starfish.chemistry
Class Residue

java.lang.Object
  starfish.chemistry.Entity
      starfish.chemistry.Compound
          starfish.chemistry.Residue

All Implemented Interfaces:

java.io.Serializable, starfish.star.STAR3Processor

public class Residue
extends Compound

See Also:

Serialized Form

Field Summary

Residue	next
Polymer	polymer
Residue	previous

Fields inherited from class starfish.chemistry.Compound

atoms, chemCompAtomLoopStrings, chemCompBondLoopStrings, chemCompEntityIndexLoopStrings, iRes, labelNum, number

Fields inherited from class starfish.chemistry.Entity

assemblyID, chemicalExchangeState, conformationalIsomer, coordSets, details, entityAssemblyLoopStrings, entityCommonNameLoopStrings, entityCompIndexLoopStrings, entityID, entityPolySeqLoopStrings, entityStrings, firstAtom, firstBond, label, lastAtom, lastBond, magneticEquivalenceGroupCode, molecule, name, physicalState, role

Constructor Summary

Residue(java.lang.String number, java.lang.String name)

Method Summary

void	addAtom(Atom atom)
void	addPseudoAtoms(java.lang.String pseudoAtomName, java.util.ArrayList<java.lang.String> atomGroup)
Atom	getAtom(java.lang.String name)
int	getIDNum()
java.lang.String	getOneLetter()
Atom[]	getPseudo(java.lang.String pseudoName)

Methods inherited from class starfish.chemistry.Compound

getAtoms, getName, getNumber, renameAtom, updateFromSTAR3ChemComp, updateNames, writeCompoundToSTAR3, writeEntityHeaderSTAR3

Methods inherited from class starfish.chemistry.Entity

addCommonName, addComponents, addCoordSet, finishSaveFrameProcessing, getCoordSets, getFirstAtom, hasEquivalentAtoms, processLoop, setHasEquivalentAtoms, setIDNum, writeEntityCommonNamesSTAR3

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

previous

public Residue previous

next

public Residue next

polymer

public Polymer polymer

Constructor Detail

Residue

public Residue(java.lang.String number,
               java.lang.String name)

Method Detail

addAtom

public void addAtom(Atom atom)

Overrides:

addAtom in class Compound

getAtom

public Atom getAtom(java.lang.String name)

Overrides:

getAtom in class Compound

getOneLetter

public java.lang.String getOneLetter()

getIDNum

public int getIDNum()

Overrides:

getIDNum in class Compound

addPseudoAtoms

public void addPseudoAtoms(java.lang.String pseudoAtomName,
                           java.util.ArrayList<java.lang.String> atomGroup)

getPseudo

public Atom[] getPseudo(java.lang.String pseudoName)