java.lang.Object

org.biojava.nbio.structure.io.mmcif.ChemCompConsumer

All Implemented Interfaces:: MMcifConsumer

public class ChemCompConsumer extends Object implements MMcifConsumer

Constructor Summary

Constructors

Constructor

Description

ChemCompConsumer()
Method Summary

Modifier and Type

Method

Description

void

documentEnd()

called at end of document

void

documentStart()

called at start of document

ChemicalComponentDictionary

getDictionary()

FileParsingParameters

getFileParsingParameters()

void

newAtomSite(AtomSite atom)

A new AtomSite record has been read.

void

newAtomSites(AtomSites atomSites)

void

newAuditAuthor(AuditAuthor aa)

AuditAuthor contains the info from the PDB-AUTHOR records.

void

newCell(Cell cell)

void

newChemComp(ChemComp c)

void

newChemCompAtom(ChemCompAtom atom)

void

newChemCompBond(ChemCompBond bond)

void

newChemCompDescriptor(ChemCompDescriptor ccd)

void

newDatabasePDBremark(DatabasePDBremark remark)

void

newDatabasePDBrev(DatabasePDBrev dbrev)

void

newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev)

void

newEntity(Entity entity)

void

newEntityPolySeq(EntityPolySeq epolseq)

void

newEntitySrcGen(EntitySrcGen entitySrcGen)

void

newEntitySrcNat(EntitySrcNat entitySrcNat)

void

newEntitySrcSyn(EntitySrcSyn entitySrcSyn)

void

newExptl(Exptl exptl)

void

newGenericData(String category, List<String> loopFields, List<String> lineData)

This method is called if no particular handler for the provided cif category has been implemented so far.

void

newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)

void

newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)

void

newPdbxEntityNonPoly(PdbxEntityNonPoly pen)

void

newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)

void

newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)

void

newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)

void

newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)

void

newPdbxStructOperList(PdbxStructOperList structOper)

void

newRefine(Refine r)

void

newStructAsym(StructAsym sasym)

void

newStructConn(StructConn structConn)

void

newStructKeywords(StructKeywords kw)

void

newStructNcsOper(StructNcsOper sNcsOper)

void

newStructRef(StructRef sref)

void

newStructRefSeq(StructRefSeq sref)

void

newStructRefSeqDif(StructRefSeqDif sref)

void

newStructSite(StructSite site)

void

newStructSiteGen(StructSiteGen gen)

void

newSymmetry(Symmetry symmetry)

void

setFileParsingParameters(FileParsingParameters params)

void

setStruct(Struct struct)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- ChemCompConsumer
  
  public ChemCompConsumer()
Method Details
- documentStart
  
  public void documentStart()
  
  Description copied from interface: MMcifConsumer
  
  called at start of document
  
  Specified by:
  
  documentStart in interface MMcifConsumer
- getDictionary
  
  public ChemicalComponentDictionary getDictionary()
- newChemComp
  
  public void newChemComp(ChemComp c)
  
  Specified by:
  
  newChemComp in interface MMcifConsumer
- documentEnd
  
  public void documentEnd()
  
  Description copied from interface: MMcifConsumer
  
  called at end of document
  
  Specified by:
  
  documentEnd in interface MMcifConsumer
- newAtomSite
  
  public void newAtomSite(AtomSite atom)
  
  Description copied from interface: MMcifConsumer
  
  A new AtomSite record has been read. Contains the Atom data
  
  Specified by:
  
  newAtomSite in interface MMcifConsumer
- newDatabasePDBremark
  
  public void newDatabasePDBremark(DatabasePDBremark remark)
  
  Specified by:
  
  newDatabasePDBremark in interface MMcifConsumer
- newDatabasePDBrev
  
  public void newDatabasePDBrev(DatabasePDBrev dbrev)
  
  Specified by:
  
  newDatabasePDBrev in interface MMcifConsumer
- newDatabasePDBrevRecord
  
  public void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev)
  
  Specified by:
  
  newDatabasePDBrevRecord in interface MMcifConsumer
- newEntity
  
  public void newEntity(Entity entity)
  
  Specified by:
  
  newEntity in interface MMcifConsumer
- newEntityPolySeq
  
  public void newEntityPolySeq(EntityPolySeq epolseq)
  
  Specified by:
  
  newEntityPolySeq in interface MMcifConsumer
- newExptl
  
  public void newExptl(Exptl exptl)
  
  Specified by:
  
  newExptl in interface MMcifConsumer
- newCell
  
  public void newCell(Cell cell)
  
  Specified by:
  
  newCell in interface MMcifConsumer
- newSymmetry
  
  public void newSymmetry(Symmetry symmetry)
  
  Specified by:
  
  newSymmetry in interface MMcifConsumer
- newStructNcsOper
  
  public void newStructNcsOper(StructNcsOper sNcsOper)
  
  Specified by:
  
  newStructNcsOper in interface MMcifConsumer
- newAtomSites
  
  public void newAtomSites(AtomSites atomSites)
  
  Specified by:
  
  newAtomSites in interface MMcifConsumer
- newPdbxEntityNonPoly
  
  public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen)
  
  Specified by:
  
  newPdbxEntityNonPoly in interface MMcifConsumer
- newPdbxNonPolyScheme
  
  public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss)
  
  Specified by:
  
  newPdbxNonPolyScheme in interface MMcifConsumer
- newPdbxPolySeqScheme
  
  public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss)
  
  Specified by:
  
  newPdbxPolySeqScheme in interface MMcifConsumer
- newRefine
  
  public void newRefine(Refine r)
  
  Specified by:
  
  newRefine in interface MMcifConsumer
- newStructAsym
  
  public void newStructAsym(StructAsym sasym)
  
  Specified by:
  
  newStructAsym in interface MMcifConsumer
- newStructKeywords
  
  public void newStructKeywords(StructKeywords kw)
  
  Specified by:
  
  newStructKeywords in interface MMcifConsumer
- newStructRef
  
  public void newStructRef(StructRef sref)
  
  Specified by:
  
  newStructRef in interface MMcifConsumer
- newStructRefSeq
  
  public void newStructRefSeq(StructRefSeq sref)
  
  Specified by:
  
  newStructRefSeq in interface MMcifConsumer
- newStructRefSeqDif
  
  public void newStructRefSeqDif(StructRefSeqDif sref)
  
  Specified by:
  
  newStructRefSeqDif in interface MMcifConsumer
- setStruct
  
  public void setStruct(Struct struct)
  
  Specified by:
  
  setStruct in interface MMcifConsumer
- newGenericData
  
  public void newGenericData(String category, List<String> loopFields, List<String> lineData)
  
  Description copied from interface: MMcifConsumer
  
  This method is called if no particular handler for the provided cif category has been implemented so far.
  
  Specified by:
  
  newGenericData in interface MMcifConsumer
  
  Parameters:
  
  category - The category that is being processed.
  
  loopFields - the fields of this category.
  
  lineData - the data that is being provided.
- newAuditAuthor
  
  public void newAuditAuthor(AuditAuthor aa)
  
  Description copied from interface: MMcifConsumer
  
  AuditAuthor contains the info from the PDB-AUTHOR records.
  
  Specified by:
  
  newAuditAuthor in interface MMcifConsumer
- getFileParsingParameters
  
  public FileParsingParameters getFileParsingParameters()
  
  Specified by:
  
  getFileParsingParameters in interface MMcifConsumer
- setFileParsingParameters
  
  public void setFileParsingParameters(FileParsingParameters params)
  
  Specified by:
  
  setFileParsingParameters in interface MMcifConsumer
- newChemCompDescriptor
  
  public void newChemCompDescriptor(ChemCompDescriptor ccd)
  
  Specified by:
  
  newChemCompDescriptor in interface MMcifConsumer
- newPdbxStructOperList
  
  public void newPdbxStructOperList(PdbxStructOperList structOper)
  
  Specified by:
  
  newPdbxStructOperList in interface MMcifConsumer
- newPdbxStrucAssembly
  
  public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly)
  
  Specified by:
  
  newPdbxStrucAssembly in interface MMcifConsumer
- newPdbxStrucAssemblyGen
  
  public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly)
  
  Specified by:
  
  newPdbxStrucAssemblyGen in interface MMcifConsumer
- newChemCompAtom
  
  public void newChemCompAtom(ChemCompAtom atom)
  
  Specified by:
  
  newChemCompAtom in interface MMcifConsumer
- newPdbxChemCompIndentifier
  
  public void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id)
  
  Specified by:
  
  newPdbxChemCompIndentifier in interface MMcifConsumer
- newChemCompBond
  
  public void newChemCompBond(ChemCompBond bond)
  
  Specified by:
  
  newChemCompBond in interface MMcifConsumer
- newPdbxChemCompDescriptor
  
  public void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc)
  
  Specified by:
  
  newPdbxChemCompDescriptor in interface MMcifConsumer
- newEntitySrcGen
  
  public void newEntitySrcGen(EntitySrcGen entitySrcGen)
  
  Specified by:
  
  newEntitySrcGen in interface MMcifConsumer
- newEntitySrcNat
  
  public void newEntitySrcNat(EntitySrcNat entitySrcNat)
  
  Specified by:
  
  newEntitySrcNat in interface MMcifConsumer
- newEntitySrcSyn
  
  public void newEntitySrcSyn(EntitySrcSyn entitySrcSyn)
  
  Specified by:
  
  newEntitySrcSyn in interface MMcifConsumer
- newStructConn
  
  public void newStructConn(StructConn structConn)
  
  Specified by:
  
  newStructConn in interface MMcifConsumer
- newStructSiteGen
  
  public void newStructSiteGen(StructSiteGen gen)
  
  Specified by:
  
  newStructSiteGen in interface MMcifConsumer
- newStructSite
  
  public void newStructSite(StructSite site)
  
  Specified by:
  
  newStructSite in interface MMcifConsumer

Class ChemCompConsumer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

ChemCompConsumer

Method Details

documentStart

getDictionary

newChemComp

documentEnd

newAtomSite

newDatabasePDBremark

newDatabasePDBrev

newDatabasePDBrevRecord

newEntity

newEntityPolySeq

newExptl

newCell

newSymmetry

newStructNcsOper

newAtomSites

newPdbxEntityNonPoly

newPdbxNonPolyScheme

newPdbxPolySeqScheme

newRefine

newStructAsym

newStructKeywords

newStructRef

newStructRefSeq

newStructRefSeqDif

setStruct

newGenericData

newAuditAuthor

getFileParsingParameters

setFileParsingParameters

newChemCompDescriptor

newPdbxStructOperList

newPdbxStrucAssembly

newPdbxStrucAssemblyGen

newChemCompAtom

newPdbxChemCompIndentifier

newChemCompBond

newPdbxChemCompDescriptor

newEntitySrcGen

newEntitySrcNat

newEntitySrcSyn

newStructConn

newStructSiteGen

newStructSite