meshi.energy.hydrogenBondsPairs
Class HydrogenBondsPairsParametersList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Parameters>
              meshi.energy.simpleEnergyTerms.ParametersList
                  meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Parameters>, java.util.Collection<Parameters>, java.util.List<Parameters>, java.util.RandomAccess

Direct Known Subclasses:

BetaParametersList, HelixParametersList

public abstract class HydrogenBondsPairsParametersList
extends ParametersList

See Also:

Serialized Form

Nested Class Summary

private static class

HydrogenBondsPairsParametersList.NoElements

Field Summary

private Parameters	nonExsisting
int	searchCounter

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

HydrogenBondsPairsParametersList()

HydrogenBondsPairsParametersList(java.lang.String parametersFileName)

Method Summary

Parameters	createParameters(java.lang.String line) Energy term specific method to create a Parameters object from a line of the parameters file.
Parameters	getKey(java.lang.Object baseElement)
Parameters	parameters(java.lang.Object baseElement) Energy term specific method to fetch parameters for the interactions between a st of atoms.

Methods inherited from class meshi.energy.simpleEnergyTerms.ParametersList

add, getParameters, iterator, sort

Methods inherited from class java.util.ArrayList

add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

nonExsisting

private final Parameters nonExsisting

searchCounter

public int searchCounter

Constructor Detail

HydrogenBondsPairsParametersList

public HydrogenBondsPairsParametersList()

HydrogenBondsPairsParametersList

public HydrogenBondsPairsParametersList(java.lang.String parametersFileName)

Method Detail

parameters

public Parameters parameters(java.lang.Object baseElement)

Description copied from class: ParametersList

Energy term specific method to fetch parameters for the interactions between a st of atoms.

Specified by:

parameters in class ParametersList

getKey

public Parameters getKey(java.lang.Object baseElement)

Parameters:

baseElement - should be instance of PairOfHydrogenBondsElements

Returns:

HydrogenBondsPairsParameters with 6 values to use un serching the freqency value

createParameters

public Parameters createParameters(java.lang.String line)

Description copied from class: ParametersList

Energy term specific method to create a Parameters object from a line of the parameters file.

Specified by:

createParameters in class ParametersList