MDLWriter.java

/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) project
 *                    2009  Egon Willighagen <egonw@users.sf.net>
 *                    2010  Mark Rijnbeek <mark_rynbeek@users.sf.net>
 * 
 * Contact: cdk-devel@lists.sourceforge.net
 * 
 * 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.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.StringTokenizer;
import java.util.TimeZone;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
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.IMolecule;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Writes MDL molfiles, which contains a single molecule.
 * For writing a MDL molfile you can this code:
 * <pre>
 * MDLWriter writer = new MDLWriter(new FileWriter(new File("output.mol")));
 * writer.write((Molecule)molecule);
 * writer.close();
 * </pre>
 *
 * See {@cdk.cite DAL92}.
 *
 * @cdk.module  io
 * @cdk.githash
 * @cdk.keyword file format, MDL molfile
 */
@TestClass("org.openscience.cdk.io.MDLWriterTest")
public class MDLWriter extends DefaultChemObjectWriter {

    private final static ILoggingTool logger =
        LoggingToolFactory.createLoggingTool(MDLWriter.class);

    private BooleanIOSetting forceWriteAs2DCoords;
    
    /* Should aromatic bonds be written as bond type 4? If true, this makes the output a query file. */
    private BooleanIOSetting writeAromaticBondTypes;

    private BufferedWriter writer;
    
    /**
     * Constructs a new MDLWriter that can write an {@link IMolecule}
     * to the MDL molfile format.
     *
     * @param   out  The Writer to write to
     */
    public MDLWriter(Writer out) {
    	if (out instanceof BufferedWriter) {
    	    writer = (BufferedWriter)out;
    	} else {
    	    writer = new BufferedWriter(out);
    	}
        initIOSettings();
    }

    /**
     * Constructs a new MDLWriter that can write an {@link IMolecule}
     * to a given OutputStream.
     *
     * @param   output  The OutputStream to write to
     */
    public MDLWriter(OutputStream output) {
        this(new OutputStreamWriter(output));
    }
    
    public MDLWriter() {
        this(new StringWriter());
    }

    @TestMethod("testGetFormat")
    public IResourceFormat getFormat() {
        return MDLFormat.getInstance();
    }
    
    public void setWriter(Writer out) throws CDKException {
    	if (out instanceof BufferedWriter) {
            writer = (BufferedWriter)out;
        } else {
            writer = new BufferedWriter(out);
        }
    }

    public void setWriter(OutputStream output) throws CDKException {
    	setWriter(new OutputStreamWriter(output));
    }
    
    /**
     * Flushes the output and closes this object.
     */
    @TestMethod("testClose")
    public void close() throws IOException {
        writer.close();
    }

	@TestMethod("testAccepts")
    public boolean accepts(Class classObject) {
		Class[] interfaces = classObject.getInterfaces();
		for (int i=0; i<interfaces.length; i++) {
			if (IAtomContainer.class.equals(interfaces[i])) return true;
			if (IChemFile.class.equals(interfaces[i])) return true;
			if (IChemModel.class.equals(interfaces[i])) return true;
		}
	    Class superClass = classObject.getSuperclass();
	    if (superClass != null) return this.accepts(superClass);
		return false;
	}

    /**
     * Writes a {@link IChemObject} to the MDL molfile formated output. 
     * It can only output ChemObjects of type {@link IChemFile},
     * {@link IMolecule} and {@link IAtomContainer}.
     *
     * @param object {@link IChemObject} to write
     *
     * @see #accepts(Class)
     */
	public void write(IChemObject object) throws CDKException {
		customizeJob();
		try {
			if (object instanceof IChemFile) {
				writeChemFile((IChemFile)object);
				return;
			} else if (object instanceof IChemModel) {
				IChemFile file = object.getBuilder().newInstance(IChemFile.class);
				IChemSequence sequence = object.getBuilder().newInstance(IChemSequence.class);
				sequence.addChemModel((IChemModel)object);
				file.addChemSequence(sequence);
				writeChemFile((IChemFile)file);
				return;
			} else if (object instanceof IAtomContainer) {
				writeMolecule((IAtomContainer)object);
				return;
			}
		} catch (Exception ex) {
			logger.error(ex.getMessage());
			logger.debug(ex);
			throw new CDKException("Exception while writing MDL file: " + ex.getMessage(), ex);
		}
		throw new CDKException("Only supported is writing of IChemFile, " +
				"IChemModel, and IAtomContainer objects.");
	}
	
	private void writeChemFile(IChemFile file) throws Exception {
	    IAtomContainer bigPile = file.getBuilder().newInstance(IAtomContainer.class);
		for (IAtomContainer container :
		     ChemFileManipulator.getAllAtomContainers(file)) {
		    bigPile.add(container);
		    if(container.getProperty(CDKConstants.TITLE)!=null){
		        if(bigPile.getProperty(CDKConstants.TITLE)!=null)
		            bigPile.setProperty(CDKConstants.TITLE, 
		                    bigPile.getProperty(CDKConstants.TITLE)+"; "
		                    +container.getProperty(CDKConstants.TITLE));
		        else
		            bigPile.setProperty(CDKConstants.TITLE, 
		                    container.getProperty(CDKConstants.TITLE));
		    }
            if(container.getProperty(CDKConstants.REMARK)!=null){
                if(bigPile.getProperty(CDKConstants.REMARK)!=null)
                    bigPile.setProperty(CDKConstants.REMARK, 
                            bigPile.getProperty(CDKConstants.REMARK)+"; "
                            +container.getProperty(CDKConstants.REMARK));
                else
                    bigPile.setProperty(CDKConstants.REMARK, 
                            container.getProperty(CDKConstants.REMARK));
            }
		}
		writeMolecule(bigPile);
	}

	/**
	 * Writes a Molecule to an OutputStream in MDL sdf format.
	 *
	 * @param   container  Molecule that is written to an OutputStream
	 */
    public void writeMolecule(IAtomContainer container) throws Exception {
        String line = "";
        List<Integer> rgroupList=null;
        // write header block
        // lines get shortened to 80 chars, that's in the spec
        String title = (String)container.getProperty(CDKConstants.TITLE);
        if (title == null) title = "";
        if(title.length()>80)
          title=title.substring(0,80);
        writer.write(title);
        writer.newLine();
        
        /* From CTX spec
         * This line has the format:
         * IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
         * (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
         * User's first and last initials (l), program name (P),
         * date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s), 
         * energy (E) if modeling program input, internal registry number (R) 
         * if input through MDL form.
         * A blank line can be substituted for line 2.
         */
        writer.write("  CDK     ");
        writer.write(new SimpleDateFormat("MMddyyHHmm").format(System.currentTimeMillis()));
        writer.newLine();
        
        String comment = (String)container.getProperty(CDKConstants.REMARK);
        if (comment == null) comment = "";
        if(comment.length()>80)
          comment=comment.substring(0,80);
        writer.write(comment);
        writer.newLine();
        
        // write Counts line
		line += formatMDLInt(container.getAtomCount(), 3);
        line += formatMDLInt(container.getBondCount(), 3);
        line += "  0  0  0  0  0  0  0  0999 V2000";
        writer.write(line);
        writer.newLine();

        // write Atom block
        for (int f = 0; f < container.getAtomCount(); f++) {
        	IAtom atom = container.getAtom(f);
        	line = "";
            if (atom.getPoint3d() != null && !forceWriteAs2DCoords.isSet()) {
        		line += formatMDLFloat((float) atom.getPoint3d().x);
        		line += formatMDLFloat((float) atom.getPoint3d().y);
        		line += formatMDLFloat((float) atom.getPoint3d().z) + " ";
        	} else if (atom.getPoint2d() != null) {
        		line += formatMDLFloat((float) atom.getPoint2d().x);
        		line += formatMDLFloat((float) atom.getPoint2d().y);
        		line += "    0.0000 ";
        	} else {
        		// if no coordinates available, then output a number
        		// of zeros
        		line += formatMDLFloat((float)0.0);
        		line += formatMDLFloat((float)0.0);
        		line += formatMDLFloat((float)0.0) + " ";
        	}
        	if(container.getAtom(f) instanceof IPseudoAtom){
        		//according to http://www.google.co.uk/url?sa=t&ct=res&cd=2&url=http%3A%2F%2Fwww.mdl.com%2Fdownloads%2Fpublic%2Fctfile%2Fctfile.pdf&ei=MsJjSMbjAoyq1gbmj7zCDQ&usg=AFQjCNGaJSvH4wYy4FTXIaQ5f7hjoTdBAw&sig2=eSfruNOSsdMFdlrn7nhdAw an R group is written as R#
        		IPseudoAtom pseudoAtom = (IPseudoAtom) container.getAtom(f);
        		if (pseudoAtom.getSymbol().equals("R") && pseudoAtom.getLabel().length()>1) {
        			line += "R# ";
        			if (rgroupList==null) {
        				rgroupList = new ArrayList<Integer>();
        			}
        			Integer rGroupNumber = new Integer(pseudoAtom.getLabel().substring(1)); 
        			rgroupList.add(f+1); 
        			rgroupList.add(rGroupNumber);
        			
        		}
        		else
        			line += formatMDLString(((IPseudoAtom) container.getAtom(f)).getLabel(), 3);
        	}else{
        		line += formatMDLString(container.getAtom(f).getSymbol(), 3);
        	}
        	line += " 0  0  0  0  0";
        	//valence 0 is defined as 15 in mol files
        	if(atom.getValency()==(Integer)CDKConstants.UNSET)
        		line += formatMDLInt(0, 3);
        	else if(atom.getValency()==0)
        		line += formatMDLInt(15, 3);
        	else
        		line += formatMDLInt(atom.getValency(), 3);
        	line += "  0  0  0";
        	
        	if (container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING) != null) {
        	    int value = ((Integer)container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue();
        	    line += formatMDLInt(value, 3);
       	    } else {
        	    line += formatMDLInt(0, 3);
        	}
      	    line += "  0  0";
        	writer.write(line);
        	writer.newLine();
        }

        // write Bond block
        Iterator<IBond> bonds = container.bonds().iterator();
        while (bonds.hasNext()) {
            IBond bond = bonds.next();

        	if (bond.getAtomCount() != 2) {
        		logger.warn("Skipping bond with more/less than two atoms: " + bond);
        	} else {
        		if (bond.getStereo() == IBond.Stereo.UP_INVERTED || 
        				bond.getStereo() == IBond.Stereo.DOWN_INVERTED ||
        				bond.getStereo() == IBond.Stereo.UP_OR_DOWN_INVERTED) {
        			// turn around atom coding to correct for inv stereo
        			line = formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
        			line += formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
        		} else {
        			line = formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
        			line += formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
        		}
                        int bondType;
                        if (writeAromaticBondTypes.isSet() && bond.getFlag(CDKConstants.ISAROMATIC))
                            bondType=4;
                        else
                            bondType=(int)bond.getOrder().ordinal()+1;
                        line += formatMDLInt(bondType,3);
                            
        		line += "  ";
        		switch(bond.getStereo()){
        		case UP:
        			line += "1";
        			break;
        		case UP_INVERTED:
        			line += "1";
        			break;
        		case DOWN:
        			line += "6";
        			break;
        		case DOWN_INVERTED:
        			line += "6";
        			break;
        		case UP_OR_DOWN:
        			line += "4";
        			break;
                case UP_OR_DOWN_INVERTED:
                    line += "4";
                    break;
           		case E_OR_Z:
          			line += "3";
          			break;
          		default:
        			line += "0";
        		}
        		line += "  0  0  0 ";
        		writer.write(line);
        		writer.newLine();
        	}
        }
        
        // Write Atom Value
        for (int i = 0; i < container.getAtomCount(); i++) {
        	IAtom atom = container.getAtom(i);
        	if(atom.getProperty(CDKConstants.COMMENT)!=null 
        	&& atom.getProperty(CDKConstants.COMMENT) instanceof String
        	&& !((String)atom.getProperty(CDKConstants.COMMENT)).trim().equals("") ) {
                writer.write("V  ");
                writer.write(formatMDLInt(i+1,3));
                writer.write(" ");
                writer.write((String)atom.getProperty(CDKConstants.COMMENT));
                writer.newLine();
        	}
        }

        // write formal atomic charges
        for (int i = 0; i < container.getAtomCount(); i++) {
        	IAtom atom = container.getAtom(i);
            Integer charge = atom.getFormalCharge();
            if (charge != null && charge != 0) {
                writer.write("M  CHG  1 ");
                writer.write(formatMDLInt(i+1,3));
                writer.write(" ");
                writer.write(formatMDLInt(charge,3));
                writer.newLine();
            }
        }
        
        // write formal isotope information
        for (int i = 0; i < container.getAtomCount(); i++) {
        	IAtom atom = container.getAtom(i);
            if (!(atom instanceof IPseudoAtom)) {
                Integer atomicMass = atom.getMassNumber();
                if (atomicMass != null) {
                	int majorMass = IsotopeFactory.getInstance(atom.getBuilder()).getMajorIsotope(atom.getSymbol()).getMassNumber();
                	if (atomicMass != majorMass) {
                		writer.write("M  ISO  1 ");
                		writer.write(formatMDLInt(i+1,3));
                		writer.write(" ");
                		writer.write(formatMDLInt(atomicMass,3));
                		writer.newLine();
                	}
                }
            }
        }

        //write RGP line (max occurrence is 16 data points per line)
        if (rgroupList!=null) {
        	StringBuffer rgpLine=new StringBuffer();
        	int cnt=0;
        	for (int i=1; i<= rgroupList.size(); i++) {
        		
        		rgpLine.append(formatMDLInt((rgroupList.get(i-1)), 4));
        		i++;
        		rgpLine.append(formatMDLInt((rgroupList.get(i-1)), 4));
        		
        		cnt++;
        		if (i==rgroupList.size() || i==16 ) { 
                	rgpLine.insert(0, "M  RGP"+formatMDLInt(cnt, 3));
                	writer.write(rgpLine.toString());
            		writer.newLine();
            		rgpLine=new StringBuffer();
            		cnt=0;
        		}
        	}
        }
        
        // close molecule
        writer.write("M  END");
        writer.newLine();
        writer.flush();
    }

	/**
	 * Formats an integer to fit into the connection table and changes it 
     * to a String.
	 *
	 * @param   i  The int to be formated
	 * @param   l  Length of the String
	 * @return     The String to be written into the connectiontable
	 */
    protected static String formatMDLInt(int i, int l) {
        String s = "", fs = "";
        NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
        nf.setParseIntegerOnly(true);
        nf.setMinimumIntegerDigits(1);
        nf.setMaximumIntegerDigits(l);
        nf.setGroupingUsed(false);
        s = nf.format(i);
        l = l - s.length();
        for (int f = 0; f < l; f++)
            fs += " ";
        fs += s;
        return fs;
    }
	
	


	/**
	 * Formats a float to fit into the connectiontable and changes it
     * to a String.
	 *
	 * @param   fl  The float to be formated
	 * @return      The String to be written into the connectiontable
	 */
    protected static String formatMDLFloat(float fl) {
        String s = "", fs = "";
        int l;
        NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
        nf.setMinimumIntegerDigits(1);
        nf.setMaximumIntegerDigits(4);
        nf.setMinimumFractionDigits(4);
        nf.setMaximumFractionDigits(4);
        nf.setGroupingUsed(false);
        s = nf.format(fl);
        l = 10 - s.length();
        for (int f = 0; f < l; f++)
            fs += " ";
        fs += s;
        return fs;
    }



	/**
	 * Formats a String to fit into the connectiontable.
	 *
	 * @param   s    The String to be formated
	 * @param   le   The length of the String
	 * @return       The String to be written in the connectiontable
	 */
    protected static String formatMDLString(String s, int le) {
        s = s.trim();
        if (s.length() > le)
            return s.substring(0, le);
        int l;
        l = le - s.length();
        for (int f = 0; f < l; f++)
            s += " ";
        return s;
    }
    
    /**
     * Initializes IO settings.<br>
     * Please note with regards to "writeAromaticBondTypes": bond type values 4 through 8 are for SSS queries only,
     * so a 'query file' is created if the container has aromatic bonds and this settings is true.
     */
    private void initIOSettings() {
        forceWriteAs2DCoords = new BooleanIOSetting(
            "ForceWriteAs2DCoordinates",
            IOSetting.LOW,
            "Should coordinates always be written as 2D?",
            "false"
        );
        writeAromaticBondTypes = new BooleanIOSetting(
            "WriteAromaticBondTypes",
            IOSetting.LOW,
            "Should aromatic bonds be written as bond type 4?",
            "false"
        );
    }

    public void customizeJob() {
        fireIOSettingQuestion(forceWriteAs2DCoords);
        fireIOSettingQuestion(writeAromaticBondTypes);

    }

    public IOSetting[] getIOSettings() {
        IOSetting[] settings = new IOSetting[2];
        settings[0] = forceWriteAs2DCoords;
        settings[1] = writeAromaticBondTypes;
        return settings;
    }
}