Package org.biojava.nbio.structure.io.mmcif

Interface MMcifConsumer

All Known Implementing Classes:
ChemCompConsumer, MetalBondConsumer, SimpleMMcifConsumer
public interface MMcifConsumer
An interface for the events triggered by a MMcifParser. The Consumer listens to the events and builds up the protein structure.
Since:
1.7
Author:
Andreas Prlic

  • Method Details

    • documentStart

      void documentStart()
      called at start of document

    • documentEnd

      void documentEnd()
      called at end of document

    • newAtomSite

      void newAtomSite(AtomSite atom)
      A new AtomSite record has been read. Contains the Atom data
      Parameters:
      atom -

    • newEntity

      void newEntity(Entity entity)

    • newEntityPolySeq

      void newEntityPolySeq(EntityPolySeq epolseq)

    • newStructAsym

      void newStructAsym(StructAsym sasym)

    • setStruct

      void setStruct(Struct struct)

    • newDatabasePDBrev

      void newDatabasePDBrev(DatabasePDBrev dbrev)

    • newDatabasePDBrevRecord

      void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev)

    • newDatabasePDBremark

      void newDatabasePDBremark(DatabasePDBremark remark)

    • newExptl

      void newExptl(Exptl exptl)

    • newCell

      void newCell(Cell cell)

    • newSymmetry

      void newSymmetry(Symmetry symmetry)

    • newStructNcsOper

      void newStructNcsOper(StructNcsOper sNcsOper)

    • newAtomSites

      void newAtomSites(AtomSites atomSites)

    • newStructRef

      void newStructRef(StructRef sref)

    • newStructRefSeq

      void newStructRefSeq(StructRefSeq sref)

    • newStructRefSeqDif

      void newStructRefSeqDif(StructRefSeqDif sref)

    • newStructSite

      void newStructSite(StructSite sref)

    • newStructSiteGen

      void newStructSiteGen(StructSiteGen sref)

    • newPdbxPolySeqScheme

      void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)

    • newPdbxNonPolyScheme

      void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)

    • newPdbxEntityNonPoly

      void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)

    • newStructKeywords

      void newStructKeywords(StructKeywords kw)

    • newRefine

      void newRefine(Refine r)

    • newChemComp

      void newChemComp(ChemComp c)

    • newChemCompDescriptor

      void newChemCompDescriptor(ChemCompDescriptor ccd)

    • newPdbxStructOperList

      void newPdbxStructOperList(PdbxStructOperList structOper)

    • newPdbxStrucAssembly

      void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)

    • newPdbxStrucAssemblyGen

      void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)

    • newChemCompAtom

      void newChemCompAtom(ChemCompAtom atom)

    • newPdbxChemCompIndentifier

      void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)

    • newChemCompBond

      void newChemCompBond(ChemCompBond bond)

    • newPdbxChemCompDescriptor

      void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)

    • newEntitySrcGen

      void newEntitySrcGen(EntitySrcGen entitySrcGen)

    • newEntitySrcNat

      void newEntitySrcNat(EntitySrcNat entitySrcNat)

    • newEntitySrcSyn

      void newEntitySrcSyn(EntitySrcSyn entitySrcSyn)

    • newStructConn

      void newStructConn(StructConn structConn)

    • newAuditAuthor

      void newAuditAuthor(AuditAuthor aa)
      AuditAuthor contains the info from the PDB-AUTHOR records.
      Parameters:
      aa -

    • newGenericData

      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.
      Parameters:
      category - The category that is being processed.
      loopFields - the fields of this category.
      lineData - the data that is being provided.

    • setFileParsingParameters

      void setFileParsingParameters(FileParsingParameters params)

    • getFileParsingParameters

      FileParsingParameters getFileParsingParameters()