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Mol2Writer.java
/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 2005-2007  Egon Willighagen <egonw@users.sf.net>
 * 
 * Contact: cdk-devel@lists.sourceforge.net
 *
 *  This library 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.
 *
 *  This library 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 library; 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.util.Iterator;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.atomtype.SybylAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.Mol2Format;
import org.openscience.cdk.tools.LoggingTool;

/**
 * An output Writer that writes molecular data into the
 * <a href="http://www.tripos.com/data/support/mol2.pdf">Tripos Mol2 format</a>.
 * Writes the atoms and the bonds only at this moment.
 *
 * @cdk.module io
 * @cdk.githash
 *
 * @author     Egon Willighagen
 */
@TestClass("org.openscience.cdk.io.Mol2WriterTest")
00056 public class Mol2Writer extends DefaultChemObjectWriter {

    private BufferedWriter writer;
      private LoggingTool logger;
        private SybylAtomTypeMatcher matcher;
    
    public Mol2Writer() {
      this(new StringWriter());
    }

    /**
     * Constructs a new Mol2 writer.
     * @param out the stream to write the Mol2 file to.
     */
00070     public Mol2Writer(Writer out) {
      logger = new LoggingTool(this);
      try {
            if (out instanceof BufferedWriter) {
                writer = (BufferedWriter)out;
            } else {
                writer = new BufferedWriter(out);
            }
        } catch (Exception exc) {
        }
    }

    public Mol2Writer(OutputStream output) {
        this(new OutputStreamWriter(output));
    }

    @TestMethod("testGetFormat")
00087     public IResourceFormat getFormat() {
        return Mol2Format.getInstance();
    }
    
00091     public void setWriter(Writer out) throws CDKException {
      if (out instanceof BufferedWriter) {
            writer = (BufferedWriter)out;
        } else {
            writer = new BufferedWriter(out);
        }
    }

00099     public void setWriter(OutputStream output) throws CDKException {
      setWriter(new OutputStreamWriter(output));
    }

    /**
     * Flushes the output and closes this object.
     */
    @TestMethod("testClose")
00107     public void close() throws IOException {
        writer.close();
    }

      @TestMethod("testAccepts")
    public boolean accepts(Class classObject) {
            Class[] interfaces = classObject.getInterfaces();
        for (Class anInterface : interfaces) {
            if (IMolecule.class.equals(anInterface)) return true;
        }
            return false;
      }

00120     public void write(IChemObject object) throws CDKException {
        if (object instanceof IMolecule) {
            try {
                writeMolecule((IMolecule)object);
            } catch(Exception ex) {
                throw new CDKException("Error while writing Mol2 file: " + ex.getMessage(), ex);
            }
        } else {
            throw new CDKException("Mol2Writer only supports output of Molecule classes.");
        }
    }

    /**
     * Writes a single frame in XYZ format to the Writer.
     *
     * @param mol the Molecule to write
     * @throws java.io.IOException if there is an error during writing
     */
00138     public void writeMolecule(IMolecule mol) throws IOException {
        matcher = SybylAtomTypeMatcher.getInstance(mol.getBuilder());
        try {
            logger.debug("Writing header...");
            if (mol.getProperty(CDKConstants.TITLE) != null) {
                writer.write("#        Name: " + mol.getProperty(CDKConstants.TITLE));
                writer.newLine();
            }
            // FIXME: add other types of meta data
            writer.newLine();

/*
@<TRIPOS>MOLECULE 
benzene 
12 12 1  0       0 
SMALL 
NO_CHARGES 
*/

            logger.debug("Writing molecule block...");
            writer.write("@<TRIPOS>MOLECULE");
            writer.newLine();
            if (mol.getID() == null) {
                writer.write("CDKMolecule");
            } else {
                writer.write(mol.getID());
            }
            writer.newLine();
            writer.write(mol.getAtomCount() + " " + 
                        mol.getBondCount()); // that's the minimum amount of info required the format
            writer.newLine();
            writer.write("SMALL"); // no biopolymer
            writer.newLine();
            writer.write("NO CHARGES"); // other options include Gasteiger charges
            writer.newLine();

/*
@<TRIPOS>ATOM 
1       C1      1.207   2.091   0.000   C.ar    1       BENZENE 0.000 
2       C2      2.414   1.394   0.000   C.ar    1       BENZENE 0.000 
3       C3      2.414   0.000   0.000   C.ar    1       BENZENE 0.000 
4       C4      1.207   -0.697  0.000   C.ar    1       BENZENE 0.000 
5       C5      0.000   0.000   0.000   C.ar    1       BENZENE 0.000 
6       C6      0.000   1.394   0.000   C.ar    1       BENZENE 0.000 
7       H1      1.207   3.175   0.000   H       1       BENZENE 0.000 
8       H2      3.353   1.936   0.000   H       1       BENZENE 0.000 
9       H3      3.353   -0.542  0.000   H       1       BENZENE 0.000 
10      H4      1.207   -1.781  0.000   H       1       BENZENE 0.000 
11      H5      -0.939  -0.542  0.000   H       1       BENZENE 0.000 
12      H6      -0.939  1.936   0.000   H       1       BENZENE 0.000 
*/

            // write atom block
            logger.debug("Writing atom block...");
            writer.write("@<TRIPOS>ATOM");
            writer.newLine();
            for (int i = 0; i < mol.getAtomCount(); i++) {
                  IAtom atom = mol.getAtom(i);
                writer.write((i+1) + " " +
                             atom.getSymbol() + (mol.getAtomNumber(atom)+1) + " ");
                if (atom.getPoint3d() != null) {
                    writer.write(atom.getPoint3d().x + " ");
                    writer.write(atom.getPoint3d().y + " ");
                    writer.write(atom.getPoint3d().z + " ");
                } else if (atom.getPoint2d() != null) {
                    writer.write(atom.getPoint2d().x + " ");
                    writer.write(atom.getPoint2d().y + " ");
                    writer.write(" 0.000 ");
                } else {
                    writer.write("0.000 0.000 0.000 ");
                }
                IAtomType sybylType = null;
                try {
                    sybylType = matcher.findMatchingAtomType(mol, atom);
                } catch ( CDKException e ) {
                    e.printStackTrace();
                }
                if (sybylType != null) {
                    writer.write(sybylType.getAtomTypeName());
                } else {
                    writer.write(atom.getSymbol());
                }
                writer.newLine();
            }

/*
@<TRIPOS>BOND 
1       1       2       ar 
2       1       6       ar 
3       2       3       ar 
4       3       4       ar 
5       4       5       ar 
6       5       6       ar 
7       1       7       1 
8       2       8       1 
9       3       9       1 
10      4       10      1 
11      5       11      1 
12      6       12      1
*/

            // write bond block
            logger.debug("Writing bond block...");
            writer.write("@<TRIPOS>BOND");
            writer.newLine();

            int counter = 0;
            for (IBond bond : mol.bonds()) {
                String sybylBondOrder = "-1";
                if (bond.getOrder().equals(IBond.Order.SINGLE)) sybylBondOrder = "1";
                else if (bond.getOrder().equals(IBond.Order.DOUBLE)) sybylBondOrder = "2";
                else if (bond.getOrder().equals(IBond.Order.TRIPLE)) sybylBondOrder = "3";
                if (bond.getFlag(CDKConstants.ISAROMATIC)) sybylBondOrder = "ar";

                // we need to check the atom types to see if we have an amide bond
                // and we're assuming a 2-centered bond
                IAtom bondAtom1 = bond.getAtom(0);
                IAtom bondAtom2 = bond.getAtom(1);
                try {
                    if ( (matcher.findMatchingAtomType(mol, bondAtom1).getAtomTypeName().equals("N.am") &&
                            matcher.findMatchingAtomType(mol, bondAtom2).getAtomTypeName().equals("C.2")) ||
                        (matcher.findMatchingAtomType(mol, bondAtom2).getAtomTypeName().equals("N.am") &&
                            matcher.findMatchingAtomType(mol, bondAtom1).getAtomTypeName().equals("C.2")) ) {
                        sybylBondOrder = "am";
                    }
                } catch (CDKException e) {
                    e.printStackTrace(); 
                }

                writer.write((counter+1) + " " +
                        (mol.getAtomNumber(bond.getAtom(0))+1) + " " +
                        (mol.getAtomNumber(bond.getAtom(1))+1) + " " +
                        sybylBondOrder);
                writer.newLine();
                counter++;
            } 

        } catch (IOException e) {
            throw e;
        }
    }
}



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