forcefield
Class Bonds

java.lang.Object
  forcefield.Bonds

public class Bonds

extends java.lang.Object

The Bonds class contains all the Bond information from the sytem.

Since:

0.1

Version:

0.2, August 2005

Author:

Mika Kastenholz, Vincent Kraeutler

Field Summary

double[]	b0 Ideal bond length of bond[num].
java.lang.String[]	bt String of the BondType.
int[]	I Atom i of bond[num].
int[]	J Atom j of bond[num].
double[]	Kb Force constant of bond[num].
int	number Number of Bonds in the object.

Constructor Summary

Bonds(int num)
The Bonds class contructor.

Method Summary

void	atomsboundto(int atom, java.util.ArrayList boundto, java.util.ArrayList bl) Determine the other atoms which are bound to a specified atom
Bonds	copies(int numCopies, int numAtoms)
Bonds	join(Bonds bonds, int numAtoms) Join this set of bonds with a set of bonds of another molecule.
Bonds	subset(int[] atomNumbers, int numAtoms) generate a new set of those bonds which only connect the atoms we're interested in.

Methods inherited from class java.lang.Object

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

Field Detail

number

public int number

Number of Bonds in the object.

I

public int[] I

Atom i of bond[num].

J

public int[] J

Atom j of bond[num].

Kb

public double[] Kb

Force constant of bond[num].

b0

public double[] b0

Ideal bond length of bond[num].

bt

public java.lang.String[] bt

String of the BondType.

Constructor Detail

Bonds

public Bonds(int num)

The Bonds class contructor.

Parameters:

num - number of Bonds to be added

See Also:

Bonds, BondType

Method Detail

copies

public Bonds copies(int numCopies,
                    int numAtoms)

Parameters:

numCopies -

numAtoms - the number of atoms in this molecule

Returns:

a new set of Bonds

See Also:

Particles.copy(int)

subset

public Bonds subset(int[] atomNumbers,
                    int numAtoms)

generate a new set of those bonds which only connect the atoms we're interested in. the new bonds have atom numbers reflecting the supplied atom numbers, i.e. if I[bb] == atomNumbers[ii], is the first matching bond, then subset(..).I[0] == ii. clear? hmm. let me put it differently. if you have a list of atoms atomNumbers, and you do particles.subset(atomNumbers), giving you a new set of particles, then bonds.subset(atomNumbers, particles.number) will give you the new set of bonds involving just atomNumbers with the correct numbering with respect to the new set of particles.

Parameters:

atomNumbers - the sorted list of atom numbers

numAtoms - the original number of atoms

Returns:

a new set of Bonds

See Also:

Particles.subset(int[])

join

public Bonds join(Bonds bonds,
                  int numAtoms)

Join this set of bonds with a set of bonds of another molecule.

Parameters:

bonds - the bonds in the other molecule

numAtoms - the atom number offset (i.e. zero for identical molecules, otherwise the number of atoms in this molecule)

Returns:

a new set of Bonds

See Also:

Particles.join(Particles)

atomsboundto

public void atomsboundto(int atom,
                         java.util.ArrayList boundto,
                         java.util.ArrayList bl)

Determine the other atoms which are bound to a specified atom

Parameters:

atom - (atom to determine bonded atoms with)

boundto - (ArrayList with bonded atoms)

bl - (bond length of bonded atoms)