic radii.

SASAweight

public double[] SASAweight

The SASA weight.

SASA

public double[] SASA

The SASA of atoms i.

Constructor Detail

Particles

public Particles()

Particles

public Particles(int num)

Parameters:

num - the number of atoms

Method Detail

copy

public Particles copy(int numCopies)

Generate a (multiple) of the particles.

Parameters:

numCopies -

Returns:

a new set of particles consisting of numCopies copies of this set

join

public Particles join(Particles particles)

Joins two sets of particles.

Parameters:

particles - the other set of particles

Returns:

a new set, containing the union of both sets

subset

public Particles subset(int[] indices)

Select a subset of particles.

Parameters:

indices - (sorted)

Returns:

a new set of particles

getAtomsByResidueNumber

public int[] getAtomsByResidueNumber(int residueNumber)

Parameters:

residueNumber -

Returns:

all atoms of that residue

getAtomsByResidueName

public int[] getAtomsByResidueName(java.lang.String residueName)

Parameters:

residueName -

Returns:

all atoms of that residue

getAtomsByMoleculeNumber

public int[] getAtomsByMoleculeNumber(int moleculeNumber)

Parameters:

moleculeNumber -

Returns:

all atoms of that molecule