org.biojava.nbio.structure.io.SandboxStyleStructureProvider 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;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.core.util.InputStreamProvider;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;


/** The "Sandbox" style of organizing files is  to have a directory structure like below, i.e. the files are organized into
 * 
 * 	directory with two characters, based on the two middle characters of a PDB ID
 * 	directory of PDB ID
 * 	several files that are available for this PDB ID
 * 
 *
 * a1/2a1v/2a1v.cif.gz
a1/2a1v/2a1v.dssp.gz
a1/2a1v/2a1v.pdb-250.jpg.gz
a1/2a1v/2a1v.pdb-500.jpg.gz
a1/2a1v/2a1v.pdb-65.jpg.gz
a1/2a1v/2a1v.pdb-80.jpg.gz
a1/2a1v/2a1v.pdb1-250.jpg.gz
a1/2a1v/2a1v.pdb1-500.jpg.gz
a1/2a1v/2a1v.pdb1-65.jpg.gz
a1/2a1v/2a1v.pdb1-80.jpg.gz
a1/2a1v/2a1v.pdb1.gz
a1/2a1v/2a1v.stride.gz
a1/2a1v/2a1v.xml.gz
a1/2a1v/pdb2a1v.ent.gz
a1/2a1v/r2a1vsf.ent.gz
a1/2a1w/2a1w-deriv.cif.gz
a1/2a1w/2a1w-extatom.xml.gz
a1/2a1w/2a1w-noatom.xml.gz
a1/2a1w/2a1w.cif.gz
a1/2a1w/2a1w.dssp.gz
a1/2a1w/2a1w.pdb-250.jpg.gz
a1/2a1w/2a1w.pdb-500.jpg.gz
a1/2a1w/2a1w.pdb-65.jpg.gz
a1/2a1w/2a1w.pdb-80.jpg.gz
a1/2a1w/2a1w.pdb1-250.jpg.gz
a1/2a1w/2a1w.pdb1-500.jpg.gz
a1/2a1w/2a1w.pdb1-65.jpg.gz
a1/2a1w/2a1w.pdb1-80.jpg.gz
a1/2a1w/2a1w.pdb1.gz
a1/2a1w/2a1w.pdb2-250.jpg.gz
a1/2a1w/2a1w.pdb2-500.jpg.gz
a1/2a1w/2a1w.pdb2-65.jpg.gz
a1/2a1w/2a1w.pdb2-80.jpg.gz
a1/2a1w/2a1w.pdb2.gz
a1/2a1w/2a1w.pdb3-250.jpg.gz
a1/2a1w/2a1w.pdb3-500.jpg.gz
a1/2a1w/2a1w.pdb3-65.jpg.gz
a1/2a1w/2a1w.pdb3-80.jpg.gz
a1/2a1w/2a1w.pdb3.gz
a1/2a1w/2a1w.pdb4-250.jpg.gz
a1/2a1w/2a1w.pdb4-500.jpg.gz
a1/2a1w/2a1w.pdb4-65.jpg.gz
a1/2a1w/2a1w.pdb4-80.jpg.gz
a1/2a1w/2a1w.pdb4.gz
a1/2a1w/2a1w.pdb5-250.jpg.gz
a1/2a1w/2a1w.pdb5-500.jpg.gz
a1/2a1w/2a1w.pdb5-65.jpg.gz
a1/2a1w/2a1w.pdb5-80.jpg.gz
a1/2a1w/2a1w.pdb5.gz
a1/2a1w/2a1w.pdb6-250.jpg.gz
a1/2a1w/2a1w.pdb6-500.jpg.gz
a1/2a1w/2a1w.pdb6-65.jpg.gz
a1/2a1w/2a1w.pdb6-80.jpg.gz
a1/2a1w/2a1w.pdb6.gz
a1/2a1w/2a1w.stride.gz
a1/2a1w/2a1w.xml.gz
a1/2a1w/pdb2a1w.ent.gz
a1/2a1w/r2a1wsf.ent.gz
a1/2a1x/2a1x-deriv.cif.gz
a1/2a1x/2a1x-extatom.xml.gz
a1/2a1x/2a1x-noatom.xml.gz

 *
 *
 * @author Andreas Prlic
 *
 *
 *@ since3.2
 */
public class SandboxStyleStructureProvider implements StructureProvider {
	FileParsingParameters params ;

	String path;
	public static final String fileSeparator = System.getProperty("file.separator");

	public SandboxStyleStructureProvider() {
		params = new FileParsingParameters();

		UserConfiguration config = new UserConfiguration();

		setPath(config.getPdbFilePath());
	}

	/** directory where to find PDB files */
	public void setPath(String p){

		path = p ;

		if ( ! (path.endsWith(fileSeparator) ) )
			path = path + fileSeparator;

	}

	@Override
	public Structure getStructureById(String pdbId) throws IOException,StructureException {


		if (pdbId == null || pdbId.length()< 4)
			throw new StructureException("This does not look like a valid PDB ID! (" + pdbId + ")");

		pdbId = pdbId.toLowerCase();

		String middle = pdbId.substring(1,3).toLowerCase();

		File f = new File(path + fileSeparator + middle + fileSeparator + pdbId  + fileSeparator + "pdb" + pdbId + ".ent.gz");

		if (! f.exists()){

		}


		InputStreamProvider isp = new InputStreamProvider();

		InputStream inputStream = isp.getInputStream(f);
		PDBFileParser pdbpars = new PDBFileParser();
		pdbpars.setFileParsingParameters(params);

		Structure struc = pdbpars.parsePDBFile(inputStream) ;
		return struc ;

		// something is wrong with the file!
		// it probably should be downloaded again...
		// TODO: add auto-download functionality...
	}

	@Override
	public void setFileParsingParameters(FileParsingParameters params) {
		this.params = params;
	}

	@Override
	public FileParsingParameters getFileParsingParameters() {
		return params;
	}

	/** Returns a list of all PDB IDs that are available in this installation
	 *
	 * @return a list of PDB IDs
	 */
	public List getAllPDBIDs() throws IOException{

		File f = new File(path);
		if ( ! f.isDirectory())
			throw new IOException("Path " + path + " is not a directory!");

		String[] dirName = f.list();

		ListpdbIds = new ArrayList();
		for (String dir : dirName) {
			File d2= new File(f,dir);
			if ( ! d2.isDirectory())
				continue;

			String[] pdbDirs = d2.list();
			for (String pdbId : pdbDirs) {
				if ( ! pdbIds.contains(pdbId))
					pdbIds.add(pdbId);

			}
		}

		return pdbIds;
	}

}