Class SimpleMMcifConsumer
- java.lang.Object
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- org.biojava.bio.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 build a 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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Field Summary
Fields Modifier and Type Field Description static java.util.logging.Logger
logger
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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 parsingStructure
getStructure()
This method will return the parsed protein structure, once the parsing has been finishedboolean
isAlignSeqRes()
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.boolean
isParseCAOnly()
void
newAtomSite(AtomSite atom)
A new AtomSite record has been read.void
newChemComp(ChemComp c)
void
newDatabasePDBremark(DatabasePDBremark remark)
void
newDatabasePDBrev(DatabasePDBrev dbrev)
void
newEntity(Entity entity)
void
newEntityPolySeq(EntityPolySeq epolseq)
The EntityPolySeq object provide the amino acid sequence objects for the Entities.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
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)
create a DBRef record from the StrucRefSeq record:void
setAlignSeqRes(boolean alignSeqRes)
define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.void
setParseCAOnly(boolean parseCAOnly)
void
setStruct(Struct struct)
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Method Detail
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isParseCAOnly
public boolean isParseCAOnly()
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setParseCAOnly
public void setParseCAOnly(boolean parseCAOnly)
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newEntity
public void newEntity(Entity entity)
- Specified by:
newEntity
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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isAlignSeqRes
public boolean isAlignSeqRes()
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.- Returns:
- flag if SEQRES - ATOM amino acids alignment is enabled
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setAlignSeqRes
public void setAlignSeqRes(boolean alignSeqRes)
define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.- Parameters:
alignSeqRes
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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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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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newExptl
public void newExptl(Exptl exptl)
- Specified by:
newExptl
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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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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