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

Class CifStructureConsumerImpl

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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.

    • Method Detail

      • 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

      • 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>