starfish.chemistry
Class Entity

java.lang.Object
  starfish.chemistry.Entity

All Implemented Interfaces:

java.io.Serializable, starfish.star.STAR3Processor

Direct Known Subclasses:

Compound, Polymer

public class Entity
extends java.lang.Object
implements java.io.Serializable, starfish.star.STAR3Processor

See Also:

Serialized Form

Field Summary

int	assemblyID
java.lang.String	chemicalExchangeState
java.lang.String	conformationalIsomer
java.util.TreeMap	coordSets
java.lang.String	details
static java.lang.String[]	entityAssemblyLoopStrings
static java.lang.String[]	entityCommonNameLoopStrings
static java.lang.String[]	entityCompIndexLoopStrings
int	entityID
static java.lang.String[]	entityPolySeqLoopStrings
static java.lang.String[]	entityStrings
Atom	firstAtom
Bond	firstBond
java.lang.String	label
Atom	lastAtom
Bond	lastBond
java.lang.String	magneticEquivalenceGroupCode
Molecule	molecule
java.lang.String	name
java.lang.String	physicalState
java.lang.String	role

Constructor Summary

Entity()

Method Summary

void	addCommonName(java.lang.String name, java.lang.String type)
void	addComponents(tcl.lang.Interp interp, starfish.star.Saveframe saveframe, java.util.ArrayList idColumn, java.util.ArrayList authSeqIDColumn, java.util.ArrayList compIDColumn, java.util.ArrayList entityIDColumn, Compound compound)
void	addCoordSet(java.lang.String setName, CoordSet coordSet)
void	finishSaveFrameProcessing(tcl.lang.Interp interp, starfish.star.Saveframe saveframe, Compound compound, java.lang.String mapID)
java.util.TreeMap	getCoordSets()
Atom	getFirstAtom()
int	getIDNum()
java.lang.String	getName()
boolean	hasEquivalentAtoms()
static void	processLoop(starfish.star.STAR3 star3, java.util.List tagList)
void	setHasEquivalentAtoms(boolean state)
void	setIDNum(int entityID)
void	writeEntityCommonNamesSTAR3(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 java.lang.Object

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

Field Detail

entityStrings

public static java.lang.String[] entityStrings

entityAssemblyLoopStrings

public static java.lang.String[] entityAssemblyLoopStrings

entityCommonNameLoopStrings

public static java.lang.String[] entityCommonNameLoopStrings

entityCompIndexLoopStrings

public static java.lang.String[] entityCompIndexLoopStrings

entityPolySeqLoopStrings

public static java.lang.String[] entityPolySeqLoopStrings

name

public java.lang.String name

label

public java.lang.String label

molecule

public Molecule molecule

firstAtom

public Atom firstAtom

lastAtom

public Atom lastAtom

firstBond

public Bond firstBond

lastBond

public Bond lastBond

coordSets

public java.util.TreeMap coordSets

entityID

public int entityID

assemblyID

public int assemblyID

physicalState

public java.lang.String physicalState

conformationalIsomer

public java.lang.String conformationalIsomer

chemicalExchangeState

public java.lang.String chemicalExchangeState

magneticEquivalenceGroupCode

public java.lang.String magneticEquivalenceGroupCode

role

public java.lang.String role

details

public java.lang.String details

Constructor Detail

Entity

public Entity()

Method Detail

getName

public java.lang.String getName()

getIDNum

public int getIDNum()

setIDNum

public void setIDNum(int entityID)

addCommonName

public void addCommonName(java.lang.String name,
                          java.lang.String type)

addCoordSet

public void addCoordSet(java.lang.String setName,
                        CoordSet coordSet)

hasEquivalentAtoms

public boolean hasEquivalentAtoms()

setHasEquivalentAtoms

public void setHasEquivalentAtoms(boolean state)

getFirstAtom

public Atom getFirstAtom()

getCoordSets

public java.util.TreeMap getCoordSets()

addComponents

public void addComponents(tcl.lang.Interp interp,
                          starfish.star.Saveframe saveframe,
                          java.util.ArrayList idColumn,
                          java.util.ArrayList authSeqIDColumn,
                          java.util.ArrayList compIDColumn,
                          java.util.ArrayList entityIDColumn,
                          Compound compound)
                   throws tcl.lang.TclException

Throws:

tcl.lang.TclException

finishSaveFrameProcessing

public void finishSaveFrameProcessing(tcl.lang.Interp interp,
                                      starfish.star.Saveframe saveframe,
                                      Compound compound,
                                      java.lang.String mapID)
                               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

Throws:

tcl.lang.TclException

writeEntityCommonNamesSTAR3

public void writeEntityCommonNamesSTAR3(tcl.lang.Interp interp,
                                        java.lang.String chanName,
                                        int entityID)
                                 throws tcl.lang.TclException

Throws:

tcl.lang.TclException

processLoop

public static void processLoop(starfish.star.STAR3 star3,
                               java.util.List tagList)