pdbconvention.java

化学图形处理软件

/* $Revision: 7981 $ $Author: egonw $ $Date: 2007-02-20 18:05:37 +0100 (Tue, 20 Feb 2007) $
 *
 * Copyright (C) 1997-2007  Egon Willighagen <[e-mail]>
 *
 * 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.cml;

import java.util.ArrayList;
import java.util.StringTokenizer;

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IPDBAtom;
import org.openscience.cdk.interfaces.IPDBMonomer;
import org.openscience.cdk.interfaces.IPDBPolymer;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.xml.sax.Attributes;

/**
 * Implements the PDB convention used by PDB2CML.
 *
 * <p>This is a lousy implementation, though. Problems that will arise:
 * <ul>
 *   <li>when this new convention is adopted in the root element no
 *     currentFrame was set. This is done when <list sequence=""> is found
 *   <li>multiple sequences are not yet supported
 *   <li>the frame is now added when the doc is ended, which will result in problems
 *     but work for one sequence files made by PDB2CML v.??
 * <ul>
 *
 * <p>What is does:
 * <ul>
 *   <li>work for now
 *   <li>give an idea on the API of the plugable CML import filter
 *     (a real one will be made)
 *   <li>read CML files generated with Steve Zara's PDB 2 CML converter
 *     (of which version 1999 produces invalid CML 1.0)
 * </ul>
 *
 * @cdk.module io
 *
 * @author Egon Willighagen <[e-mail]>
 */
public class PDBConvention extends CMLCoreModule {

    private boolean connectionTable;
    private boolean isELSYM;
    private boolean isBond;
    private String connect_root;
	private boolean hasScalar;
	private String idValue = "";
	private ArrayList altLocV;
	private ArrayList chainIDV;
	private ArrayList hetAtomV;
	private ArrayList iCodeV;
	private ArrayList nameV;
	private ArrayList oxtV;
	private ArrayList recordV;
	private ArrayList resNameV;
	private ArrayList resSeqV;
	private ArrayList segIDV;
	private ArrayList serialV;
	private ArrayList tempFactorV;
	
    public PDBConvention(IChemFile chemFile) {
        super(chemFile);
    }
    
    public PDBConvention(ICMLModule conv) {
        super(conv);
    }

    public void endDocument() {
        storeData();
        super.endDocument();
    }
    
    public void startElement(CMLStack xpath, String uri, String local, String raw, 
                              Attributes atts) {
        String name = raw;
        isELSYM = false;
        if ("molecule".equals(name)) {
        	
            for (int j = 0; j < atts.getLength(); j++) {
            	logger.debug("StartElement");
                currentChars = "";
                
                BUILTIN = "";
                DICTREF = "";

                for (int i=0; i<atts.getLength(); i++) {
                    String qname = atts.getQName(i);
                    if (qname.equals("builtin")) {
                        BUILTIN = atts.getValue(i);
                        logger.debug(name, "->BUILTIN found: ", atts.getValue(i));
                    } else if (qname.equals("dictRef")) {
                        DICTREF = atts.getValue(i);
                        logger.debug(name, "->DICTREF found: ", atts.getValue(i));
                    } else if (qname.equals("title")) {
                        elementTitle = atts.getValue(i);
                        logger.debug(name, "->TITLE found: ", atts.getValue(i));
                    } else {
                        logger.debug("Qname: ", qname);
                    }
                }
                if (atts.getQName(j).equals("convention") && atts.getValue(j).equals("PDB")) {
//                    cdo.startObject("PDBPolymer");
                	currentStrand = currentChemFile.getBuilder().newStrand();
                	currentStrand.setStrandName("A");
                    currentMolecule = currentChemFile.getBuilder().newPDBPolymer();
                }else if (atts.getQName(j).equals("dictRef") && atts.getValue(j).equals("pdb:sequence")) {
                    
                    newSequence();
                    BUILTIN = "";
                    for (int i = 0; i < atts.getLength(); i++) {
                        if (atts.getQName(i).equals("id")) {
//                            cdo.setObjectProperty("Molecule", "id", atts.getValue(i));
                            currentMolecule.setID(atts.getValue(i));
                        } else if (atts.getQName(i).equals("dictRef")) {
//                        	cdo.setObjectProperty("Molecule", "dictRef", atts.getValue(i));
                        	// FIXME: has no equivalent in ChemFileCDO
                        }
                    }
                	
                } else if (atts.getQName(j).equals("title") && 
                         atts.getValue(j).equals("connections")) {
                    // assume that Atom's have been read
                    logger.debug("Assuming that Atom's have been read: storing them");
                    super.storeAtomData();
                    connectionTable = true;
                    logger.debug("Start Connection Table");
                } else if (atts.getQName(j).equals("title") && 
                         atts.getValue(j).equals("connect")) {
                    logger.debug("New connection");
                    isBond = true;
                } else if (atts.getQName(j).equals("id") && isBond) {
                    connect_root = atts.getValue(j);
                }

                // ignore other list items at this moment
            }
        }else if ("scalar".equals(name)) {
        	hasScalar = true;
        	for (int i = 0; i < atts.getLength(); i++) {
                if(atts.getQName(i).equals("dictRef"))
                	idValue = atts.getValue(i);
        	}
        }else if ("label".equals(name)) {
        	hasScalar = true;
        	for (int i = 0; i < atts.getLength(); i++) {
                if(atts.getQName(i).equals("dictRef"))
                	idValue = atts.getValue(i);
        	}
        }else if ("atom".equals(name)) {
        	super.startElement(xpath, uri, local, raw, atts);
        }
    }
    
    public void newSequence(){
    	altLocV = new ArrayList();
    	chainIDV = new ArrayList();
    	hetAtomV = new ArrayList();
    	iCodeV = new ArrayList();
    	nameV = new ArrayList();
    	oxtV = new ArrayList();
    	recordV = new ArrayList();
    	resNameV = new ArrayList();
    	resSeqV = new ArrayList();
    	segIDV = new ArrayList();
    	serialV = new ArrayList();
    	tempFactorV = new ArrayList();
    	
    }
    public void endElement(CMLStack xpath, String uri, String local, String raw) {
        String name = raw;

        // OLD +++++++++++++++++++++++++++++++++++++++++++++
        if (name.equals("list") && connectionTable && !isBond) {
            logger.debug("End Connection Table");
            connectionTable = false;
        // OLD +++++++++++++++++++++++++++++++++++++++++++++

         
        } else if(name.equals("molecule")){
        	storeData();
            if(xpath.sp == 1){
//	        	cdo.endObject("Molecule");
            	if (currentMolecule instanceof IMolecule) {
                    logger.debug("Adding molecule to set");
                    currentMoleculeSet.addMolecule((IMolecule)currentMolecule);
                    logger.debug("#mols in set: " + currentMoleculeSet.getMoleculeCount());
                } else if (currentMolecule instanceof ICrystal) {
                    logger.debug("Adding crystal to chemModel");
                    currentChemModel.setCrystal((ICrystal)currentMolecule);
                    currentChemSequence.addChemModel(currentChemModel);
                }
        	}
        }
        isELSYM = false;
        isBond = false;
        
    }

    public void characterData(CMLStack xpath, char[] ch, int start, int length) {

        String s = new String(ch, start, length).trim();
        StringTokenizer st1 = new StringTokenizer(s);
        String dictpdb = "";
        while (st1.hasMoreElements()) {
        	
            dictpdb += (String)st1.nextElement();
            if(st1.hasMoreElements())
            	dictpdb += " ";
            else if(idValue.equals("pdb:record"))
            	dictpdb += " ";
        }

        if(idValue.equals("pdb:altLoc"))
            altLocV.add(dictpdb);
        else if(idValue.equals("pdb:chainID"))
        	chainIDV.add(dictpdb);
        else if(idValue.equals("pdb:hetAtom"))
        	hetAtomV.add(dictpdb);
        else if(idValue.equals("pdb:iCode"))
        	iCodeV.add(dictpdb);
        else if(idValue.equals("pdb:name"))
        	nameV.add(dictpdb);
        else if(idValue.equals("pdb:oxt"))
        	oxtV.add(dictpdb);
        else if(idValue.equals("pdb:record"))
        	recordV.add(dictpdb);
        else if(idValue.equals("pdb:resName"))
        	resNameV.add(dictpdb);
        else if(idValue.equals("pdb:resSeq"))
        	resSeqV.add(dictpdb);
        else if(idValue.equals("pdb:segID"))
        	segIDV.add(dictpdb);
        else if(idValue.equals("pdb:serial"))
        	serialV.add(dictpdb);
        else if(idValue.equals("pdb:tempFactor"))
        	tempFactorV.add(dictpdb);
        
        idValue = "";
        
        if (isELSYM) {
            elsym.add(s);
        } else if (isBond) {
            logger.debug("CD (bond): " + s);
            if (connect_root.length() > 0) {
                StringTokenizer st = new StringTokenizer(s);
                while (st.hasMoreElements()) {
                    String atom = (String)st.nextElement();
                    if (!atom.equals("0")) {
                        logger.debug("new bond: " + connect_root + "-" + 
                                     atom);
//                        cdo.startObject("Bond");
//                        int atom1 = Integer.parseInt(connect_root) - 1;
//                        int atom2 = Integer.parseInt(atom) - 1;
//                        cdo.setObjectProperty("Bond", "atom1", 
//                                (new Integer(atom1)).toString());
//                        cdo.setObjectProperty("Bond", "atom2", 
//                                (new Integer(atom2)).toString());
                        currentBond = currentMolecule.getBuilder().newBond(
                        	currentMolecule.getAtom(Integer.parseInt(connect_root) - 1),
                        	currentMolecule.getAtom(Integer.parseInt(atom) - 1),
                        	CDKConstants.BONDORDER_SINGLE
                        );
                        currentMolecule.addBond(currentBond);
                    }
                }
            }
        } 
    }
    
    
    protected void storeData() {
        if (inchi != null) {
//            cdo.setObjectProperty("Molecule", "inchi", inchi);
            currentMolecule.setProperty(CDKConstants.INCHI, inchi);
        }
        storeAtomData();
        storeBondData();
    }

    protected void storeAtomData() {
        logger.debug("No atoms: ", atomCounter);