meshi.geometry
Class TorsionPairList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<TorsionPair>
              meshi.geometry.TorsionPairList

All Implemented Interfaces:

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

public class TorsionPairList
extends java.util.ArrayList<TorsionPair>
implements Updateable

A list of torsion pairs, used mainly for the various two torsion energies.

See Also:

Serialized Form

Field Summary

private int

numberOfUpdates

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

TorsionPairList()

TorsionPairList(TorsionList torsions)
A TorsionPair list based on a Torsion list.

Method Summary

static TorsionPairList	createQuickAndDirtyTorsionPairList(Protein protein, DistanceMatrix distanceMatrix)
static TorsionPairList	createQuickAndDirtyTorsionPairList(Protein protein, DistanceMatrix distanceMatrix, Filter torsionsListFilter)
static TorsionPairList	createTorsionPairList(Protein protein, DistanceMatrix distanceMatrix) Create a torsion pair list from a protein.
TorsionPairList	filter(Filter filter)
boolean	sortable()
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

private int numberOfUpdates

Constructor Detail

TorsionPairList

public TorsionPairList()

TorsionPairList

public TorsionPairList(TorsionList torsions)

A TorsionPair list based on a Torsion list. Currently, only torsion pairs from the same residue are considered. Mixed torsion pairs from different residues are not treated nor created. Also, only torsions with known biological names (PHI , CHI1, etc.) are treated.

Method Detail

update

public void update(int numberOfUpdates)
            throws UpdateableException

Specified by:

update in interface Updateable

Throws:

UpdateableException

sortable

public boolean sortable()

createTorsionPairList

public static TorsionPairList createTorsionPairList(Protein protein,
                                                    DistanceMatrix distanceMatrix)

Create a torsion pair list from a protein. Note, that many of the torsion pairs created are considered not relevent, such as {PSI , CHI4}.

createQuickAndDirtyTorsionPairList

public static TorsionPairList createQuickAndDirtyTorsionPairList(Protein protein,
                                                                 DistanceMatrix distanceMatrix)

createQuickAndDirtyTorsionPairList

public static TorsionPairList createQuickAndDirtyTorsionPairList(Protein protein,
                                                                 DistanceMatrix distanceMatrix,
                                                                 Filter torsionsListFilter)

filter

public TorsionPairList filter(Filter filter)