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* $Date: 2007-08-28 10:29:51 +0200 (Tue, 28 Aug 2007) $
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* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
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* Contact: cdk-devel@lists.sourceforge.net
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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* All we ask is that proper credit is given for our work, which includes
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* - but is not limited to - adding the above copyright notice to the beginning
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* of your source code files, and to any copyright notice that you may distribute
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* with programs based on this work.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.io;
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import org.openscience.cdk.CDKConstants;
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import org.openscience.cdk.config.IsotopeFactory;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.interfaces.*;
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import org.openscience.cdk.io.formats.IResourceFormat;
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import org.openscience.cdk.io.formats.MDLFormat;
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import org.openscience.cdk.tools.LoggingTool;
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import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
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import java.text.NumberFormat;
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import java.text.SimpleDateFormat;
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* Writes MDL mol files and SD files.
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* A MDL mol file contains a single molecule, whereas a MDL SD file contains
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* one or more molecules. This class is capable of writing both mol files and
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* SD files. The correct format is automatically chosen:
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* <li>if {@link #write(IChemObject)} is called with a {@link org.openscience.cdk.MoleculeSet MoleculeSet}
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* as an argument a SD files is written</li>
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* <li>if one of the two writeMolecule methods (either {@link #writeMolecule(IMolecule) this one} or
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* {@link #writeMolecule(org.openscience.cdk.interfaces.IMolecule)} that one}) is called the first time, a mol file is written</li>
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* <li>if one of the two writeMolecule methods is called more than once the output is a SD file</li>
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* <p>Thus, to write several molecules to a single SD file you can either use {@link #write(IChemObject)} and pass
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* a {@link org.openscience.cdk.MoleculeSet MoleculeSet} or you can repeatedly call one of the two
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* writeMolecule methods.
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* <p>For writing a MDL molfile you can this code:
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* MDLWriter writer = new MDLWriter(new FileWriter(new File("output.mol")));
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* writer.write((Molecule)molecule);
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* See {@cdk.cite DAL92}.
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* @cdk.keyword file format, MDL molfile
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public class MDLWriter extends DefaultChemObjectWriter {
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private BufferedWriter writer;
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private LoggingTool logger;
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private int moleculeNumber;
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public Map sdFields=null;
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//private boolean writeAromatic=true;
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* Contructs a new MDLWriter that can write an array of
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* Molecules to a Writer.
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* @param out The Writer to write to
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public MDLWriter(Writer out) {
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logger = new LoggingTool(this);
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if (out instanceof BufferedWriter) {
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writer = (BufferedWriter)out;
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writer = new BufferedWriter(out);
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} catch (Exception exc) {
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this.moleculeNumber = 1;
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* Contructs a new MDLWriter that can write an array of
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* Molecules to a given OutputStream.
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* @param output The OutputStream to write to
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public MDLWriter(OutputStream output) {
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this(new OutputStreamWriter(output));
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this(new StringWriter());
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public IResourceFormat getFormat() {
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return MDLFormat.getInstance();
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public void setWriter(Writer out) throws CDKException {
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if (out instanceof BufferedWriter) {
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writer = (BufferedWriter)out;
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writer = new BufferedWriter(out);
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public void setWriter(OutputStream output) throws CDKException {
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setWriter(new OutputStreamWriter(output));
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* Method does not do anything until now.
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public void dontWriteAromatic(){
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//writeAromatic=false;
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* Here you can set a map which will be used to build sd fields in the file.
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* The entries will be translated to sd fields like this:<br>
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* > <key><br>
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* @param map The map to be used, map of String-String pairs
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public void setSdFields(Map map){
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* Flushes the output and closes this object.
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public void close() throws IOException {
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public boolean accepts(Class classObject) {
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Class[] interfaces = classObject.getInterfaces();
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for (int i=0; i<interfaces.length; i++) {
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if (IMolecule.class.equals(interfaces[i])) return true;
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if (IChemFile.class.equals(interfaces[i])) return true;
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if (IChemModel.class.equals(interfaces[i])) return true;
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if (IMoleculeSet.class.equals(interfaces[i])) return true;
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* Writes a IChemObject to the MDL molfile formated output.
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* It can only output ChemObjects of type ChemFile, Molecule and
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* @param object class must be of type ChemFile, Molecule or MoleculeSet.
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* @see org.openscience.cdk.ChemFile
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public void write(IChemObject object) throws CDKException {
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if (object instanceof IMoleculeSet) {
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writeMoleculeSet((IMoleculeSet)object);
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} else if (object instanceof IChemFile) {
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writeChemFile((IChemFile)object);
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} else if (object instanceof IChemModel) {
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IChemFile file = object.getBuilder().newChemFile();
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IChemSequence sequence = object.getBuilder().newChemSequence();
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sequence.addChemModel((IChemModel)object);
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file.addChemSequence(sequence);
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writeChemFile((IChemFile)file);
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} else if (object instanceof IMolecule) {
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writeMolecule((IMolecule)object);
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} catch (Exception ex) {
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logger.error(ex.getMessage());
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throw new CDKException("Exception while writing MDL file: " + ex.getMessage(), ex);
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throw new CDKException("Only supported is writing of ChemFile, MoleculeSet, AtomContainer and Molecule objects.");
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* Writes an array of Molecules to an OutputStream in MDL sdf format.
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* @param som Array of Molecules that is written to an OutputStream
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private void writeMoleculeSet(IMoleculeSet som)
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java.util.Iterator molecules = som.molecules();
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while (molecules.hasNext())
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IMolecule mol = (IMolecule)molecules.next();
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boolean[] isVisible=new boolean[mol.getAtomCount()];
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for(int k=0;k<isVisible.length;k++){
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catch (Exception exc)
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private void writeChemFile(IChemFile file) throws Exception {
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List moleculesList = ChemFileManipulator.getAllAtomContainers(file);
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for (int i=0; i<moleculesList.size(); i++) {
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writeMolecule(file.getBuilder().newMolecule((IAtomContainer)moleculesList.get(i)));
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* Writes a Molecule to an OutputStream in MDL sdf format.
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* @param container Molecule that is written to an OutputStream
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public void writeMolecule(IMolecule container) throws Exception {
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// taking care of the $$$$ signs:
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// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
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if(moleculeNumber == 2) {
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writer.write("$$$$");
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// write header block
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// lines get shortened to 80 chars, that's in the spec
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String title = (String)container.getProperty(CDKConstants.TITLE);
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if (title == null) title = "";
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if(title.length()>80)
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title=title.substring(0,80);
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writer.write(title + "\n");
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* This line has the format:
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* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
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* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
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* User's first and last initials (l), program name (P),
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* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
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* energy (E) if modeling program input, internal registry number (R)
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* if input through MDL form.
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* A blank line can be substituted for line 2.
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writer.write(" CDK ");
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writer.write(new SimpleDateFormat("M/d/y,H:m",Locale.US).format(
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Calendar.getInstance(TimeZone.getDefault()).getTime())
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String comment = (String)container.getProperty(CDKConstants.REMARK);
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if (comment == null) comment = "";
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if(comment.length()>80)
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comment=comment.substring(0,80);
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writer.write(comment + "\n");
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line += formatMDLInt(container.getAtomCount(), 3);
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line += formatMDLInt(container.getBondCount(), 3);
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line += " 0 0 0 0 0 0 0 0999 V2000\n";
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for (int f = 0; f < container.getAtomCount(); f++) {
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IAtom atom = container.getAtom(f);
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if (atom.getPoint3d() != null) {
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line += formatMDLFloat((float) atom.getPoint3d().x);
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line += formatMDLFloat((float) atom.getPoint3d().y);
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line += formatMDLFloat((float) atom.getPoint3d().z) + " ";
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} else if (atom.getPoint2d() != null) {
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line += formatMDLFloat((float) atom.getPoint2d().x);
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line += formatMDLFloat((float) atom.getPoint2d().y);
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// if no coordinates available, then output a number
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line += formatMDLFloat((float)0.0);
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line += formatMDLFloat((float)0.0);
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line += formatMDLFloat((float)0.0) + " ";
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if(container.getAtom(f) instanceof IPseudoAtom)
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line += formatMDLString(((IPseudoAtom) container.getAtom(f)).getLabel(), 3);
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line += formatMDLString(container.getAtom(f).getSymbol(), 3);
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line += " 0 0 0 0 0 0 0 0 0 0 0 0";
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Iterator bonds = container.bonds();
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while (bonds.hasNext()) {
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IBond bond = (IBond) bonds.next();
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if (bond.getAtomCount() != 2) {
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logger.warn("Skipping bond with more/less than two atoms: " + bond);
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if (bond.getStereo() == CDKConstants.STEREO_BOND_UP_INV ||
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bond.getStereo() == CDKConstants.STEREO_BOND_DOWN_INV) {
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// turn around atom coding to correct for inv stereo
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line = formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
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line += formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
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line = formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
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line += formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
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line += formatMDLInt((int)bond.getOrder(),3);
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switch(bond.getStereo()){
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case CDKConstants.STEREO_BOND_UP:
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case CDKConstants.STEREO_BOND_UP_INV:
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case CDKConstants.STEREO_BOND_DOWN:
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case CDKConstants.STEREO_BOND_DOWN_INV:
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// write formal atomic charges
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for (int i = 0; i < container.getAtomCount(); i++) {
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IAtom atom = container.getAtom(i);
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int charge = atom.getFormalCharge();
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writer.write("M CHG 1 ");
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writer.write(formatMDLInt(i+1,3));
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writer.write(formatMDLInt(charge,3));
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// write formal isotope information
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for (int i = 0; i < container.getAtomCount(); i++) {
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IAtom atom = container.getAtom(i);
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if (!(atom instanceof IPseudoAtom)) {
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int atomicMass = atom.getMassNumber();
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int majorMass = IsotopeFactory.getInstance(atom.getBuilder()).getMajorIsotope(atom.getSymbol()).getMassNumber();
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if (atomicMass != 0 && atomicMass != majorMass) {
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writer.write("M ISO 1 ");
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writer.write(formatMDLInt(i+1,3));
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writer.write(formatMDLInt(atomicMass,3));
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writer.write("M END");
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//write sdfields, if any
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Set set = sdFields.keySet();
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Iterator iterator = set.iterator();
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while (iterator.hasNext()) {
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Object element = iterator.next();
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writer.write("> <"+(String)element+">");
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writer.write(sdFields.get(element).toString());
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// taking care of the $$$$ signs:
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// we write such a sign at the end of all except the first molecule
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if(moleculeNumber != 1) {
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writer.write("$$$$");
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* Formats an int to fit into the connectiontable and changes it
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* @param i The int to be formated
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* @param l Length of the String
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* @return The String to be written into the connectiontable
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private String formatMDLInt(int i, int l) {
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String s = "", fs = "";
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NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
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nf.setParseIntegerOnly(true);
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nf.setMinimumIntegerDigits(1);
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nf.setMaximumIntegerDigits(l);
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nf.setGroupingUsed(false);
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for (int f = 0; f < l; f++)
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* Formats a float to fit into the connectiontable and changes it
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* @param fl The float to be formated
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* @return The String to be written into the connectiontable
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private String formatMDLFloat(float fl) {
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String s = "", fs = "";
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NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
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nf.setMinimumIntegerDigits(1);
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nf.setMaximumIntegerDigits(4);
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nf.setMinimumFractionDigits(4);
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nf.setMaximumFractionDigits(4);
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nf.setGroupingUsed(false);
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for (int f = 0; f < l; f++)
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* Formats a String to fit into the connectiontable.
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* @param s The String to be formated
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* @param le The length of the String
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* @return The String to be written in the connectiontable
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private String formatMDLString(String s, int le) {
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return s.substring(0, le);
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for (int f = 0; f < l; f++)
added
removed
src/org/openscience/cdk/io/MDLWriter.java
