meshi.energy.simpleEnergyTerms.compositeTorsions
Class ResidueTorsionsList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<ResidueTorsions>
              meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList

All Implemented Interfaces:

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

public class ResidueTorsionsList
extends java.util.ArrayList<ResidueTorsions>
implements Updateable

An updateable list of ResidueTorsions.

See Also:

Serialized Form

Nested Class Summary

static class	ResidueTorsionsList.CompleteResidueFilter
static class	ResidueTorsionsList.IncompleteResidueFilter
static class	ResidueTorsionsList.PhiPsiResidueFilter

Field Summary

(package private) int

numberOfUpdates

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ResidueTorsionsList()

ResidueTorsionsList(Protein protein, DistanceMatrix dm)
Creates ResidueTorsionsList from protein.

Method Summary

ResidueTorsionsList	filterCompleteResidues() A method to filter residues that have all torsions
ResidueTorsionsList	filterIncompleteResidues() A method to filter for incomplete residues.
ResidueTorsionsList	filterPhiPsiResidues() A method to filter residues that have {PHI,PSI} torsions.
ResidueTorsions	findResidueInList(int num)
private void	tagPreProline() A method to tag as Pre-Proline all the residues that are such.
void	update(int numberOfUpdates)

Methods inherited from class java.util.ArrayList

add, 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, iterator, 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, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

numberOfUpdates

int numberOfUpdates

Constructor Detail

ResidueTorsionsList

public ResidueTorsionsList()

ResidueTorsionsList

public ResidueTorsionsList(Protein protein,
                           DistanceMatrix dm)

Creates ResidueTorsionsList from protein.

Method Detail

update

public void update(int numberOfUpdates)
            throws UpdateableException

Specified by:

update in interface Updateable

Throws:

UpdateableException

filterPhiPsiResidues

public ResidueTorsionsList filterPhiPsiResidues()

A method to filter residues that have {PHI,PSI} torsions. This method removes residues at chain termini or Ca traces, but keeps incomplete residues.

filterIncompleteResidues

public ResidueTorsionsList filterIncompleteResidues()

A method to filter for incomplete residues. Note that the resulting list CONTAINS all the INCOMPLETE residues of the protein. It is inverse of the filterCompleteResidues() method.

filterCompleteResidues

public ResidueTorsionsList filterCompleteResidues()

A method to filter residues that have all torsions

tagPreProline

private void tagPreProline()

A method to tag as Pre-Proline all the residues that are such.

findResidueInList

public ResidueTorsions findResidueInList(int num)