starfish.chemistry
Class Polymer

java.lang.Object
  starfish.chemistry.Entity
      starfish.chemistry.Polymer

All Implemented Interfaces:

java.io.Serializable, starfish.star.STAR3Processor

Direct Known Subclasses:

Water

public class Polymer
extends Entity

See Also:

Serialized Form

Field Summary

static java.lang.String[]	entityCompIndexLoopStrings
static java.lang.String[]	entityPolySeqLoopStrings
Residue	firstResidue
Residue	lastResidue
java.util.Hashtable	residues
java.util.Vector	residueVector

Fields inherited from class starfish.chemistry.Entity

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

Constructor Summary

Polymer(java.lang.String name)

Polymer(java.lang.String label, java.lang.String name)

Method Summary

void	addResidue(Residue residue)
void	addResidueOld(Residue residue)
void	finishSaveFrameProcessing(tcl.lang.Interp interp, starfish.star.Saveframe saveframe, java.lang.String nomenclature)
java.lang.String	getNomenclature()
java.lang.String	getOneLetterCode()
java.lang.String	getPolymerType()
Residue	getResidue(int resNum)
Residue	getResidue(java.lang.String name)
java.util.Vector	getResidues()
java.lang.String	getStrandID()
void	removeResidue(Residue residue)
int	renumberResidue(java.lang.String oldNumber, java.lang.String newNumber)
void	setNomenclature(java.lang.String nomenclature)
void	setPolymerType(java.lang.String s)
void	setStrandID(java.lang.String s)
void	writeEntitySeqSTAR3(tcl.lang.Interp interp, java.lang.String chanName, int entityID)

Methods inherited from class starfish.chemistry.Entity

addCommonName, addComponents, addCoordSet, finishSaveFrameProcessing, getCoordSets, getFirstAtom, getIDNum, getName, hasEquivalentAtoms, processLoop, setHasEquivalentAtoms, setIDNum, writeEntityCommonNamesSTAR3, writeEntityHeaderSTAR3

Methods inherited from class java.lang.Object

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

Field Detail

residues

public java.util.Hashtable residues

residueVector

public java.util.Vector residueVector

firstResidue

public Residue firstResidue

lastResidue

public Residue lastResidue

entityCompIndexLoopStrings

public static java.lang.String[] entityCompIndexLoopStrings

entityPolySeqLoopStrings

public static java.lang.String[] entityPolySeqLoopStrings

Constructor Detail

Polymer

public Polymer(java.lang.String name)

Polymer

public Polymer(java.lang.String label,
               java.lang.String name)

Method Detail

addResidueOld

public void addResidueOld(Residue residue)

getResidue

public Residue getResidue(java.lang.String name)

getResidue

public Residue getResidue(int resNum)

addResidue

public void addResidue(Residue residue)

removeResidue

public void removeResidue(Residue residue)

getResidues

public java.util.Vector getResidues()

renumberResidue

public int renumberResidue(java.lang.String oldNumber,
                           java.lang.String newNumber)

getPolymerType

public java.lang.String getPolymerType()

getNomenclature

public java.lang.String getNomenclature()

setNomenclature

public void setNomenclature(java.lang.String nomenclature)

getStrandID

public java.lang.String getStrandID()

setStrandID

public void setStrandID(java.lang.String s)

setPolymerType

public void setPolymerType(java.lang.String s)

getOneLetterCode

public java.lang.String getOneLetterCode()

writeEntitySeqSTAR3

public void writeEntitySeqSTAR3(tcl.lang.Interp interp,
                                java.lang.String chanName,
                                int entityID)
                         throws tcl.lang.TclException

Throws:

tcl.lang.TclException

finishSaveFrameProcessing

public void finishSaveFrameProcessing(tcl.lang.Interp interp,
                                      starfish.star.Saveframe saveframe,
                                      java.lang.String nomenclature)
                               throws tcl.lang.TclException

Throws:

tcl.lang.TclException