org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of biojava-structure Show documentation
The protein structure modules of BioJava.
There is a newer version: 7.2.2
/*
 *                    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.quaternary.io;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;



/** A provider for information about biological units for PDB files that is based on reading local MMcif files.
 *
 * @author Andreas Prlic
 *
 */
public class MmCifPDBBiolAssemblyProvider implements RawBioUnitDataProvider{

	private static final Logger logger = LoggerFactory.getLogger(MmCifPDBBiolAssemblyProvider.class);

	private String pdbId;
	private List pdbxStructAssemblies;
	private List pdbxStructAssemblyGens;
	private List pdbxStructOperList;
	private Structure asymUnit;

	private AtomCache cache ;

	public MmCifPDBBiolAssemblyProvider(){
		//reset();
	}

	@Override
	public void setPdbId(String pdbId) {
		if ( cache == null)
			cache =new AtomCache();

		if (
				this.pdbId != null &&
				(this.pdbId.equals(pdbId))
				) {
			// we already have all the data we need...
			return;
		}

		this.pdbId= pdbId;

		reset();

		MMCIFFileReader reader = new MMCIFFileReader(cache.getPath());
		FileParsingParameters params = cache.getFileParsingParams();
		params.setAlignSeqRes(true);
		params.setParseBioAssembly(true);
		reader.setFileParsingParameters(params);
		reader.setFetchBehavior(cache.getFetchBehavior());
		reader.setObsoleteBehavior(cache.getObsoleteBehavior());

		try{
			asymUnit = reader.getStructureById(pdbId);
			if ( asymUnit.nrModels() > 1) {
				// why do some NMR structures have bio units???
				asymUnit = StructureTools.removeModels(asymUnit);
			}

			SimpleMMcifConsumer consumer = reader.getMMcifConsumer();


			pdbxStructOperList 		= consumer.getStructOpers();
			pdbxStructAssemblies 	= consumer.getStructAssemblies();
			pdbxStructAssemblyGens 	= consumer.getStructAssemblyGens();

			//System.out.println(asymUnit.getPDBHeader());

			//System.out.println("OPER:" + pdbxStructOperList);
			//System.out.println("ASSEMBLIES:" + pdbxStructAssemblies);
			//System.out.println("ASSEMBLYGENS:" + pdbxStructAssemblyGens);

			// reset the consumer data to avoid memory leaks
			consumer.documentStart();


			// here we trim in the same way as we do in SimpleMmcifConsumer, removing PAU and XAU bioassemblies, see #230 in github
			Iterator it = pdbxStructAssemblies.iterator();
			while (it.hasNext()) {
				PdbxStructAssembly psa = it.next();
				try {
					Integer.parseInt(psa.getId());
				} catch (NumberFormatException e) {
					logger.info("Ignoring bioassembly with id {} for PDB id {}", psa.getId(), pdbId);
					it.remove();
				}
			}

		} catch (IOException e){
			// TODO this should be thrown but setPdbId doesn't have a throws in contract, we need a better solution - JD 2016-01-27
			logger.error("IOException caught when reading mmcif file to get bioassembly for PDB " + pdbId, e);

		}
	}

	private void reset() {

		pdbxStructOperList   	= new ArrayList();
		pdbxStructAssemblies	= new ArrayList();
		pdbxStructAssemblyGens 	= new ArrayList();
		asymUnit = null;
	}

	public String getPdbId(){
		return pdbId;
	}

	@Override
	public List getPdbxStructAssemblies() {
		return pdbxStructAssemblies;
	}

	@Override
	public List getPdbxStructAssemblyGens() {
		return pdbxStructAssemblyGens;
	}

	@Override
	public List getPdbxStructOperList() {
		return pdbxStructOperList;
	}

	@Override
	public int getNrBiolAssemblies() {
		return pdbxStructAssemblies.size();
	}

	@Override
	public boolean hasBiolAssembly() {
		int nrAssemblies = getNrBiolAssemblies();
		if ( nrAssemblies > 0)
			return true;

		return false;
	}

	@Override
	public PdbxStructAssembly getPdbxStructAssembly(int biolAssemblyNr) {
		if ( biolAssemblyNr < getNrBiolAssemblies())
			return pdbxStructAssemblies.get(biolAssemblyNr);
		return null;
	}

	@Override
	public List getPdbxStructAssemblyGen(int biolAssemblyNr) {
		if ( biolAssemblyNr > getNrBiolAssemblies())
			return null;

		List psags = new ArrayList();
		for (PdbxStructAssemblyGen psag : pdbxStructAssemblyGens){
			if ( psag.getAssembly_id().equals((biolAssemblyNr +1)+ ""))
				psags.add(psag);
		}
		return psags;
	}

	/** get the asym unit for this PDB ID
	 *
	 * @return
	 */
	public Structure getAsymUnit(){
		return asymUnit;
	}

	public void setAsymUnit(Structure s){
		this.asymUnit = s;
	}

	public AtomCache getAtomCache() {
		return cache;
	}

	public void setAtomCache(AtomCache cache) {
		this.cache = cache;
	}



}