meshi.geometry
Class QuickAndDirtyAngleList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Angle>
              meshi.geometry.AngleList
                  meshi.geometry.QuickAndDirtyAngleList

All Implemented Interfaces:

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

public class QuickAndDirtyAngleList
extends AngleList

A list of quick and dirty angles. These angles may use approximate angle calculations if ArcCos.useFastArcCos() is called.

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

QuickAndDirtyAngleList()

QuickAndDirtyAngleList(AtomPairList bonds, DistanceMatrix distanceMatrix)

Method Summary

Angle	getAngle(AtomPair atomPair1, AtomPair atomPair2, DistanceMatrix distanceMatrix)
static QuickAndDirtyAngleList	getCaAnglesQuickAndDirty(Protein protein, DistanceMatrix distanceMatrix)
QuickAndDirtyAngleList	namedFilterQD() Returns a sub-list containing angles that have a known name

Methods inherited from class meshi.geometry.AngleList

angleAt, atomList, getCaAngles, isNamed, namedFilter, update

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

Constructor Detail

QuickAndDirtyAngleList

public QuickAndDirtyAngleList()

QuickAndDirtyAngleList

public QuickAndDirtyAngleList(AtomPairList bonds,
                              DistanceMatrix distanceMatrix)

Method Detail

getAngle

public Angle getAngle(AtomPair atomPair1,
                      AtomPair atomPair2,
                      DistanceMatrix distanceMatrix)

Overrides:

getAngle in class AngleList

getCaAnglesQuickAndDirty

public static QuickAndDirtyAngleList getCaAnglesQuickAndDirty(Protein protein,
                                                              DistanceMatrix distanceMatrix)

namedFilterQD

public QuickAndDirtyAngleList namedFilterQD()

Returns a sub-list containing angles that have a known name