public class SimpleMMcifConsumer extends java.lang.Object implements MMcifConsumer
Modifier and Type | Field and Description |
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static java.util.logging.Logger |
logger |
Constructor and Description |
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SimpleMMcifConsumer() |
Modifier and Type | Method and Description |
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void |
documentEnd()
called at end of document
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void |
documentStart()
Start the parsing
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Structure |
getStructure()
This method will return the parsed protein structure, once the parsing has been finished
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boolean |
isAlignSeqRes()
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
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boolean |
isParseCAOnly() |
void |
newAtomSite(AtomSite atom)
A new AtomSite record has been read.
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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.
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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.
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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:
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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.
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void |
setParseCAOnly(boolean parseCAOnly) |
void |
setStruct(Struct struct) |
public boolean isParseCAOnly()
public void setParseCAOnly(boolean parseCAOnly)
public void newEntity(Entity entity)
newEntity
in interface MMcifConsumer
public void newStructAsym(StructAsym sasym)
newStructAsym
in interface MMcifConsumer
public void newStructKeywords(StructKeywords kw)
newStructKeywords
in interface MMcifConsumer
public void setStruct(Struct struct)
setStruct
in interface MMcifConsumer
public void newAtomSite(AtomSite atom)
MMcifConsumer
newAtomSite
in interface MMcifConsumer
public void documentStart()
documentStart
in interface MMcifConsumer
public boolean isAlignSeqRes()
public void setAlignSeqRes(boolean alignSeqRes)
alignSeqRes
- public void documentEnd()
MMcifConsumer
documentEnd
in interface MMcifConsumer
public Structure getStructure()
public void newDatabasePDBrev(DatabasePDBrev dbrev)
newDatabasePDBrev
in interface MMcifConsumer
public void newDatabasePDBremark(DatabasePDBremark remark)
newDatabasePDBremark
in interface MMcifConsumer
public void newRefine(Refine r)
newRefine
in interface MMcifConsumer
public void newExptl(Exptl exptl)
newExptl
in interface MMcifConsumer
public void newStructRef(StructRef sref)
newStructRef
in interface MMcifConsumer
public void newStructRefSeq(StructRefSeq sref)
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
newStructRefSeq
in interface MMcifConsumer
public void newEntityPolySeq(EntityPolySeq epolseq)
newEntityPolySeq
in interface MMcifConsumer
epolseq
- the EntityPolySeq record for one amino acidpublic void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)
newPdbxPolySeqScheme
in interface MMcifConsumer
public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)
newPdbxNonPolyScheme
in interface MMcifConsumer
public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)
newPdbxEntityNonPoly
in interface MMcifConsumer
public void newChemComp(ChemComp c)
newChemComp
in interface MMcifConsumer
public void newGenericData(java.lang.String category, java.util.List<java.lang.String> loopFields, java.util.List<java.lang.String> lineData)
MMcifConsumer
newGenericData
in interface MMcifConsumer
category
- The category that is being processed.loopFields
- the fields of this category.lineData
- the data that is being provided.