meshi.applications.prediction
Class AbitSmarterLoopBuilder.Loop

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Residue>
              meshi.molecularElements.ResidueList
                  meshi.applications.prediction.AbitSmarterLoopBuilder.Loop

All Implemented Interfaces:

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

Enclosing class:

AbitSmarterLoopBuilder

private static class AbitSmarterLoopBuilder.Loop
extends ResidueList

Nested Class Summary

private static class

AbitSmarterLoopBuilder.Loop.End

Nested classes/interfaces inherited from class meshi.molecularElements.ResidueList

ResidueList.NonDummyFilter

Field Summary

private double	clashDistance
private int	nTrys
private int	optimalNumberOfClashes
private int	rank

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

AbitSmarterLoopBuilder.Loop(double clashDistance, int optimalNumberOfClashes, int nTrys)

Method Summary

boolean	assignCoordinates(Protein protein, int fromI, int assignMeI, int toI)
void	build(Protein protein)
void	build(Protein protein, int first, int last, AbitSmarterLoopBuilder.Loop.End flag)
private static int	getClashes(Atom atom, java.util.ArrayList<Atom> neighbors, double clashDistance)
int	rank()

Methods inherited from class meshi.molecularElements.ResidueList

atoms, filter, print, residue, sort, toString

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

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

clashDistance

private double clashDistance

optimalNumberOfClashes

private int optimalNumberOfClashes

nTrys

private int nTrys

rank

private int rank

Constructor Detail

AbitSmarterLoopBuilder.Loop

public AbitSmarterLoopBuilder.Loop(double clashDistance,
                                   int optimalNumberOfClashes,
                                   int nTrys)

Method Detail

build

public void build(Protein protein)

build

public void build(Protein protein,
                  int first,
                  int last,
                  AbitSmarterLoopBuilder.Loop.End flag)

assignCoordinates

public boolean assignCoordinates(Protein protein,
                                 int fromI,
                                 int assignMeI,
                                 int toI)

getClashes

private static int getClashes(Atom atom,
                              java.util.ArrayList<Atom> neighbors,
                              double clashDistance)

rank

public int rank()