starfish.chemistry
Class Compound

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

All Implemented Interfaces:

java.io.Serializable, starfish.star.STAR3Processor

Direct Known Subclasses:

Residue

public class Compound
extends Entity

See Also:

Serialized Form

Field Summary

protected java.util.HashMap	atoms
static java.lang.String[]	chemCompAtomLoopStrings
static java.lang.String[]	chemCompBondLoopStrings
static java.lang.String[]	chemCompEntityIndexLoopStrings
int	iRes
int	labelNum
java.lang.String	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

protected	Compound()
	Compound(java.lang.String number, java.lang.String name)
	Compound(java.lang.String number, java.lang.String name, java.lang.String label)

Method Summary

void	addAtom(Atom atom)
Atom	getAtom(java.lang.String name)
java.util.ArrayList<Atom>	getAtoms(java.lang.String match)
int	getIDNum()
java.lang.String	getName()
java.lang.String	getNumber()
int	renameAtom(java.lang.String oldName, java.lang.String newName)
void	updateFromSTAR3ChemComp(tcl.lang.Interp interp, starfish.star.Saveframe saveframe)
void	updateNames()
void	writeCompoundToSTAR3(tcl.lang.Interp interp, java.lang.String chanName, int entityID)
void	writeEntityHeaderSTAR3(tcl.lang.Interp interp, java.lang.String chanName, int entityID)

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

atoms

protected java.util.HashMap atoms

number

public java.lang.String number

iRes

public int iRes

labelNum

public int labelNum

chemCompEntityIndexLoopStrings

public static java.lang.String[] chemCompEntityIndexLoopStrings

chemCompBondLoopStrings

public static java.lang.String[] chemCompBondLoopStrings

chemCompAtomLoopStrings

public static java.lang.String[] chemCompAtomLoopStrings

Constructor Detail

Compound

protected Compound()

Compound

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

Compound

public Compound(java.lang.String number,
                java.lang.String name,
                java.lang.String label)

Method Detail

getName

public java.lang.String getName()

Overrides:

getName in class Entity

getNumber

public java.lang.String getNumber()

getIDNum

public int getIDNum()

Overrides:

getIDNum in class Entity

addAtom

public void addAtom(Atom atom)

getAtom

public Atom getAtom(java.lang.String name)

getAtoms

public java.util.ArrayList<Atom> getAtoms(java.lang.String match)

renameAtom

public int renameAtom(java.lang.String oldName,
                      java.lang.String newName)

updateNames

public void updateNames()

updateFromSTAR3ChemComp

public void updateFromSTAR3ChemComp(tcl.lang.Interp interp,
                                    starfish.star.Saveframe saveframe)
                             throws tcl.lang.TclException

Throws:

tcl.lang.TclException

writeEntityHeaderSTAR3

public void writeEntityHeaderSTAR3(tcl.lang.Interp interp,
                                   java.lang.String chanName,
                                   int entityID)
                            throws tcl.lang.TclException

Overrides:

writeEntityHeaderSTAR3 in class Entity

Throws:

tcl.lang.TclException

writeCompoundToSTAR3

public void writeCompoundToSTAR3(tcl.lang.Interp interp,
                                 java.lang.String chanName,
                                 int entityID)
                          throws tcl.lang.TclException

Throws:

tcl.lang.TclException