meshi.geometry
Class TorsionList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Torsion>
              meshi.geometry.TorsionList

All Implemented Interfaces:

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

Direct Known Subclasses:

QuickAndDirtyTorsionList

public class TorsionList
extends java.util.ArrayList<Torsion>
implements Updateable

See Also:

Serialized Form

Nested Class Summary

static class	TorsionList.FilterChi1
static class	TorsionList.FilterChi2
static class	TorsionList.FilterChi3
static class	TorsionList.FilterChi4
static class	TorsionList.FilterOOP
static class	TorsionList.FilterPhi
static class	TorsionList.FilterPsi
static class	TorsionList.FilterSideChain

Field Summary

private int

numberOfUpdates

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

TorsionList()
An Torsion list based on a angle list

TorsionList(AngleList angles, DistanceMatrix distanceMatrix)

Method Summary

AtomList	atomList()
TorsionList	chi1Filter() Returns a sub-list that is accepted by the parameter
static TorsionList	createQuickAndDirtyTorsionList(Protein protein, DistanceMatrix distanceMatrix)
static TorsionList	createTorsionList(Protein protein, DistanceMatrix distanceMatrix)
boolean	equivalentExists(Torsion findMe)
TorsionList	filter(Filter filter)
TorsionList	filterEquivalents()
void	freeze()
Torsion	getTorsion(Angle angle1, Angle angle2, DistanceMatrix distanceMatrix)
static boolean	isChi1(Torsion torsion)
static boolean	isChi2(Torsion torsion)
static boolean	isChi3(Torsion torsion)
static boolean	isChi4(Torsion torsion)
static boolean	isChi5(Torsion torsion)
static boolean	isCimp(Torsion torsion)
static boolean	isNamed(Torsion torsion)
static boolean	isNimp(Torsion torsion)
static boolean	isOmega(Torsion torsion)
static boolean	isOOP(Torsion torsion)
static boolean	isPhi(Torsion torsion)
static boolean	isPsi(Torsion torsion)
TorsionList	namedFilter() Returns a sub-list that is has a known name
Torsion	torsionAt(int i)
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

TorsionList

public TorsionList()

An Torsion list based on a angle list

TorsionList

public TorsionList(AngleList angles,
                   DistanceMatrix distanceMatrix)

Method Detail

getTorsion

public Torsion getTorsion(Angle angle1,
                          Angle angle2,
                          DistanceMatrix distanceMatrix)

update

public void update(int numberOfUpdates)
            throws UpdateableException

Specified by:

update in interface Updateable

Throws:

UpdateableException

torsionAt

public Torsion torsionAt(int i)

atomList

public AtomList atomList()

equivalentExists

public boolean equivalentExists(Torsion findMe)

filterEquivalents

public TorsionList filterEquivalents()

chi1Filter

public TorsionList chi1Filter()

Returns a sub-list that is accepted by the parameter

namedFilter

public TorsionList namedFilter()

Returns a sub-list that is has a known name

isNamed

public static boolean isNamed(Torsion torsion)

isPhi

public static boolean isPhi(Torsion torsion)

isPsi

public static boolean isPsi(Torsion torsion)

isOmega

public static boolean isOmega(Torsion torsion)

isCimp

public static boolean isCimp(Torsion torsion)

isNimp

public static boolean isNimp(Torsion torsion)

isChi1

public static boolean isChi1(Torsion torsion)

isChi2

public static boolean isChi2(Torsion torsion)

isChi3

public static boolean isChi3(Torsion torsion)

isChi4

public static boolean isChi4(Torsion torsion)

isChi5

public static boolean isChi5(Torsion torsion)

isOOP

public static boolean isOOP(Torsion torsion)

createTorsionList

public static TorsionList createTorsionList(Protein protein,
                                            DistanceMatrix distanceMatrix)

createQuickAndDirtyTorsionList

public static TorsionList createQuickAndDirtyTorsionList(Protein protein,
                                                         DistanceMatrix distanceMatrix)

freeze

public void freeze()

filter

public TorsionList filter(Filter filter)