Class SimpleMMcifConsumer
- java.lang.Object
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- org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
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- All Implemented Interfaces:
MMcifConsumer
public class SimpleMMcifConsumer extends java.lang.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
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Constructor Summary
Constructors Constructor Description SimpleMMcifConsumer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
documentEnd()
called at end of documentvoid
documentStart()
Start the parsingFileParsingParameters
getFileParsingParameters()
java.util.List<PdbxStructAssembly>
getStructAssemblies()
java.util.List<PdbxStructAssemblyGen>
getStructAssemblyGens()
java.util.List<PdbxStructOperList>
getStructOpers()
Structure
getStructure()
This method will return the parsed protein structure, once the parsing has been finishedvoid
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 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(java.lang.String category, java.util.List<java.lang.String> loopFields, java.util.List<java.lang.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)
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Method Detail
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newEntity
public void newEntity(Entity entity)
- Specified by:
newEntity
in interfaceMMcifConsumer
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newPdbxStructOperList
public void newPdbxStructOperList(PdbxStructOperList structOper)
- Specified by:
newPdbxStructOperList
in interfaceMMcifConsumer
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newStructAsym
public void newStructAsym(StructAsym sasym)
- Specified by:
newStructAsym
in interfaceMMcifConsumer
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newStructKeywords
public void newStructKeywords(StructKeywords kw)
- Specified by:
newStructKeywords
in interfaceMMcifConsumer
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setStruct
public void setStruct(Struct struct)
- Specified by:
setStruct
in interfaceMMcifConsumer
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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 interfaceMMcifConsumer
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documentStart
public void documentStart()
Start the parsing- Specified by:
documentStart
in interfaceMMcifConsumer
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documentEnd
public void documentEnd()
Description copied from interface:MMcifConsumer
called at end of document- Specified by:
documentEnd
in interfaceMMcifConsumer
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getStructure
public Structure getStructure()
This method will return the parsed protein structure, once the parsing has been finished- Returns:
- a BioJava protein structure object
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newDatabasePDBrevRecord
public void newDatabasePDBrevRecord(DatabasePdbrevRecord record)
- Specified by:
newDatabasePDBrevRecord
in interfaceMMcifConsumer
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newDatabasePDBrev
public void newDatabasePDBrev(DatabasePDBrev dbrev)
- Specified by:
newDatabasePDBrev
in interfaceMMcifConsumer
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newDatabasePDBremark
public void newDatabasePDBremark(DatabasePDBremark remark)
- Specified by:
newDatabasePDBremark
in interfaceMMcifConsumer
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newRefine
public void newRefine(Refine r)
- Specified by:
newRefine
in interfaceMMcifConsumer
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newAuditAuthor
public void newAuditAuthor(AuditAuthor aa)
Description copied from interface:MMcifConsumer
AuditAuthor contains the info from the PDB-AUTHOR records.- Specified by:
newAuditAuthor
in interfaceMMcifConsumer
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newExptl
public void newExptl(Exptl exptl)
- Specified by:
newExptl
in interfaceMMcifConsumer
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newCell
public void newCell(Cell cell)
- Specified by:
newCell
in interfaceMMcifConsumer
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newSymmetry
public void newSymmetry(Symmetry symmetry)
- Specified by:
newSymmetry
in interfaceMMcifConsumer
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newStructNcsOper
public void newStructNcsOper(StructNcsOper sNcsOper)
- Specified by:
newStructNcsOper
in interfaceMMcifConsumer
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newAtomSites
public void newAtomSites(AtomSites atomSites)
- Specified by:
newAtomSites
in interfaceMMcifConsumer
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newStructRef
public void newStructRef(StructRef sref)
- Specified by:
newStructRef
in interfaceMMcifConsumer
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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 interfaceMMcifConsumer
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newStructRefSeqDif
public void newStructRefSeqDif(StructRefSeqDif sref)
- Specified by:
newStructRefSeqDif
in interfaceMMcifConsumer
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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 interfaceMMcifConsumer
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newEntitySrcNat
public void newEntitySrcNat(EntitySrcNat entitySrcNat)
- Specified by:
newEntitySrcNat
in interfaceMMcifConsumer
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newEntitySrcSyn
public void newEntitySrcSyn(EntitySrcSyn entitySrcSyn)
- Specified by:
newEntitySrcSyn
in interfaceMMcifConsumer
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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 interfaceMMcifConsumer
- Parameters:
epolseq
- the EntityPolySeq record for one amino acid
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newPdbxPolySeqScheme
public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)
- Specified by:
newPdbxPolySeqScheme
in interfaceMMcifConsumer
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newPdbxNonPolyScheme
public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)
- Specified by:
newPdbxNonPolyScheme
in interfaceMMcifConsumer
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newPdbxEntityNonPoly
public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)
- Specified by:
newPdbxEntityNonPoly
in interfaceMMcifConsumer
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newChemComp
public void newChemComp(ChemComp c)
- Specified by:
newChemComp
in interfaceMMcifConsumer
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newGenericData
public void newGenericData(java.lang.String category, java.util.List<java.lang.String> loopFields, java.util.List<java.lang.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 interfaceMMcifConsumer
- Parameters:
category
- The category that is being processed.loopFields
- the fields of this category.lineData
- the data that is being provided.
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getFileParsingParameters
public FileParsingParameters getFileParsingParameters()
- Specified by:
getFileParsingParameters
in interfaceMMcifConsumer
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setFileParsingParameters
public void setFileParsingParameters(FileParsingParameters params)
- Specified by:
setFileParsingParameters
in interfaceMMcifConsumer
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newChemCompDescriptor
public void newChemCompDescriptor(ChemCompDescriptor ccd)
- Specified by:
newChemCompDescriptor
in interfaceMMcifConsumer
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getStructOpers
public java.util.List<PdbxStructOperList> getStructOpers()
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newPdbxStrucAssembly
public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)
- Specified by:
newPdbxStrucAssembly
in interfaceMMcifConsumer
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getStructAssemblies
public java.util.List<PdbxStructAssembly> getStructAssemblies()
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newPdbxStrucAssemblyGen
public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)
- Specified by:
newPdbxStrucAssemblyGen
in interfaceMMcifConsumer
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getStructAssemblyGens
public java.util.List<PdbxStructAssemblyGen> getStructAssemblyGens()
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newChemCompAtom
public void newChemCompAtom(ChemCompAtom atom)
- Specified by:
newChemCompAtom
in interfaceMMcifConsumer
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newPdbxChemCompIndentifier
public void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)
- Specified by:
newPdbxChemCompIndentifier
in interfaceMMcifConsumer
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newChemCompBond
public void newChemCompBond(ChemCompBond bond)
- Specified by:
newChemCompBond
in interfaceMMcifConsumer
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newPdbxChemCompDescriptor
public void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)
- Specified by:
newPdbxChemCompDescriptor
in interfaceMMcifConsumer
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newStructConn
public void newStructConn(StructConn structConn)
- Specified by:
newStructConn
in interfaceMMcifConsumer
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newStructSiteGen
public void newStructSiteGen(StructSiteGen siteGen)
- Specified by:
newStructSiteGen
in interfaceMMcifConsumer
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newStructSite
public void newStructSite(StructSite structSite)
- Specified by:
newStructSite
in interfaceMMcifConsumer
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