Class CifStructureConsumerImpl
java.lang.Object
org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
- All Implemented Interfaces:
CifFileConsumer<Structure>
,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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
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 datavoid
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.Retrieve the created container representing a CIF file.void
prepare()
Setup routine which initializes a new container.
-
Constructor Details
-
CifStructureConsumerImpl
-
-
Method Details
-
prepare
public void prepare()Description copied from interface:CifFileConsumer
Setup routine which initializes a new container.- Specified by:
prepare
in interfaceCifFileConsumer<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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- Parameters:
em3dReconstruction
-
-
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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifStructureConsumer
- 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 interfaceCifFileConsumer<Structure>
-
getContainer
Description copied from interface:CifFileConsumer
Retrieve the created container representing a CIF file.- Specified by:
getContainer
in interfaceCifFileConsumer<Structure>
- Returns:
- all desired information wrapped as object of type
S
-