Package org.biojava.nbio.structure.io.mmcif

Interface MMcifConsumer

All Known Implementing Classes:

ChemCompConsumer, MetalBondConsumer, SimpleMMcifConsumer

public interface MMcifConsumer

An interface for the events triggered by a MMcifParser. The Consumer listens to the events and builds up the protein structure.

Since:

1.7

Author:

Andreas Prlic

Method Summary

Modifier and Type	Method	Description
void	documentEnd()	called at end of document
void	documentStart()	called at start of document
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 sref)
void	newStructSiteGen(StructSiteGen sref)
void	newSymmetry(Symmetry symmetry)
void	setFileParsingParameters(FileParsingParameters params)
void	setStruct(Struct struct)

Method Detail

documentStart

void documentStart()

called at start of document

documentEnd

void documentEnd()

called at end of document

newAtomSite

void newAtomSite(AtomSite atom)

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

Parameters:

atom -

newEntity

void newEntity(Entity entity)

newEntityPoly

void newEntityPoly(EntityPoly entityPoly)

newEntityPolySeq

void newEntityPolySeq(EntityPolySeq epolseq)

newStructAsym

void newStructAsym(StructAsym sasym)

setStruct

void setStruct(Struct struct)

newDatabasePDBrev

void newDatabasePDBrev(DatabasePDBrev dbrev)

newDatabasePDBrevRecord

void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev)

newDatabasePDBremark

void newDatabasePDBremark(DatabasePDBremark remark)

newExptl

void newExptl(Exptl exptl)

newCell

void newCell(Cell cell)

newSymmetry

void newSymmetry(Symmetry symmetry)

newStructNcsOper

void newStructNcsOper(StructNcsOper sNcsOper)

newAtomSites

void newAtomSites(AtomSites atomSites)

newStructRef

void newStructRef(StructRef sref)

newStructRefSeq

void newStructRefSeq(StructRefSeq sref)

newStructRefSeqDif

void newStructRefSeqDif(StructRefSeqDif sref)

newStructSite

void newStructSite(StructSite sref)

newStructSiteGen

void newStructSiteGen(StructSiteGen sref)

newPdbxAuditRevisionHistory

void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history)

newPdbxDatabaseStatus

void newPdbxDatabaseStatus(PdbxDatabaseStatus status)

newPdbxPolySeqScheme

void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)

newPdbxNonPolyScheme

void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)

newPdbxEntityNonPoly

void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)

newStructKeywords

void newStructKeywords(StructKeywords kw)

newRefine

void newRefine(Refine r)

newChemComp

void newChemComp(ChemComp c)

newChemCompDescriptor

void newChemCompDescriptor(ChemCompDescriptor ccd)

newPdbxStructOperList

void newPdbxStructOperList(PdbxStructOperList structOper)

newPdbxStrucAssembly

void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)

newPdbxStrucAssemblyGen

void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)

newChemCompAtom

void newChemCompAtom(ChemCompAtom atom)

newPdbxChemCompIndentifier

void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)

newChemCompBond

void newChemCompBond(ChemCompBond bond)

newPdbxChemCompDescriptor

void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)

newEntitySrcGen

void newEntitySrcGen(EntitySrcGen entitySrcGen)

newEntitySrcNat

void newEntitySrcNat(EntitySrcNat entitySrcNat)

newEntitySrcSyn

void newEntitySrcSyn(EntitySrcSyn entitySrcSyn)

newStructConn

void newStructConn(StructConn structConn)

newAuditAuthor

void newAuditAuthor(AuditAuthor aa)

AuditAuthor contains the info from the PDB-AUTHOR records.

Parameters:

aa -

newGenericData

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.

Parameters:

category - The category that is being processed.

loopFields - the fields of this category.

lineData - the data that is being provided.

setFileParsingParameters

void setFileParsingParameters(FileParsingParameters params)

getFileParsingParameters

FileParsingParameters getFileParsingParameters()