meshi.symmetryComplex.geometryImage
Class DistanceMatrixNoImageAtoms

java.lang.Object
  meshi.util.MeshiProgram
      meshi.geometry.DistanceMatrix
          meshi.symmetryComplex.geometryImage.DistanceMatrixNoImageAtoms

All Implemented Interfaces:

Updateable

public class DistanceMatrixNoImageAtoms
extends DistanceMatrix

Nested Class Summary

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

DistanceMatrix.Indicator

Field Summary

private DistanceMatrix.Indicator

indicatorToUpdateHB

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, numberOfUpdates, rMax, rMax2, rMaxPlusBuffer, rMaxPlusBuffer2, terminator

Fields inherited from class meshi.util.MeshiProgram

commandLine, name

Constructor Summary

DistanceMatrixNoImageAtoms(MolecularSystem molecularSystem, double rMax, double buffer, double edge, int bondedListDepth, ResidueList imageResidues)

Method Summary

private void	reset()
protected void	update()

Methods inherited from class meshi.geometry.DistanceMatrix

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

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

indicatorToUpdateHB

private DistanceMatrix.Indicator indicatorToUpdateHB

Constructor Detail

DistanceMatrixNoImageAtoms

public DistanceMatrixNoImageAtoms(MolecularSystem molecularSystem,
                                  double rMax,
                                  double buffer,
                                  double edge,
                                  int bondedListDepth,
                                  ResidueList imageResidues)

Method Detail

reset

private void reset()

update

protected void update()
               throws UpdateableException

Overrides:

update in class DistanceMatrix

Throws:

UpdateableException