org.biojava.nbio.structure.io.mmcif

Class SimpleMMcifConsumer

java.lang.Object

org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer

All Implemented Interfaces:

MMcifConsumer

public class SimpleMMcifConsumer
extends Object
implements MMcifConsumer

A MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object.

Since:

1.7

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
SimpleMMcifConsumer()

Method Summary

Modifier and Type	Method and Description
void	documentEnd() called at end of document
void	documentStart() Start the parsing
FileParsingParameters	getFileParsingParameters()
List<PdbxStructAssembly>	getStructAssemblies()
List<PdbxStructAssemblyGen>	getStructAssemblyGens()
List<PdbxStructOperList>	getStructOpers()
Structure	getStructure() This method will return the parsed protein structure, once the parsing has been finished
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	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 record)
void	newEntity(Entity entity)
void	newEntityPolySeq(EntityPolySeq epolseq) The EntityPolySeq object provide the amino acid sequence objects for the Entities.
void	newEntitySrcGen(EntitySrcGen entitySrcGen) Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
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	newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)
void	newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)
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) create a DBRef record from the StrucRefSeq record:
void	newStructRefSeqDif(StructRefSeqDif sref)
void	newStructSite(StructSite structSite)
void	newStructSiteGen(StructSiteGen siteGen)
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

SimpleMMcifConsumer

public SimpleMMcifConsumer()

Method Detail

newEntity

public void newEntity(Entity entity)

Specified by:

newEntity in interface MMcifConsumer

newPdbxStructOperList

public void newPdbxStructOperList(PdbxStructOperList structOper)

Specified by:

newPdbxStructOperList 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

setStruct

public void setStruct(Struct struct)

Specified by:

setStruct 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

documentStart

public void documentStart()

Start the parsing

Specified by:

documentStart in interface MMcifConsumer

documentEnd

public void documentEnd()

Description copied from interface: MMcifConsumer

called at end of document

Specified by:

documentEnd in interface MMcifConsumer

getStructure

public Structure getStructure()

This method will return the parsed protein structure, once the parsing has been finished

Returns:

a BioJava protein structure object

newDatabasePDBrevRecord

public void newDatabasePDBrevRecord(DatabasePdbrevRecord record)

Specified by:

newDatabasePDBrevRecord in interface MMcifConsumer

newDatabasePDBrev

public void newDatabasePDBrev(DatabasePDBrev dbrev)

Specified by:

newDatabasePDBrev in interface MMcifConsumer

newDatabasePDBremark

public void newDatabasePDBremark(DatabasePDBremark remark)

Specified by:

newDatabasePDBremark in interface MMcifConsumer

newRefine

public void newRefine(Refine r)

Specified by:

newRefine in interface MMcifConsumer

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

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

newStructRef

public void newStructRef(StructRef sref)

Specified by:

newStructRef in interface MMcifConsumer

newStructRefSeq

public void newStructRefSeq(StructRefSeq sref)

create a DBRef record from the StrucRefSeq record:

 PDB record                    DBREF
 Field Name                    mmCIF Data Item
 Section                       n.a.
 PDB_ID_Code                   _struct_ref_seq.pdbx_PDB_id_code
 Strand_ID                     _struct_ref_seq.pdbx_strand_id
 Begin_Residue_Number          _struct_ref_seq.pdbx_auth_seq_align_beg
 Begin_Ins_Code                _struct_ref_seq.pdbx_seq_align_beg_ins_code
 End_Residue_Number            _struct_ref_seq.pdbx_auth_seq_align_end
 End_Ins_Code                  _struct_ref_seq.pdbx_seq_align_end_ins_code
 Database                      _struct_ref.db_name
 Database_Accession_No         _struct_ref_seq.pdbx_db_accession
 Database_ID_Code              _struct_ref.db_code
 Database_Begin_Residue_Number _struct_ref_seq.db_align_beg
 Databaes_Begin_Ins_Code       _struct_ref_seq.pdbx_db_align_beg_ins_code
 Database_End_Residue_Number   _struct_ref_seq.db_align_end
 Databaes_End_Ins_Code         _struct_ref_seq.pdbx_db_align_end_ins_code
 

Specified by:

newStructRefSeq in interface MMcifConsumer

newStructRefSeqDif

public void newStructRefSeqDif(StructRefSeqDif sref)

Specified by:

newStructRefSeqDif in interface MMcifConsumer

newEntitySrcGen

public void newEntitySrcGen(EntitySrcGen entitySrcGen)

Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).

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

newEntityPolySeq

public void newEntityPolySeq(EntityPolySeq epolseq)

The EntityPolySeq object provide the amino acid sequence objects for the Entities. Later on the entities are mapped to the BioJava Chain and Compound objects.

Specified by:

newEntityPolySeq in interface MMcifConsumer

Parameters:

epolseq - the EntityPolySeq record for one amino acid

newPdbxPolySeqScheme

public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)

Specified by:

newPdbxPolySeqScheme in interface MMcifConsumer

newPdbxNonPolyScheme

public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)

Specified by:

newPdbxNonPolyScheme in interface MMcifConsumer

newPdbxEntityNonPoly

public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)

Specified by:

newPdbxEntityNonPoly in interface MMcifConsumer

newChemComp

public void newChemComp(ChemComp c)

Specified by:

newChemComp 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.

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

getStructOpers

public List<PdbxStructOperList> getStructOpers()

newPdbxStrucAssembly

public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)

Specified by:

newPdbxStrucAssembly in interface MMcifConsumer

getStructAssemblies

public List<PdbxStructAssembly> getStructAssemblies()

newPdbxStrucAssemblyGen

public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)

Specified by:

newPdbxStrucAssemblyGen in interface MMcifConsumer

getStructAssemblyGens

public List<PdbxStructAssemblyGen> getStructAssemblyGens()

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

newStructConn

public void newStructConn(StructConn structConn)

Specified by:

newStructConn in interface MMcifConsumer

newStructSiteGen

public void newStructSiteGen(StructSiteGen siteGen)

Specified by:

newStructSiteGen in interface MMcifConsumer

newStructSite

public void newStructSite(StructSite structSite)

Specified by:

newStructSite in interface MMcifConsumer