Package etomica.association

Class AssociationHelperMolecule

java.lang.Object

etomica.association.AssociationHelperMolecule

All Implemented Interfaces:

IAssociationHelperMolecule

public class AssociationHelperMolecule
extends java.lang.Object
implements IAssociationHelperMolecule

AssociationHelperBranched is capable of populating a list of molecules in an smer within a simulation with multiple association sites per molecule. The number of sites per molecule can be set, but ought to be at least 3 (AssociationManagerSingle or AssociationManagerDouble are more efficient for single-site and double-site bonding). With at least 3 sites, branching can occur and is handled by this class. AssociationHelperBranched verifies that each atom has (at most) maxBonds bonds and that all atoms bonded to a single atom have a minimum distance from each other, which ensures that none of the atoms are bonded to the same site of the central atom. AssociationHelperBranched does not attempt to verify that bonding information is consistent.

Field Summary

Fields

Modifier and Type	Field	Description
protected AssociationManagerMolecule	associationManager
protected Boundary	boundary
protected Vector	dr
protected int	maxBonds
protected double	minR2

Constructor Summary

Constructors

Constructor	Description
AssociationHelperMolecule(Space space, Box box, AssociationManagerMolecule associationManager)

Method Summary

Modifier and Type	Method	Description
int	getMaxBonds()
double	getMinBondedMoleculeDistance()
protected boolean	populate(MoleculeArrayList smerList, IMolecule molecule, boolean mightBeBroken)
boolean	populateList(MoleculeArrayList smerList, IMolecule molecule, boolean mightBeBroken)	Populates smerList with all molecules in the smer that contains molecule.
void	setMaxBonds(int newMaxBonds)
void	setMinBondedMoleculeDistance(double newDistance)
protected boolean	validateBondList(IMolecule molecule, IMoleculeList bondList, boolean mightBeBroken)	Returns false if invalid bonding is recognized

Methods inherited from class java.lang.Object

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

Field Detail

associationManager

protected final AssociationManagerMolecule associationManager

maxBonds

protected int maxBonds

boundary

protected final Boundary boundary

minR2

protected double minR2

dr

protected final Vector dr

Constructor Detail

AssociationHelperMolecule

public AssociationHelperMolecule(Space space,
                                 Box box,
                                 AssociationManagerMolecule associationManager)

Method Detail

setMaxBonds

public void setMaxBonds(int newMaxBonds)

getMaxBonds

public int getMaxBonds()

setMinBondedMoleculeDistance

public void setMinBondedMoleculeDistance(double newDistance)

getMinBondedMoleculeDistance

public double getMinBondedMoleculeDistance()

populateList

public boolean populateList(MoleculeArrayList smerList,
                            IMolecule molecule,
                            boolean mightBeBroken)

Description copied from interface: IAssociationHelperMolecule

Populates smerList with all molecules in the smer that contains molecule. If mightBeBroken is false, an exception is throw if any invalid bonding is encountered (along with potentially useful information about the invalid bonding). If mightBeBroken is true, then populateList returns true if any invalid bonding is encountered. populateList returns false if invalid bonding is not encountered.

Specified by:

populateList in interface IAssociationHelperMolecule

populate

protected boolean populate(MoleculeArrayList smerList,
                           IMolecule molecule,
                           boolean mightBeBroken)

validateBondList

protected boolean validateBondList(IMolecule molecule,
                                   IMoleculeList bondList,
                                   boolean mightBeBroken)

Returns false if invalid bonding is recognized