Package org.biojava.nbio.structure.io.cif

Class CifStructureConsumerImpl

java.lang.Object
org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
All Implemented Interfaces:
CifFileConsumer<Structure>, CifStructureConsumer
public class CifStructureConsumerImpl extends Object implements CifStructureConsumer
An implementation of a CifFileConsumer for BioJava. Will process the information provided by a CifFile instance and use it to build up a Structure object.
Since:
6.0.0
Author:
Sebastian Bittrich

  • Constructor Summary

    Constructors
    Constructor
    Description
    CifStructureConsumerImpl(FileParsingParameters params)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    consumeAtomSite(org.rcsb.cif.schema.mm.AtomSite atomSite)
    Consume a particular Cif category.
    void
    consumeAtomSites(org.rcsb.cif.schema.mm.AtomSites atomSites)
    Consume a particular Cif category.
    void
    consumeAuditAuthor(org.rcsb.cif.schema.mm.AuditAuthor auditAuthor)
    Consume a particular Cif category.
    void
    consumeCell(org.rcsb.cif.schema.mm.Cell cell)
    Consume a particular Cif category.
    void
    consumeChemComp(org.rcsb.cif.schema.mm.ChemComp chemComp)
    Consume a particular Cif category.
    void
    consumeChemCompBond(org.rcsb.cif.schema.mm.ChemCompBond chemCompBond)
    Consume a particular Cif category.
    void
    consumeDatabasePDBRemark(org.rcsb.cif.schema.mm.DatabasePDBRemark databasePDBremark)
    Consume a particular Cif category.
    void
    consumeDatabasePDBRev(org.rcsb.cif.schema.mm.DatabasePDBRev databasePDBrev)
    Consume a particular Cif category.
    void
    consumeDatabasePDBRevRecord(org.rcsb.cif.schema.mm.DatabasePDBRevRecord databasePDBrevRecord)
    Consume a particular Cif category.
    void
    consumeEm3dReconstruction(org.rcsb.cif.schema.mm.Em3dReconstruction em3dReconstruction)
    Consume Electron Microscopy 3D reconstruction data
    void
    consumeEntity(org.rcsb.cif.schema.mm.Entity entity)
    Consume a particular Cif category.
    void
    consumeEntityPoly(org.rcsb.cif.schema.mm.EntityPoly entityPoly)
    Consume a particular Cif category.
    void
    consumeEntityPolySeq(org.rcsb.cif.schema.mm.EntityPolySeq entityPolySeq)
    Consume a particular Cif category.
    void
    consumeEntitySrcGen(org.rcsb.cif.schema.mm.EntitySrcGen entitySrcGen)
    Consume a particular Cif category.
    void
    consumeEntitySrcNat(org.rcsb.cif.schema.mm.EntitySrcNat entitySrcNat)
    Consume a particular Cif category.
    void
    consumeEntitySrcSyn(org.rcsb.cif.schema.mm.PdbxEntitySrcSyn entitySrcSyn)
    Consume a particular Cif category.
    void
    consumeExptl(org.rcsb.cif.schema.mm.Exptl exptl)
    Consume a particular Cif category.
    void
    consumePdbxAuditRevisionHistory(org.rcsb.cif.schema.mm.PdbxAuditRevisionHistory pdbxAuditRevisionHistory)
    Consume a particular Cif category.
    void
    consumePdbxChemCompIdentifier(org.rcsb.cif.schema.mm.PdbxChemCompIdentifier pdbxChemCompIdentifier)
    Consume a particular Cif category.
    void
    consumePdbxDatabaseStatus(org.rcsb.cif.schema.mm.PdbxDatabaseStatus pdbxDatabaseStatus)
    Consume a particular Cif category.
    void
    consumePdbxEntityBranchDescriptor(org.rcsb.cif.schema.mm.PdbxEntityBranchDescriptor pdbxEntityBranchDescriptor)
    Consume a particular Cif category.
    void
    consumePdbxMolecule(org.rcsb.cif.schema.mm.PdbxMolecule pdbxMolecule)
    Consume a particular Cif category.
    void
    consumePdbxMoleculeFeatures(org.rcsb.cif.schema.mm.PdbxMoleculeFeatures pdbxMoleculeFeatures)
    Consume a particular Cif category.
    void
    consumePdbxNonpolyScheme(org.rcsb.cif.schema.mm.PdbxNonpolyScheme pdbxNonpolyScheme)
    Consume a particular Cif category.
    void
    consumePdbxReferenceEntityLink(org.rcsb.cif.schema.mm.PdbxReferenceEntityLink pdbxReferenceEntityLink)
    Consume a particular Cif category.
    void
    consumePdbxReferenceEntityList(org.rcsb.cif.schema.mm.PdbxReferenceEntityList pdbxReferenceEntityList)
    Consume a particular Cif category.
    void
    consumePdbxReferenceEntityPolyLink(org.rcsb.cif.schema.mm.PdbxReferenceEntityPolyLink pdbxReferenceEntityPolyLink)
    Consume a particular Cif category.
    void
    consumePdbxStructAssembly(org.rcsb.cif.schema.mm.PdbxStructAssembly pdbxStructAssembly)
    Consume a particular Cif category.
    void
    consumePdbxStructAssemblyGen(org.rcsb.cif.schema.mm.PdbxStructAssemblyGen pdbxStructAssemblyGen)
    Consume a particular Cif category.
    void
    consumePdbxStructModResidue(org.rcsb.cif.schema.mm.PdbxStructModResidue pdbxStructModResidue)
    Consume a particular Cif category.
    void
    consumePdbxStructOperList(org.rcsb.cif.schema.mm.PdbxStructOperList pdbxStructOperList)
    Consume a particular Cif category.
    void
    consumeRefine(org.rcsb.cif.schema.mm.Refine refine)
    Consume a particular Cif category.
    void
    consumeStruct(org.rcsb.cif.schema.mm.Struct struct)
    Consume a particular Cif category.
    void
    consumeStructAsym(org.rcsb.cif.schema.mm.StructAsym structAsym)
    Consume a particular Cif category.
    void
    consumeStructConf(org.rcsb.cif.schema.mm.StructConf structConf)
    Consume a particular Cif category.
    void
    consumeStructConn(org.rcsb.cif.schema.mm.StructConn structConn)
    Consume a particular Cif category.
    void
    consumeStructConnType(org.rcsb.cif.schema.mm.StructConnType structConnType)
    Consume a particular Cif category.
    void
    consumeStructKeywords(org.rcsb.cif.schema.mm.StructKeywords structKeywords)
    Consume a particular Cif category.
    void
    consumeStructNcsOper(org.rcsb.cif.schema.mm.StructNcsOper structNcsOper)
    Consume a particular Cif category.
    void
    consumeStructRef(org.rcsb.cif.schema.mm.StructRef structRef)
    Consume a particular Cif category.
    void
    consumeStructRefSeq(org.rcsb.cif.schema.mm.StructRefSeq structRefSeq)
    Consume a particular Cif category.
    void
    consumeStructRefSeqDif(org.rcsb.cif.schema.mm.StructRefSeqDif structRefSeqDif)
    Consume a particular Cif category.
    void
    consumeStructSheetRange(org.rcsb.cif.schema.mm.StructSheetRange structSheetRange)
    Consume a particular Cif category.
    void
    consumeStructSite(org.rcsb.cif.schema.mm.StructSite structSite)
    Consume a particular Cif category.
    void
    consumeStructSiteGen(org.rcsb.cif.schema.mm.StructSiteGen structSiteGen)
    Consume a particular Cif category.
    void
    consumeSymmetry(org.rcsb.cif.schema.mm.Symmetry symmetry)
    Consume a particular Cif category.
    void
    finish()
    Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.
    Structure
    getContainer()
    Retrieve the created container representing a CIF file.
    void
    prepare()
    Setup routine which initializes a new container.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait