maciereader.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.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.LineNumberReader;
import java.io.Reader;
import java.util.Iterator;
import java.util.List;
import java.util.StringTokenizer;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemSequence;
import org.openscience.cdk.EnzymeResidueLocator;
import org.openscience.cdk.PseudoAtom;
import org.openscience.cdk.Reaction;
import org.openscience.cdk.ReactionSet;
import org.openscience.cdk.dict.DictRef;
import org.openscience.cdk.dict.DictionaryDatabase;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
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.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MACiEFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.io.setting.IntegerIOSetting;
import org.openscience.cdk.io.setting.StringIOSetting;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;

/**
 * Reads an export from the MACiE enzyme reaction database.
 * Information about this database can be obtained from
 * Gemma Holiday, Cambridge University, UK, and Gail Bartlett,
 * European Bioinformatics Institute, Hinxton, UK.
 *
 * <p>This implementation is based on a dump from their database
 * on 2003-07-14.
 *
 * @cdk.module experimental
 *
 * @author     Egon Willighagen
 * @cdk.created    2003-07-24
 *
 * @cdk.keyword    file format, MACiE RDF
 * @cdk.require java1.4+
 */
public class MACiEReader extends DefaultChemObjectReader {

    /** Property it will put on ChemModel */
    public final static String CreationDate = "org.openscience.cdk.io.MACiE.CreationDate";
    /** Property it will put on ChemModel */
    public final static String MedlineID = "org.openscience.cdk.io.MACiE.MedlineID";
    /** Property it will put on ChemModel */
    public final static String PDBCode = "org.openscience.cdk.io.MACiE.PDBCode";
    /** Property it will put on ChemModel */
    public final static String ECNumber = "org.openscience.cdk.io.MACiE.ECNumber";
    /** Property it will put on ChemModel */
    public final static String EnzymeName = "org.openscience.cdk.io.MACiE.EnzymeName";
    
    private LineNumberReader input = null;
    private LoggingTool logger = null;

    private IntegerIOSetting selectedEntry;
    private BooleanIOSetting readSecondaryFiles;
    private StringIOSetting readSecondaryDir;

    private Pattern topLevelDatum;
    private Pattern subLevelDatum;
    private Pattern annotationTuple;
    private Pattern residueLocator;
    
    private ChemModel currentEntry;
    private Reaction currentReaction;
    private ReactionSet currentReactionStepSet;
    
    private String reactionStepAnnotation;
    private String reactionStepComments;
    
    private boolean readThisEntry = true;
    
    /**
     * Contructs a new MACiEReader that can read Molecule from a given Reader.
     *
     * @param  in  The Reader to read from
     */
    public MACiEReader(Reader in) {
        this();
        this.input = new LineNumberReader(in);
    }

    public MACiEReader(InputStream input) {
        this(new InputStreamReader(input));
    }
    
    public MACiEReader() {
        logger = new LoggingTool(this);
        
        /* compile patterns */
        topLevelDatum = Pattern.compile("(.+):(.+)");
        subLevelDatum = Pattern.compile("(.+):(.+)\\((.+)\\):(.+)");
        annotationTuple = Pattern.compile("(\\w+)=\\((.+?)\\);(.*)");
        residueLocator = Pattern.compile("[A-Z][a-z][a-z]\\d{1,5}"); // e.g. Lys150
        
        initIOSettings();
    }

    public IResourceFormat getFormat() {
        return MACiEFormat.getInstance();
    }

    public void setReader(Reader input) throws CDKException {
        if (input instanceof LineNumberReader) {
            this.input = (LineNumberReader)input;
        } else {
            this.input = new LineNumberReader(input);
        }
    }

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

	public boolean accepts(Class classObject) {
		Class[] interfaces = classObject.getInterfaces();
		for (int i=0; i<interfaces.length; i++) {
			if (IChemModel.class.equals(interfaces[i])) return true;
			if (IChemFile.class.equals(interfaces[i])) return true;
			if (IChemSequence.class.equals(interfaces[i])) return true;
		}
		return false;
	}

    /**
     * Takes an object which subclasses IChemObject, e.g. Molecule, and will read
     * this (from file, database, internet etc). If the specific implementation
     * does not support a specific IChemObject it will throw an Exception.
     *
     * @param  object The object that subclasses IChemObject
     * @return        The IChemObject read
     * @exception     CDKException
     */
     public IChemObject read(IChemObject object) throws CDKException {
         customizeJob();
         
         try {
             if (object instanceof IChemSequence) {
                 return readReactions(false);
             } else if (object instanceof IChemModel) {
                 return readReactions(true);
             } else if (object instanceof IChemFile) {
                 IChemFile chemFile = object.getBuilder().newChemFile();
                 chemFile.addChemSequence((ChemSequence)readReactions(false));
                 return chemFile;
             }
         } catch (IOException exception) {
             String message = "Error while reading file, line number: " + input.getLineNumber();
             logger.error(message);
             logger.debug(exception);
             throw new CDKException(message, exception);
         }
         throw new CDKException("Only supported are ChemSequence and ChemModel.");
     }

     public boolean accepts(IChemObject object) {
         if (object instanceof ChemSequence) {
             return true;
         } else if (object instanceof ChemModel) {
             return true;
         } else if (object instanceof ChemFile) {
             return true;
         } else if (object == null) {
             logger.warn("MACiEReader can not read null objects.");
         } else {
             logger.warn("MACiEReader can not read IChemObject of type: ", 
                         object.getClass().getName());
         }
         return false;
    }
    


    /**
     * Read a Reaction from a file in MACiE RDF format.
     *
     * @return  The Reaction that was read from the MDL file.
     */
    private IChemObject readReactions(boolean selectEntry) throws CDKException, IOException {
        ChemSequence entries = new ChemSequence();
        currentEntry = null;
        int entryCounter = 0;
        currentReactionStepSet = null;
        
        while (input.ready()) {
            String line = input.readLine();
            if (line.startsWith("$RDFILE")) {
                entries = new ChemSequence();
            } else if (line.startsWith("$DATM")) {
                entries.setProperty(CreationDate, line.substring(7));
            } else if (line.startsWith("$RIREG")) {
                // new entry, store previous entry if any
                if (currentEntry != null) {
                    // store previous entry
                    currentEntry.setReactionSet(currentReactionStepSet);
                    createNiceMACiETitle(currentEntry);
                    entries.addChemModel(currentEntry);
                    fireFrameRead();
                    if (selectEntry && (entryCounter == selectedEntry.getSettingValue())) {
                        logger.info("Starting reading wanted frame: ", selectedEntry);
                        return currentEntry;
                    } else {
                        logger.debug("Not reading unwanted frame: " + entryCounter);
                    }
                }
                currentEntry = new ChemModel();
                entryCounter++;
                if (!selectEntry || entryCounter == selectedEntry.getSettingValue()) {
                    readThisEntry = true;
                } else {
                    readThisEntry = false;
                }
                currentReactionStepSet = new ReactionSet();
            } else if (line.startsWith("$DTYPE")) {
                String[] tuple = readDtypeDatumTuple(line);
                String dataType = tuple[0];
                String datum   = tuple[1];
                
                // now some regular expression wizardry
                Matcher subLevelMatcher = subLevelDatum.matcher(dataType);
                if (subLevelMatcher.matches()) {
                    // sub level field found
                    String field = subLevelMatcher.group(2);
                    String fieldNumber = subLevelMatcher.group(3);
                    String subfield = subLevelMatcher.group(4);
                    processSubLevelField(field, fieldNumber, subfield, datum);
                } else {
                    Matcher topLevelMatcher = topLevelDatum.matcher(dataType);
                    if (topLevelMatcher.matches()) {
                        // top level field found
                        String field = topLevelMatcher.group(2);
                        processTopLevelField(field, datum);
                    } else {
                        logger.error("Could not parse datum tuple of type ", dataType,
                                     " around line " + input.getLineNumber());
                    }
                }
            } else {
                logger.warn("Unrecognized command on line " + input.getLineNumber(), ": ", line);
            }
        }
        
        if (currentEntry != null) {
            createNiceMACiETitle(currentEntry);
            // store last entry
            currentEntry.setReactionSet(currentReactionStepSet);
            entries.addChemModel(currentEntry);
            fireFrameRead();
        }
        
        if (selectEntry) {
            // apparently selected last one, other already returned
            return currentEntry;
        }