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

Constructor Detail

CifStructureConsumerImpl

public CifStructureConsumerImpl(FileParsingParameters params)

Method Detail

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