Package ffx.algorithms.optimize

Class TitrationManyBody

java.lang.Object

ffx.algorithms.optimize.TitrationManyBody

public class TitrationManyBody
extends Object

Constructor Summary

Constructors

Constructor	Description
TitrationManyBody(String filename, ForceField forceField, List<Integer> resNumberList, double pH)
TitrationManyBody(String filename, ForceField forceField, List<Integer> resNumberList, double pH, ManyBodyOptions manyBodyOptions)

Method Summary

Modifier and Type	Method	Description
boolean	excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, MolecularAssembly molecularAssembly, List<Residue> residueList)
boolean	excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, List<Residue> residueList)
Set<Atom>	getExcludeAtoms()
MolecularAssembly[]	getProtonatedAssemblies()
MolecularAssembly	getProtonatedAssembly()
void	setExcludeAtoms(Set<Atom> excludeAtoms)

Methods inherited from class java.lang.Object

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

Constructor Details

TitrationManyBody

public TitrationManyBody(String filename,
 ForceField forceField,
 List<Integer> resNumberList,
 double pH)

TitrationManyBody

public TitrationManyBody(String filename,
 ForceField forceField,
 List<Integer> resNumberList,
 double pH,
 ManyBodyOptions manyBodyOptions)

Method Details

getExcludeAtoms

public Set<Atom> getExcludeAtoms()

setExcludeAtoms

public void setExcludeAtoms(Set<Atom> excludeAtoms)

getProtonatedAssembly

public MolecularAssembly getProtonatedAssembly()

getProtonatedAssemblies

public MolecularAssembly[] getProtonatedAssemblies()

excludeExcessAtoms

public boolean excludeExcessAtoms(Set<Atom> excludeAtoms,
 int[] optimalRotamers,
 List<Residue> residueList)

excludeExcessAtoms

public boolean excludeExcessAtoms(Set<Atom> excludeAtoms,
 int[] optimalRotamers,
 MolecularAssembly molecularAssembly,
 List<Residue> residueList)