/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.io.mmcif;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
import org.biojava.nbio.structure.io.mmcif.model.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.List;
public class ChemCompConsumer implements MMcifConsumer {
private static final Logger logger = LoggerFactory.getLogger(ChemCompConsumer.class);
ChemicalComponentDictionary dictionary;
String latestChemCompId;
public ChemCompConsumer(){
dictionary = new ChemicalComponentDictionary();
}
@Override
public void documentStart() {
}
public ChemicalComponentDictionary getDictionary(){
return dictionary;
}
@Override
public void newChemComp(ChemComp c) {
if ( c.getId() == null)
logger.warn("chem comp ID == null " + c);
latestChemCompId = c.getId();
dictionary.addChemComp(c);
if ( c.getResidueType() == ResidueType.nonPolymer)
return;
if ( c.getResidueType() == ResidueType.saccharide)
return;
if ( c.getResidueType() == ResidueType.dSaccharide)
return;
//if ( c.isStandard())
// System.out.println(c);
}
@Override
public void documentEnd() {
}
@Override
public void newAtomSite(AtomSite atom) {
}
@Override
public void newDatabasePDBremark(DatabasePDBremark remark) {
}
@Override
public void newDatabasePDBrev(DatabasePDBrev dbrev) {
}
@Override
public void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev) {
}
@Override
public void newEntity(Entity entity) {
}
@Override
public void newEntityPolySeq(EntityPolySeq epolseq) {
}
@Override
public void newExptl(Exptl exptl) {
}
@Override
public void newCell(Cell cell) {
}
@Override
public void newSymmetry(Symmetry symmetry) {
}
@Override
public void newStructNcsOper(StructNcsOper sNcsOper) {
}
@Override
public void newAtomSites(AtomSites atomSites) {
}
@Override
public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen) {
}
@Override
public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss) {
}
@Override
public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss) {
}
@Override
public void newRefine(Refine r) {
}
@Override
public void newStructAsym(StructAsym sasym) {
}
@Override
public void newStructKeywords(StructKeywords kw) {
}
@Override
public void newStructRef(StructRef sref) {
}
@Override
public void newStructRefSeq(StructRefSeq sref) {
}
@Override
public void newStructRefSeqDif(StructRefSeqDif sref) {
}
@Override
public void setStruct(Struct struct) {
}
@Override
public void newGenericData(String category, List<String> loopFields,
List<String> lineData) {
//System.out.println("unhandled category: " + category);
}
@Override
public void newAuditAuthor(AuditAuthor aa)
{
}
@Override
public FileParsingParameters getFileParsingParameters()
{
// can be ingored in this case...
return null;
}
@Override
public void setFileParsingParameters(FileParsingParameters params)
{
}
@Override
public void newChemCompDescriptor(ChemCompDescriptor ccd) {
ChemComp cc = dictionary.getChemComp(latestChemCompId);
cc.getDescriptors().add(ccd);
}
@Override
public void newPdbxStructOperList(PdbxStructOperList structOper) {
}
@Override
public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly) {
}
@Override
public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly) {
}
@Override
public void newChemCompAtom(ChemCompAtom atom) {
dictionary.getChemComp(latestChemCompId).getAtoms().add(atom);
}
@Override
public void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id) {
}
@Override
public void newChemCompBond(ChemCompBond bond) {
dictionary.getChemComp(latestChemCompId).getBonds().add(bond);
}
@Override
public void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc) {
}
@Override
public void newEntitySrcGen(EntitySrcGen entitySrcGen) {
}
@Override
public void newEntitySrcNat(EntitySrcNat entitySrcNat) {
}
@Override
public void newEntitySrcSyn(EntitySrcSyn entitySrcSyn) {
}
@Override
public void newStructConn(StructConn structConn) {
}
@Override
public void newStructSiteGen(StructSiteGen gen) {
}
@Override
public void newStructSite(StructSite site) {
}
@Override
public void newEntityPoly(EntityPoly entityPoly) {
}
}