meshi.geometry
Class DistanceMatrixBondedOnly

java.lang.Object
  meshi.util.MeshiProgram
      meshi.geometry.DistanceMatrix
          meshi.geometry.DistanceMatrixBondedOnly

All Implemented Interfaces:

Updateable

public class DistanceMatrixBondedOnly
extends DistanceMatrix

Nested Class Summary

private class

DistanceMatrixBondedOnly.DistanceComparator

Nested classes/interfaces inherited from class meshi.geometry.DistanceMatrix

DistanceMatrix.Indicator

Field Summary

private static double	d2
private Distance[]	distanceArray
private static double	dx
private static double	dy
private static double	dz
private int	numberOfUpdates

Fields inherited from class meshi.geometry.DistanceMatrix

bondedList, bondedListDepth, buffer, bufferOneThirdSqr, debug, DEFAULT_BONDED_LIST_DEPTH, DEFAULT_BUFFER, DEFAULT_RMAX, edge, energyTermsDistanceLists, grid, matrix, molecularSystem, nonBondedList, rMax, rMax2, rMaxPlusBuffer, rMaxPlusBuffer2, terminator

Fields inherited from class meshi.util.MeshiProgram

commandLine, name

Constructor Summary

DistanceMatrixBondedOnly(MolecularSystem molecularSystem, int bondedListDepth)

Method Summary

Distance	distance(Atom atom1, Atom atom2) Returns the Distance object of the parameters.
Distance	distance(AtomPair atomPair)
Distance	distance(int atom1Number, int atom2Number) Returns the Distance object of the parameters.
static AtomList	getBonded(Atom atom, int depth)
static void	getBonded(Atom atom, int depth, AtomList out, int rootNumber)
static DistanceList	getBondedList(MolecularSystem molecularSystem, int depth)
private void	reset()
void	testNonBondedList()
java.lang.String	toString()
protected void	update()
void	update(int numberOfUpdates) Updates the distance matrix.

Methods inherited from class meshi.geometry.DistanceMatrix

bondedList, buffer, DebugOFF, debugON, DEFAULT_EDGE, doNotUpdateNonBondedList, energyTermsDistanceLists, getBondedList, indicatorToUpdateHB, nonBondedList, nonBondedListSize, radius, rMax, rMax2, rMaxPlusBuffer, rMaxPlusBuffer2, rowIterator, rowNumber

Methods inherited from class meshi.util.MeshiProgram

about, debug, get2ndString, getb, getB, getd, getD, getFlag, getFlagedArgument, geti, getI, getOrderedArgument, getS, getS, initRandom, initRandom, initRandom, printGlobalTable, randomNumberGenerator, seed, tableGet, tableIncludes, tableSet, verbose

Methods inherited from class java.lang.Object

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

Field Detail

dx

private static double dx

dy

private static double dy

dz

private static double dz

d2

private static double d2

numberOfUpdates

private int numberOfUpdates

distanceArray

private Distance[] distanceArray

Constructor Detail

DistanceMatrixBondedOnly

public DistanceMatrixBondedOnly(MolecularSystem molecularSystem,
                                int bondedListDepth)

Method Detail

reset

private void reset()

getBondedList

public static DistanceList getBondedList(MolecularSystem molecularSystem,
                                         int depth)

getBonded

public static AtomList getBonded(Atom atom,
                                 int depth)

getBonded

public static void getBonded(Atom atom,
                             int depth,
                             AtomList out,
                             int rootNumber)

update

public void update(int numberOfUpdates)
            throws UpdateableException

Updates the distance matrix.

Specified by:

update in interface Updateable

Overrides:

update in class DistanceMatrix

Throws:

UpdateableException

update

protected void update()
               throws UpdateableException

Overrides:

update in class DistanceMatrix

Throws:

UpdateableException

distance

public Distance distance(Atom atom1,
                         Atom atom2)

Returns the Distance object of the parameters.

Overrides:

distance in class DistanceMatrix

distance

public Distance distance(AtomPair atomPair)

Overrides:

distance in class DistanceMatrix

distance

public Distance distance(int atom1Number,
                         int atom2Number)

Description copied from class: DistanceMatrix

Returns the Distance object of the parameters.

Overrides:

distance in class DistanceMatrix

toString

public java.lang.String toString()

Overrides:

toString in class DistanceMatrix

testNonBondedList

public void testNonBondedList()