meshi.molecularElements
Class ResidueList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Residue>
              meshi.molecularElements.ResidueList

All Implemented Interfaces:

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

Direct Known Subclasses:

AbitSmarterLoopBuilder.Loop, Chain, HomologyModeling.Loop

public class ResidueList
extends java.util.ArrayList<Residue>

A list of residues.

See Also:

Serialized Form

Nested Class Summary

static class

ResidueList.NonDummyFilter

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ResidueList()

ResidueList(ChainList chains)

Method Summary

AtomList	atoms()
ResidueList	filter(Filter residueFilter) Extracts the residues accepted by the filter.
void	print()
Residue	residue(ResidueIdentifier residueID) Fetches a residue by its residue identifier.
void	sort()
java.lang.String	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

Constructor Detail

ResidueList

public ResidueList()

ResidueList

public ResidueList(ChainList chains)

Method Detail

residue

public Residue residue(ResidueIdentifier residueID)

Fetches a residue by its residue identifier.

filter

public ResidueList filter(Filter residueFilter)

Extracts the residues accepted by the filter.

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<Residue>

atoms

public AtomList atoms()

print

public void print()

sort

public void sort()