org.biojava.nbio.structure.io.mmcif

Class ChemCompConsumer

java.lang.Object

org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

All Implemented Interfaces:

MMcifConsumer

public class ChemCompConsumer
extends Object
implements MMcifConsumer

Constructor Summary

Constructors

Constructor and Description
ChemCompConsumer()

Method Summary

Modifier and Type	Method and Description
void	documentEnd() called at end of document
void	documentStart() called at start of document
ChemicalComponentDictionary	getDictionary()
FileParsingParameters	getFileParsingParameters()
void	newAtomSite(AtomSite atom) A new AtomSite record has been read.
void	newAtomSites(AtomSites atomSites)
void	newAuditAuthor(AuditAuthor aa) AuditAuthor contains the info from the PDB-AUTHOR records.
void	newCell(Cell cell)
void	newChemComp(ChemComp c)
void	newChemCompAtom(ChemCompAtom atom)
void	newChemCompBond(ChemCompBond bond)
void	newChemCompDescriptor(ChemCompDescriptor ccd)
void	newDatabasePDBremark(DatabasePDBremark remark)
void	newDatabasePDBrev(DatabasePDBrev dbrev)
void	newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev)
void	newEntity(Entity entity)
void	newEntityPoly(EntityPoly entityPoly)
void	newEntityPolySeq(EntityPolySeq epolseq)
void	newEntitySrcGen(EntitySrcGen entitySrcGen)
void	newEntitySrcNat(EntitySrcNat entitySrcNat)
void	newEntitySrcSyn(EntitySrcSyn entitySrcSyn)
void	newExptl(Exptl exptl)
void	newGenericData(String category, List<String> loopFields, List<String> lineData) This method is called if no particular handler for the provided cif category has been implemented so far.
void	newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history)
void	newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)
void	newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)
void	newPdbxDatabaseStatus(PdbxDatabaseStatus status)
void	newPdbxEntityNonPoly(PdbxEntityNonPoly pen)
void	newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)
void	newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)
void	newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)
void	newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)
void	newPdbxStructOperList(PdbxStructOperList structOper)
void	newRefine(Refine r)
void	newStructAsym(StructAsym sasym)
void	newStructConn(StructConn structConn)
void	newStructKeywords(StructKeywords kw)
void	newStructNcsOper(StructNcsOper sNcsOper)
void	newStructRef(StructRef sref)
void	newStructRefSeq(StructRefSeq sref)
void	newStructRefSeqDif(StructRefSeqDif sref)
void	newStructSite(StructSite site)
void	newStructSiteGen(StructSiteGen gen)
void	newSymmetry(Symmetry symmetry)
void	setFileParsingParameters(FileParsingParameters params)
void	setStruct(Struct struct)

Methods inherited from class java.lang.Object

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

Constructor Detail

ChemCompConsumer

public ChemCompConsumer()

Method Detail

documentStart

public void documentStart()

Description copied from interface: MMcifConsumer

called at start of document

Specified by:

documentStart in interface MMcifConsumer

getDictionary

public ChemicalComponentDictionary getDictionary()

newChemComp

public void newChemComp(ChemComp c)

Specified by:

newChemComp in interface MMcifConsumer

documentEnd

public void documentEnd()

Description copied from interface: MMcifConsumer

called at end of document

Specified by:

documentEnd in interface MMcifConsumer

newAtomSite

public void newAtomSite(AtomSite atom)

Description copied from interface: MMcifConsumer

A new AtomSite record has been read. Contains the Atom data

Specified by:

newAtomSite in interface MMcifConsumer

newDatabasePDBremark

public void newDatabasePDBremark(DatabasePDBremark remark)

Specified by:

newDatabasePDBremark in interface MMcifConsumer

newDatabasePDBrev

public void newDatabasePDBrev(DatabasePDBrev dbrev)

Specified by:

newDatabasePDBrev in interface MMcifConsumer

newDatabasePDBrevRecord

public void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev)

Specified by:

newDatabasePDBrevRecord in interface MMcifConsumer

newEntity

public void newEntity(Entity entity)

Specified by:

newEntity in interface MMcifConsumer

newEntityPolySeq

public void newEntityPolySeq(EntityPolySeq epolseq)

Specified by:

newEntityPolySeq in interface MMcifConsumer

newExptl

public void newExptl(Exptl exptl)

Specified by:

newExptl in interface MMcifConsumer

newCell

public void newCell(Cell cell)

Specified by:

newCell in interface MMcifConsumer

newSymmetry

public void newSymmetry(Symmetry symmetry)

Specified by:

newSymmetry in interface MMcifConsumer

newStructNcsOper

public void newStructNcsOper(StructNcsOper sNcsOper)

Specified by:

newStructNcsOper in interface MMcifConsumer

newAtomSites

public void newAtomSites(AtomSites atomSites)

Specified by:

newAtomSites in interface MMcifConsumer

newPdbxEntityNonPoly

public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)

Specified by:

newPdbxEntityNonPoly in interface MMcifConsumer

newPdbxNonPolyScheme

public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)

Specified by:

newPdbxNonPolyScheme in interface MMcifConsumer

newPdbxPolySeqScheme

public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)

Specified by:

newPdbxPolySeqScheme in interface MMcifConsumer

newRefine

public void newRefine(Refine r)

Specified by:

newRefine in interface MMcifConsumer

newStructAsym

public void newStructAsym(StructAsym sasym)

Specified by:

newStructAsym in interface MMcifConsumer

newStructKeywords

public void newStructKeywords(StructKeywords kw)

Specified by:

newStructKeywords in interface MMcifConsumer

newStructRef

public void newStructRef(StructRef sref)

Specified by:

newStructRef in interface MMcifConsumer

newStructRefSeq

public void newStructRefSeq(StructRefSeq sref)

Specified by:

newStructRefSeq in interface MMcifConsumer

newStructRefSeqDif

public void newStructRefSeqDif(StructRefSeqDif sref)

Specified by:

newStructRefSeqDif in interface MMcifConsumer

setStruct

public void setStruct(Struct struct)

Specified by:

setStruct in interface MMcifConsumer

newGenericData

public void newGenericData(String category,
                           List<String> loopFields,
                           List<String> lineData)

Description copied from interface: MMcifConsumer

This method is called if no particular handler for the provided cif category has been implemented so far.

Specified by:

newGenericData in interface MMcifConsumer

Parameters:

category - The category that is being processed.

loopFields - the fields of this category.

lineData - the data that is being provided.

newAuditAuthor

public void newAuditAuthor(AuditAuthor aa)

Description copied from interface: MMcifConsumer

AuditAuthor contains the info from the PDB-AUTHOR records.

Specified by:

newAuditAuthor in interface MMcifConsumer

getFileParsingParameters

public FileParsingParameters getFileParsingParameters()

Specified by:

getFileParsingParameters in interface MMcifConsumer

setFileParsingParameters

public void setFileParsingParameters(FileParsingParameters params)

Specified by:

setFileParsingParameters in interface MMcifConsumer

newChemCompDescriptor

public void newChemCompDescriptor(ChemCompDescriptor ccd)

Specified by:

newChemCompDescriptor in interface MMcifConsumer

newPdbxStructOperList

public void newPdbxStructOperList(PdbxStructOperList structOper)

Specified by:

newPdbxStructOperList in interface MMcifConsumer

newPdbxStrucAssembly

public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)

Specified by:

newPdbxStrucAssembly in interface MMcifConsumer

newPdbxStrucAssemblyGen

public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)

Specified by:

newPdbxStrucAssemblyGen in interface MMcifConsumer

newChemCompAtom

public void newChemCompAtom(ChemCompAtom atom)

Specified by:

newChemCompAtom in interface MMcifConsumer

newPdbxChemCompIndentifier

public void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)

Specified by:

newPdbxChemCompIndentifier in interface MMcifConsumer

newChemCompBond

public void newChemCompBond(ChemCompBond bond)

Specified by:

newChemCompBond in interface MMcifConsumer

newPdbxChemCompDescriptor

public void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)

Specified by:

newPdbxChemCompDescriptor in interface MMcifConsumer

newEntitySrcGen

public void newEntitySrcGen(EntitySrcGen entitySrcGen)

Specified by:

newEntitySrcGen in interface MMcifConsumer

newEntitySrcNat

public void newEntitySrcNat(EntitySrcNat entitySrcNat)

Specified by:

newEntitySrcNat in interface MMcifConsumer

newEntitySrcSyn

public void newEntitySrcSyn(EntitySrcSyn entitySrcSyn)

Specified by:

newEntitySrcSyn in interface MMcifConsumer

newStructConn

public void newStructConn(StructConn structConn)

Specified by:

newStructConn in interface MMcifConsumer

newStructSiteGen

public void newStructSiteGen(StructSiteGen gen)

Specified by:

newStructSiteGen in interface MMcifConsumer

newStructSite

public void newStructSite(StructSite site)

Specified by:

newStructSite in interface MMcifConsumer

newEntityPoly

public void newEntityPoly(EntityPoly entityPoly)

Specified by:

newEntityPoly in interface MMcifConsumer

newPdbxAuditRevisionHistory

public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history)

Specified by:

newPdbxAuditRevisionHistory in interface MMcifConsumer

newPdbxDatabaseStatus

public void newPdbxDatabaseStatus(PdbxDatabaseStatus status)

Specified by:

newPdbxDatabaseStatus in interface MMcifConsumer