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
     
  • 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
    Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.
    Retrieve the created container representing a CIF file.
    void
    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
  • Constructor Details

  • Method Details

    • prepare

      public void prepare()
      Description copied from interface: CifFileConsumer
      Setup routine which initializes a new container.
      Specified by:
      prepare in interface CifFileConsumer<Structure>
    • consumeAtomSite

      public void consumeAtomSite(org.rcsb.cif.schema.mm.AtomSite atomSite)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeAtomSite in interface CifStructureConsumer
      Parameters:
      atomSite - data
    • consumeAtomSites

      public void consumeAtomSites(org.rcsb.cif.schema.mm.AtomSites atomSites)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeAtomSites in interface CifStructureConsumer
      Parameters:
      atomSites - data
    • consumeAuditAuthor

      public void consumeAuditAuthor(org.rcsb.cif.schema.mm.AuditAuthor auditAuthor)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeAuditAuthor in interface CifStructureConsumer
      Parameters:
      auditAuthor - data
    • consumeCell

      public void consumeCell(org.rcsb.cif.schema.mm.Cell cell)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeCell in interface CifStructureConsumer
      Parameters:
      cell - data
    • consumeChemComp

      public void consumeChemComp(org.rcsb.cif.schema.mm.ChemComp chemComp)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeChemComp in interface CifStructureConsumer
      Parameters:
      chemComp - data
    • consumeChemCompBond

      public void consumeChemCompBond(org.rcsb.cif.schema.mm.ChemCompBond chemCompBond)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeChemCompBond in interface CifStructureConsumer
      Parameters:
      chemCompBond - data
    • consumeDatabasePDBRemark

      public void consumeDatabasePDBRemark(org.rcsb.cif.schema.mm.DatabasePDBRemark databasePDBremark)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeDatabasePDBRemark in interface CifStructureConsumer
      Parameters:
      databasePDBremark - data
    • consumeDatabasePDBRev

      public void consumeDatabasePDBRev(org.rcsb.cif.schema.mm.DatabasePDBRev databasePDBrev)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeDatabasePDBRev in interface CifStructureConsumer
      Parameters:
      databasePDBrev - data
    • consumeDatabasePDBRevRecord

      public void consumeDatabasePDBRevRecord(org.rcsb.cif.schema.mm.DatabasePDBRevRecord databasePDBrevRecord)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeDatabasePDBRevRecord in interface CifStructureConsumer
      Parameters:
      databasePDBrevRecord - data
    • consumeEm3dReconstruction

      public void consumeEm3dReconstruction(org.rcsb.cif.schema.mm.Em3dReconstruction em3dReconstruction)
      Description copied from interface: CifStructureConsumer
      Consume Electron Microscopy 3D reconstruction data
      Specified by:
      consumeEm3dReconstruction in interface CifStructureConsumer
    • consumeEntity

      public void consumeEntity(org.rcsb.cif.schema.mm.Entity entity)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeEntity in interface CifStructureConsumer
      Parameters:
      entity - data
    • consumeEntityPoly

      public void consumeEntityPoly(org.rcsb.cif.schema.mm.EntityPoly entityPoly)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeEntityPoly in interface CifStructureConsumer
      Parameters:
      entityPoly - data
    • consumeEntitySrcGen

      public void consumeEntitySrcGen(org.rcsb.cif.schema.mm.EntitySrcGen entitySrcGen)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeEntitySrcGen in interface CifStructureConsumer
      Parameters:
      entitySrcGen - data
    • consumeEntitySrcNat

      public void consumeEntitySrcNat(org.rcsb.cif.schema.mm.EntitySrcNat entitySrcNat)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeEntitySrcNat in interface CifStructureConsumer
      Parameters:
      entitySrcNat - data
    • consumeEntitySrcSyn

      public void consumeEntitySrcSyn(org.rcsb.cif.schema.mm.PdbxEntitySrcSyn entitySrcSyn)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeEntitySrcSyn in interface CifStructureConsumer
      Parameters:
      entitySrcSyn - data
    • consumeEntityPolySeq

      public void consumeEntityPolySeq(org.rcsb.cif.schema.mm.EntityPolySeq entityPolySeq)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeEntityPolySeq in interface CifStructureConsumer
      Parameters:
      entityPolySeq - data
    • consumeExptl

      public void consumeExptl(org.rcsb.cif.schema.mm.Exptl exptl)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeExptl in interface CifStructureConsumer
      Parameters:
      exptl - data
    • consumePdbxAuditRevisionHistory

      public void consumePdbxAuditRevisionHistory(org.rcsb.cif.schema.mm.PdbxAuditRevisionHistory pdbxAuditRevisionHistory)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxAuditRevisionHistory in interface CifStructureConsumer
      Parameters:
      pdbxAuditRevisionHistory - data
    • consumePdbxChemCompIdentifier

      public void consumePdbxChemCompIdentifier(org.rcsb.cif.schema.mm.PdbxChemCompIdentifier pdbxChemCompIdentifier)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxChemCompIdentifier in interface CifStructureConsumer
      Parameters:
      pdbxChemCompIdentifier - data
    • consumePdbxDatabaseStatus

      public void consumePdbxDatabaseStatus(org.rcsb.cif.schema.mm.PdbxDatabaseStatus pdbxDatabaseStatus)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxDatabaseStatus in interface CifStructureConsumer
      Parameters:
      pdbxDatabaseStatus - data
    • consumePdbxEntityBranchDescriptor

      public void consumePdbxEntityBranchDescriptor(org.rcsb.cif.schema.mm.PdbxEntityBranchDescriptor pdbxEntityBranchDescriptor)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxEntityBranchDescriptor in interface CifStructureConsumer
      Parameters:
      pdbxEntityBranchDescriptor - data
    • consumePdbxMolecule

      public void consumePdbxMolecule(org.rcsb.cif.schema.mm.PdbxMolecule pdbxMolecule)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxMolecule in interface CifStructureConsumer
      Parameters:
      pdbxMolecule - data
    • consumePdbxMoleculeFeatures

      public void consumePdbxMoleculeFeatures(org.rcsb.cif.schema.mm.PdbxMoleculeFeatures pdbxMoleculeFeatures)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxMoleculeFeatures in interface CifStructureConsumer
      Parameters:
      pdbxMoleculeFeatures - data
    • consumePdbxNonpolyScheme

      public void consumePdbxNonpolyScheme(org.rcsb.cif.schema.mm.PdbxNonpolyScheme pdbxNonpolyScheme)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxNonpolyScheme in interface CifStructureConsumer
      Parameters:
      pdbxNonpolyScheme - data
    • consumePdbxReferenceEntityLink

      public void consumePdbxReferenceEntityLink(org.rcsb.cif.schema.mm.PdbxReferenceEntityLink pdbxReferenceEntityLink)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxReferenceEntityLink in interface CifStructureConsumer
      Parameters:
      pdbxReferenceEntityLink - data
    • consumePdbxReferenceEntityList

      public void consumePdbxReferenceEntityList(org.rcsb.cif.schema.mm.PdbxReferenceEntityList pdbxReferenceEntityList)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxReferenceEntityList in interface CifStructureConsumer
      Parameters:
      pdbxReferenceEntityList - data
    • consumePdbxReferenceEntityPolyLink

      public void consumePdbxReferenceEntityPolyLink(org.rcsb.cif.schema.mm.PdbxReferenceEntityPolyLink pdbxReferenceEntityPolyLink)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxReferenceEntityPolyLink in interface CifStructureConsumer
      Parameters:
      pdbxReferenceEntityPolyLink - data
    • consumePdbxStructAssembly

      public void consumePdbxStructAssembly(org.rcsb.cif.schema.mm.PdbxStructAssembly pdbxStructAssembly)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxStructAssembly in interface CifStructureConsumer
      Parameters:
      pdbxStructAssembly - data
    • consumePdbxStructAssemblyGen

      public void consumePdbxStructAssemblyGen(org.rcsb.cif.schema.mm.PdbxStructAssemblyGen pdbxStructAssemblyGen)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxStructAssemblyGen in interface CifStructureConsumer
      Parameters:
      pdbxStructAssemblyGen - data
    • consumePdbxStructModResidue

      public void consumePdbxStructModResidue(org.rcsb.cif.schema.mm.PdbxStructModResidue pdbxStructModResidue)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxStructModResidue in interface CifStructureConsumer
      Parameters:
      pdbxStructModResidue - data
    • consumePdbxStructOperList

      public void consumePdbxStructOperList(org.rcsb.cif.schema.mm.PdbxStructOperList pdbxStructOperList)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumePdbxStructOperList in interface CifStructureConsumer
      Parameters:
      pdbxStructOperList - data
    • consumeRefine

      public void consumeRefine(org.rcsb.cif.schema.mm.Refine refine)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeRefine in interface CifStructureConsumer
      Parameters:
      refine - data
    • consumeStruct

      public void consumeStruct(org.rcsb.cif.schema.mm.Struct struct)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStruct in interface CifStructureConsumer
      Parameters:
      struct - data
    • consumeStructAsym

      public void consumeStructAsym(org.rcsb.cif.schema.mm.StructAsym structAsym)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructAsym in interface CifStructureConsumer
      Parameters:
      structAsym - data
    • consumeStructConf

      public void consumeStructConf(org.rcsb.cif.schema.mm.StructConf structConf)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructConf in interface CifStructureConsumer
      Parameters:
      structConf - data
    • consumeStructConn

      public void consumeStructConn(org.rcsb.cif.schema.mm.StructConn structConn)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructConn in interface CifStructureConsumer
      Parameters:
      structConn - data
    • consumeStructConnType

      public void consumeStructConnType(org.rcsb.cif.schema.mm.StructConnType structConnType)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructConnType in interface CifStructureConsumer
      Parameters:
      structConnType - data
    • consumeStructKeywords

      public void consumeStructKeywords(org.rcsb.cif.schema.mm.StructKeywords structKeywords)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructKeywords in interface CifStructureConsumer
      Parameters:
      structKeywords - data
    • consumeStructNcsOper

      public void consumeStructNcsOper(org.rcsb.cif.schema.mm.StructNcsOper structNcsOper)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructNcsOper in interface CifStructureConsumer
      Parameters:
      structNcsOper - data
    • consumeStructRef

      public void consumeStructRef(org.rcsb.cif.schema.mm.StructRef structRef)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructRef in interface CifStructureConsumer
      Parameters:
      structRef - data
    • consumeStructRefSeq

      public void consumeStructRefSeq(org.rcsb.cif.schema.mm.StructRefSeq structRefSeq)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructRefSeq in interface CifStructureConsumer
      Parameters:
      structRefSeq - data
    • consumeStructRefSeqDif

      public void consumeStructRefSeqDif(org.rcsb.cif.schema.mm.StructRefSeqDif structRefSeqDif)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructRefSeqDif in interface CifStructureConsumer
      Parameters:
      structRefSeqDif - data
    • consumeStructSheetRange

      public void consumeStructSheetRange(org.rcsb.cif.schema.mm.StructSheetRange structSheetRange)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructSheetRange in interface CifStructureConsumer
      Parameters:
      structSheetRange - data
    • consumeStructSite

      public void consumeStructSite(org.rcsb.cif.schema.mm.StructSite structSite)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructSite in interface CifStructureConsumer
      Parameters:
      structSite - data
    • consumeStructSiteGen

      public void consumeStructSiteGen(org.rcsb.cif.schema.mm.StructSiteGen structSiteGen)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeStructSiteGen in interface CifStructureConsumer
      Parameters:
      structSiteGen - data
    • consumeSymmetry

      public void consumeSymmetry(org.rcsb.cif.schema.mm.Symmetry symmetry)
      Description copied from interface: CifStructureConsumer
      Consume a particular Cif category.
      Specified by:
      consumeSymmetry in interface CifStructureConsumer
      Parameters:
      symmetry - data
    • finish

      public void finish()
      Description copied from interface: CifFileConsumer
      Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.
      Specified by:
      finish in interface CifFileConsumer<Structure>
    • getContainer

      public Structure getContainer()
      Description copied from interface: CifFileConsumer
      Retrieve the created container representing a CIF file.
      Specified by:
      getContainer in interface CifFileConsumer<Structure>
      Returns:
      all desired information wrapped as object of type S