meshi.energy.hydrogenBond
Class HydrogenBondsParametersList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Parameters>
              meshi.energy.simpleEnergyTerms.ParametersList
                  meshi.energy.hydrogenBond.LennardJonesParametersList
                      meshi.energy.hydrogenBond.HydrogenBondsParametersList

All Implemented Interfaces:

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

public class HydrogenBondsParametersList
extends LennardJonesParametersList

See Also:

Serialized Form

Field Summary

(package private) AtomList

nitrogens

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

HydrogenBondsParametersList(java.lang.String parametersFileName)

HydrogenBondsParametersList(java.lang.String parametersFileName, AtomList nitrogens)

Method Summary

Parameters	createParameters(java.lang.String line) Energy term specific method to create a Parameters object from a line of the parameters file.
AtomList	nitrogens()
Parameters	parameters(java.lang.Object obj) 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

nitrogens

AtomList nitrogens

Constructor Detail

HydrogenBondsParametersList

public HydrogenBondsParametersList(java.lang.String parametersFileName,
                                   AtomList nitrogens)

HydrogenBondsParametersList

public HydrogenBondsParametersList(java.lang.String parametersFileName)

Method Detail

parameters

public Parameters parameters(java.lang.Object obj)

Description copied from class: ParametersList

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

Overrides:

parameters in class LennardJonesParametersList

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.

Overrides:

createParameters in class LennardJonesParametersList

nitrogens

public AtomList nitrogens()

Returns:

nitrogens