org.biojava.bio.structure.io.mmcif

Class ChemCompConsumer

java.lang.Object

org.biojava.bio.structure.io.mmcif.ChemCompConsumer

All Implemented Interfaces:

MMcifConsumer

public class ChemCompConsumer
extends Object
implements MMcifConsumer

Constructor Summary

Constructors

Constructor and Description
ChemCompConsumer()

Method Summary

Methods

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	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)

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

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

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

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