cifreader.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 * $Revision: 7636 $
 *
 * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 *
 * Contact: [e-mail]
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 */
package org.openscience.cdk.io;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.StringTokenizer;

import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.CrystalGeometryTools;
import org.openscience.cdk.io.formats.CIFFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.tools.LoggingTool;

/**
 * This is not a reader for the CIF and mmCIF crystallographic formats.
 * It is able, however, to extract some content from such files. 
 * It's very ad hoc, not written
 * using any dictionary. So please complain if something is not working.
 * In addition, the things it does read are considered experimental.
 *
 * <p>The CIF example on the IUCR website has been tested, as well as Crambin (1CRN)
 * in the PDB database.
 *
 * @cdk.module io
 *
 * @cdk.keyword file format, CIF
 * @cdk.keyword file format, mmCIF
 *
 * @author  E.L. Willighagen
 * @cdk.created 2003-10-12
 */
public class CIFReader extends DefaultChemObjectReader {

    private BufferedReader input;
    private LoggingTool logger;

    private ICrystal crystal = null;
    // cell parameters
    private double a = 0.0;
    private double b = 0.0;
    private double c = 0.0;
    private double alpha = 0.0;
    private double beta = 0.0;
    private double gamma = 0.0;
    
    /**
     * Create an CIF like file reader.
     *
     * @param input source of CIF data
     */
    public CIFReader(Reader input) {
        this.input = new BufferedReader(input);
        this.logger = new LoggingTool(this);
    }
    
    public CIFReader(InputStream input) {
        this(new InputStreamReader(input));
    }
    
    public CIFReader() {
        this(new StringReader(""));
    }
    
    public IResourceFormat getFormat() {
        return CIFFormat.getInstance();
    }

    public void setReader(Reader reader) throws CDKException {
        this.input = new BufferedReader(input);
    }

    public void setReader(InputStream input) throws CDKException {
        setReader(new InputStreamReader(input));
    }

    public boolean accepts(Class testClass) {
		Class[] interfaces = testClass.getInterfaces();
		for (int i=0; i<interfaces.length; i++) {
			if (IChemFile.class.equals(interfaces[i])) return true;
		}
		return false;
    }
    
    /**
     * Read a ChemFile from input
     *
     * @return the content in a ChemFile object
     */
    public IChemObject read(IChemObject object) throws CDKException {
        if (object instanceof IChemFile) {
            IChemFile cf = (IChemFile)object;
            try {
                cf = readChemFile(cf);
            } catch (IOException e) {
                logger.error("Input/Output error while reading from input.");
            }
            return cf;
        } else {
            throw new CDKException("Only supported is reading of ChemFile.");
        }
    }

    /**
     * Read the ShelX from input. Each ShelX document is expected to contain
     * one crystal structure.
     *
     * @return a ChemFile with the coordinates, charges, vectors, etc.
     */
    private IChemFile readChemFile(IChemFile file) throws IOException {
        IChemSequence seq = file.getBuilder().newChemSequence();
        IChemModel model = file.getBuilder().newChemModel();
        crystal = file.getBuilder().newCrystal();

        String line = input.readLine();
        boolean end_found = false;
        while (input.ready() && line != null && !end_found) {
            if (line.startsWith("#")) {
                logger.warn("Skipping comment: " + line);
                // skip comment lines
            } else if (line.length() == 0) {
                logger.debug("Skipping empty line");
                // skip empty lines
            } else if (!(line.startsWith("_") || 
                  line.startsWith("loop_"))) {
                logger.warn("Skipping unrecognized line: " + line);
                // skip line
            } else {
                
                /* determine CIF command */
                String command = "";
                int spaceIndex = line.indexOf(" ");
                if (spaceIndex != -1) {
                    // everything upto space is command
                    try {
                        command = new String(line.substring(0, spaceIndex));
                    } catch (StringIndexOutOfBoundsException sioobe) {
                        // disregard this line
                        break;
                    }
                } else {
                    // complete line is command
                    command = line;
                }
                
                logger.debug("command: " + command);
                if (command.startsWith("_cell")) {
                    processCellParameter(command, line);
                } else if (command.equals("loop_")) {
                    processLoopBlock();
                } else if (command.equals("_symmetry_space_group_name_H-M")) {
                    String value = line.substring(29).trim();
                    crystal.setSpaceGroup(value);
                } else {
                    // skip command
                    logger.warn("Skipping command: " + command);
                    line = input.readLine();
                    if (line.startsWith(";")) {
                        logger.debug("Skipping block content");
                        line = input.readLine().trim();
                        while (!line.equals(";")) { 
                            line = input.readLine().trim();
                            logger.debug("Skipping block line: " + line);
                        }
                        line = input.readLine();
                    }
                }
            }
            line = input.readLine();
        }
        logger.info("Adding crystal to file with #atoms: " + crystal.getAtomCount());
        model.setCrystal(crystal);
        seq.addChemModel(model);
        file.addChemSequence(seq);
        return file;
    }

    private void processCellParameter(String command, String line) {
        command = command.substring(6); // skip the "_cell." part
        if (command.equals("length_a")) {