meshi.energy.hydrogenBond
Class HBondList

java.lang.Object
  meshi.geometry.DistanceList
      meshi.energy.hydrogenBond.HBdistanceList
          meshi.energy.hydrogenBond.HBondList

All Implemented Interfaces:

java.lang.Iterable<Distance>, Updateable

public class HBondList
extends HBdistanceList
implements Updateable

Nested Class Summary

(package private) static class	HBondList.IsAlive
(package private) static class	HBondList.IsWithInRmax
private class	HBondList.WithinRmaxIterator

Field Summary

private int	countUpdates
int	deletionFromList
private DistanceMatrix	distanceMatrix
private GoodResiduesForHB	goodResiduesForHB
protected static HBdistanceList	inputNewHBList
int	insertionToList
private HBondList.IsAlive	isAlive
protected DistanceList	newhBondList
private int	numberOfUpdates
private int	oldSize to find easily the last element that was in this list before the new update
private HydrogenBondsParametersList	parametersList
private java.util.ArrayList<java.lang.Integer>	relevantRows
private int	UPDATE_EVERY_X_STEPS

Fields inherited from class meshi.geometry.DistanceList

capacity, filter, internalArray, size

Constructor Summary

HBondList(DistanceMatrix distanceMatrix, HydrogenBondsParametersList parametersList)

HBondList(DistanceMatrix distanceMatrix, HydrogenBondsParametersList parametersList, DistanceList specialDistances)

Method Summary

void	cleanList_dm() save only the live elements in this list
int	countUpdates()
int	getOldSize()
static HBdistanceList	inputNewHBList()
DistanceList	newhBondList()
java.util.Iterator	newWithinRmaxIterator()
private void	update_dm()
private void	update()
void	update(int numberOfUpdates)
private void	updateTwoLists(HBdistanceList atomPairList)
java.util.Iterator	withinRmaxIterator()

Methods inherited from class meshi.geometry.DistanceList

add, clear, get, isEmpty, iterator, size, sort, toArray

Methods inherited from class java.lang.Object

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

Field Detail

insertionToList

public int insertionToList

deletionFromList

public int deletionFromList

UPDATE_EVERY_X_STEPS

private final int UPDATE_EVERY_X_STEPS

See Also:

Constant Field Values

newhBondList

protected DistanceList newhBondList

inputNewHBList

protected static HBdistanceList inputNewHBList

relevantRows

private java.util.ArrayList<java.lang.Integer> relevantRows

parametersList

private HydrogenBondsParametersList parametersList

distanceMatrix

private DistanceMatrix distanceMatrix

numberOfUpdates

private int numberOfUpdates

countUpdates

private int countUpdates

goodResiduesForHB

private GoodResiduesForHB goodResiduesForHB

isAlive

private final HBondList.IsAlive isAlive

oldSize

private int oldSize

to find easily the last element that was in this list before the new update

Constructor Detail

HBondList

public HBondList(DistanceMatrix distanceMatrix,
                 HydrogenBondsParametersList parametersList)

Parameters:

distanceMatrix -

HBondList

public HBondList(DistanceMatrix distanceMatrix,
                 HydrogenBondsParametersList parametersList,
                 DistanceList specialDistances)

Method Detail

getOldSize

public final int getOldSize()

newhBondList

public final DistanceList newhBondList()

inputNewHBList

public static HBdistanceList inputNewHBList()

countUpdates

public final int countUpdates()

update

public void update(int numberOfUpdates)

Specified by:

update in interface Updateable

update

private void update()

updateTwoLists

private void updateTwoLists(HBdistanceList atomPairList)

Parameters:

atomPairList - of new distances that where added after HbondList was updated in the last time

update_dm

private void update_dm()

newWithinRmaxIterator

public java.util.Iterator newWithinRmaxIterator()

cleanList_dm

public void cleanList_dm()

save only the live elements in this list

withinRmaxIterator

public java.util.Iterator withinRmaxIterator()