org.biojava.bio.structure.io.mmcif

Interface MMcifConsumer

All Known Implementing Classes:

ChemCompConsumer, 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

Methods

Modifier and Type	Method and 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	newAuditAuthor(AuditAuthor aa) AuditAuthor contains the info from the PDB-AUTHOR records.
void	newChemComp(ChemComp c)
void	newChemCompDescriptor(ChemCompDescriptor ccd)
void	newDatabasePDBremark(DatabasePDBremark remark)
void	newDatabasePDBrev(DatabasePDBrev dbrev)
void	newEntity(Entity entity)
void	newEntityPolySeq(EntityPolySeq epolseq)
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	newPdbxEntityNonPoly(PdbxEntityNonPoly pen)
void	newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)
void	newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)
void	newRefine(Refine r)
void	newStructAsym(StructAsym sasym)
void	newStructKeywords(StructKeywords kw)
void	newStructRef(StructRef sref)
void	newStructRefSeq(StructRefSeq sref)
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)

newEntityPolySeq

void newEntityPolySeq(EntityPolySeq epolseq)

newStructAsym

void newStructAsym(StructAsym sasym)

setStruct

void setStruct(Struct struct)

newDatabasePDBrev

void newDatabasePDBrev(DatabasePDBrev dbrev)

newDatabasePDBremark

void newDatabasePDBremark(DatabasePDBremark remark)

newExptl

void newExptl(Exptl exptl)

newStructRef

void newStructRef(StructRef sref)

newStructRefSeq

void newStructRefSeq(StructRefSeq sref)

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)

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()