meshi.geometry
Class DistanceMatrixCaOnly

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

All Implemented Interfaces:

Updateable

public class DistanceMatrixCaOnly
extends DistanceMatrix

A Distance Matrix specifically tailored for Calpha model. It is O(N2) but takes into account the geometrical constrains of CA model. If the chain is not very long, it may run much faster than the assimptotically more efficient

Nested Class Summary

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

DistanceMatrix.Indicator

Field Summary

private static int

counter

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

DistanceMatrixCaOnly(MolecularSystem molecularSystem, double rMax, int bondedListDepth)

Method Summary

void	refresh()
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, distance, distance, distance, doNotUpdateNonBondedList, energyTermsDistanceLists, getBonded, getBonded, 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

counter

private static int counter

Constructor Detail

DistanceMatrixCaOnly

public DistanceMatrixCaOnly(MolecularSystem molecularSystem,
                            double rMax,
                            int bondedListDepth)

Method Detail

refresh

public void refresh()

reset

private void reset()

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

testNonBondedList

public void testNonBondedList()

toString

public java.lang.String toString()

Overrides:

toString in class DistanceMatrix