core
Class G96SolventTopology

java.lang.Object
  core.G96SolventTopology

public class G96SolventTopology

extends java.lang.Object

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

personally, i think the solvent concept in G96 is a fairly lame performance hack. so i'd suggest to not introduce it in esra and use this class only for topology postprocessing.

Author:

vincent

Field Summary

double[]	charge
Bonds	constraints
int[]	IAC
double[]	mass
java.lang.String[]	name
int	numAtoms

Constructor Summary

G96SolventTopology()

G96SolventTopology(int nn)

Method Summary

Particles	addSolvents(Particles solute, int numSolvents)
Particles	particles()
Particles	solvate(Particles solute, double[][] coords)

Methods inherited from class java.lang.Object

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

Field Detail

numAtoms

public int numAtoms

name

public java.lang.String[] name

IAC

public int[] IAC

mass

public double[] mass

charge

public double[] charge

constraints

public Bonds constraints

Constructor Detail

G96SolventTopology

public G96SolventTopology()

G96SolventTopology

public G96SolventTopology(int nn)

Method Detail

particles

public Particles particles()

addSolvents

public Particles addSolvents(Particles solute,
                             int numSolvents)

solvate

public Particles solvate(Particles solute,
                         double[][] coords)