meshi.molecularElements
Class Chain

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

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:

ImageChain, Pdb2Fasta.MyChain

public class Chain
extends ResidueList

A list of residues of the same chain. Note that some of the residues may be dummy. Specifically, the first residue may be dummy in order to be compatible with the biologists convention that the first residue is 1 (they grew up on FORTRAN). Residue positions in the list are equal to their residue number. Holes are filed by DummyResidue objects

See Also:

Serialized Form

Nested Class Summary

(package private) static class

Chain.IsResidue

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

ResidueList.NonDummyFilter

Field Summary

static java.lang.String	GENERIC_CHAIN_NAME
java.lang.String	name The first Non Dummy Residue (may but also may not be number 1).
Protein	protein

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Chain(AtomList atomList, ResidueCreator creator, Protein protein)
Constructs a Chain from a list of atoms.

Chain(AtomList atomList, ResidueCreator creator, java.lang.String chainName, Protein protein)
Constructs a Chain from a list of atoms.

Chain(AtomList atomList, ResidueCreator creator, java.lang.String chainName, Protein protein, MolecularSystem current, MolecularSystem newms)

Chain(Sequence sequence, ResidueCreator creator, Protein protein)
Constructs a Chain from a sequence (a string of one letter codes).

Chain(Sequence sequence, ResidueCreator creator, java.lang.String chainName, Protein protein)
Constructs a Chain from a sequence (a string of one letter codes).

Chain(java.lang.String name, Protein protein)
Empty list.

Method Summary

void	assertChain() Asserts that this chain is comprised of residues with the same chain string.
AtomList	atoms()
private void	createAndAddResidue(ResidueCreator creator, AtomList newAtomList, ResidueMode mode)
ResidueList	filter(Filter residueFilter) Extracts the residues accepted by the filter.
Residue	firstNonDummyResidue()
private static AtomList	getCaAtomList(char c, Coordinates coordinates)
ResidueList	missingResidues()
java.lang.String	name()
AtomList	nowhereAtoms()
int	numberOfNonDummyResidues()
Residue	residue(ResidueIdentifier residueID) Fetches a residue by its residue identifier.
Residue	residueAt(int index) Fetch a residue by its position in the list.
ResidueSequence	sequence()
java.lang.String	toString()

Methods inherited from class meshi.molecularElements.ResidueList

print, sort

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

name

public final java.lang.String name

The first Non Dummy Residue (may but also may not be number 1).

GENERIC_CHAIN_NAME

public static final java.lang.String GENERIC_CHAIN_NAME

See Also:

Constant Field Values

protein

public final Protein protein

Constructor Detail

Chain

public Chain(java.lang.String name,
             Protein protein)

Empty list.

Chain

public Chain(Sequence sequence,
             ResidueCreator creator,
             Protein protein)

Constructs a Chain from a sequence (a string of one letter codes). The residueCreator is responsible for the interpretation of the letters to actual residues and thus determines the molecular model.

Chain

public Chain(Sequence sequence,
             ResidueCreator creator,
             java.lang.String chainName,
             Protein protein)

Constructs a Chain from a sequence (a string of one letter codes). The residueCreator is responsible for the interpretation of the letters to actual residues and thus determines the molecular model.

Chain

public Chain(AtomList atomList,
             ResidueCreator creator,
             Protein protein)

Constructs a Chain from a list of atoms. The residueCreator allows the use of information that is not stored in the atoms themselves. Note that the chain is going to havewill get a genergic name.

Chain

public Chain(AtomList atomList,
             ResidueCreator creator,
             java.lang.String chainName,
             Protein protein)

Constructs a Chain from a list of atoms. The residueCreator allows the use of information that is not stored in the atoms themselves.

Chain

public Chain(AtomList atomList,
             ResidueCreator creator,
             java.lang.String chainName,
             Protein protein,
             MolecularSystem current,
             MolecularSystem newms)

Method Detail

name

public final java.lang.String name()

getCaAtomList

private static AtomList getCaAtomList(char c,
                                      Coordinates coordinates)

createAndAddResidue

private void createAndAddResidue(ResidueCreator creator,
                                 AtomList newAtomList,
                                 ResidueMode mode)

residueAt

public Residue residueAt(int index)

Fetch a residue by its position in the list.

residue

public Residue residue(ResidueIdentifier residueID)

Fetches a residue by its residue identifier.

Overrides:

residue in class ResidueList

filter

public ResidueList filter(Filter residueFilter)

Extracts the residues accepted by the filter.

Overrides:

filter in class ResidueList

numberOfNonDummyResidues

public int numberOfNonDummyResidues()

toString

public java.lang.String toString()

Overrides:

toString in class ResidueList

sequence

public ResidueSequence sequence()

atoms

public AtomList atoms()

Overrides:

atoms in class ResidueList

assertChain

public void assertChain()

Asserts that this chain is comprised of residues with the same chain string.

Throws:

MeshiException - if the assertion fails.

missingResidues

public ResidueList missingResidues()

nowhereAtoms

public AtomList nowhereAtoms()

firstNonDummyResidue

public Residue firstNonDummyResidue()