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 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
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Constructor Detail
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SimpleMMcifConsumer
public SimpleMMcifConsumer()
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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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newEntityPoly
public void newEntityPoly(EntityPoly entityPoly)
- Specified by:
newEntityPoly
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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newPdbxAuditRevisionHistory
public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history)
- Specified by:
newPdbxAuditRevisionHistory
in interfaceMMcifConsumer
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newPdbxDatabaseStatus
public void newPdbxDatabaseStatus(PdbxDatabaseStatus status)
- Specified by:
newPdbxDatabaseStatus
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 BioJavaChain
andEntityInfo
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(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 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 List<PdbxStructOperList> getStructOpers()
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newPdbxStrucAssembly
public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)
- Specified by:
newPdbxStrucAssembly
in interfaceMMcifConsumer
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getStructAssemblies
public List<PdbxStructAssembly> getStructAssemblies()
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newPdbxStrucAssemblyGen
public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)
- Specified by:
newPdbxStrucAssemblyGen
in interfaceMMcifConsumer
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getStructAssemblyGens
public 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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