org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider 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.io.mmcif;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.zip.GZIPInputStream;

import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;


/** Unlike the {@link DownloadChemCompProvider}, this  {@link ChemCompProvider} does not download any chem comp definitions.
 * It has access to a limited set of files that are part of the biojava distribution.
 *
 * @author Andreas Prlic
 * @since 3.0
 */
public class ReducedChemCompProvider implements ChemCompProvider {

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

	public ReducedChemCompProvider(){
		logger.debug("Initialising ReducedChemCompProvider");
	}


	@Override
	public ChemComp getChemComp(String recordName) {
		String name = recordName.toUpperCase().trim();
		try(InputStream inStream = this.getClass().getResourceAsStream("/chemcomp/"+name + ".cif.gz")) {

			logger.debug("Reading chemcomp/"+name+".cif.gz");

			if ( inStream == null){
				//System.out.println("Could not find chem comp: " + name + " ... using generic Chem Comp");
				// could not find the chem comp definition for this in the jar file
				logger.debug("Getting empty chem comp for {}",name);
				ChemComp cc = ChemComp.getEmptyChemComp();
				cc.setId(name);
				return cc;
			}

			MMcifParser parser = new SimpleMMcifParser();

			ChemCompConsumer consumer = new ChemCompConsumer();

			// The Consumer builds up the BioJava - structure object.
			// you could also hook in your own and build up you own data model.
			parser.addMMcifConsumer(consumer);

			parser.parse(new BufferedReader(new InputStreamReader(new GZIPInputStream(inStream))));

			ChemicalComponentDictionary dict = consumer.getDictionary();

			ChemComp chemComp = dict.getChemComp(name);

			return chemComp;

		} catch (IOException e){
			logger.error("IOException caught while reading chem comp {}.",name,e);
		}
		logger.warn("Problem when loading chem comp {}, will use an empty chem comp for it", name);
		ChemComp cc = ChemComp.getEmptyChemComp();
		cc.setId(name);
		return cc;
	}


}