/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2003-2007 Egon Willighagen <egonw@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.util.Iterator;
import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
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.IChemObject;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.io.formats.CDKSourceCodeFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.tools.DataFeatures;
import org.openscience.cdk.tools.IDCreator;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Converts a Molecule into CDK source code that would build the same
* molecule. It's typical use is:
* <pre>
* StringWriter stringWriter = new StringWriter();
* ChemObjectWriter writer = new CDKSourceCodeWriter(stringWriter);
* writer.write((Molecule)molecule);
* writer.close();
* System.out.print(stringWriter.toString());
* </pre>
*
* @cdk.module io
* @cdk.githash
*
* @author Egon Willighagen <egonw@sci.kun.nl>
* @cdk.created 2003-10-01
*
* @cdk.keyword file format, CDK source code
*/
@TestClass("org.openscience.cdk.io.CDKSourceCodeWriterTest")
public class CDKSourceCodeWriter extends DefaultChemObjectWriter {
private BufferedWriter writer;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(CDKSourceCodeWriter.class);
private BooleanIOSetting write2DCoordinates;
private BooleanIOSetting write3DCoordinates;
/**
* Constructs a new CDKSourceCodeWriter.
*
* @param out The Writer to write to
*/
public CDKSourceCodeWriter(Writer out) {
initIOSettings();
try {
setWriter(out);
} catch (Exception exc) {
}
}
public CDKSourceCodeWriter(OutputStream out) {
this(new OutputStreamWriter(out));
}
public CDKSourceCodeWriter() {
this(new StringWriter());
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return CDKSourceCodeFormat.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.flush();
writer.close();
}
@TestMethod("testAccepts")
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (int i=0; i<interfaces.length; i++) {
if (IMolecule.class.equals(interfaces[i])) return true;
if (IAtomContainer.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
public void write(IChemObject object) throws CDKException {
customizeJob();
if (object instanceof IMolecule) {
try {
writeMolecule((IMolecule)object);
writer.flush();
} catch (Exception ex) {
logger.error(ex.getMessage());
logger.debug(ex);
throw new CDKException("Exception while writing to CDK source code: " + ex.getMessage(), ex);
}
} else if (object instanceof IAtomContainer) {
try {
writeAtomContainer((IAtomContainer)object);
writer.flush();
} catch (Exception ex) {
logger.error(ex.getMessage());
logger.debug(ex);
throw new CDKException("Exception while writing to CDK source code: " + ex.getMessage(), ex);
}
} else {
throw new CDKException("Only supported is writing of IMolecule and IAtomContainer objects.");
}
}
private void writeAtoms(IAtomContainer molecule) throws Exception {
Iterator<IAtom> atoms = molecule.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = (IAtom)atoms.next();
writeAtom(atom);
writer.write(" mol.addAtom(" + atom.getID() + ");");
writer.newLine();
}
}
private void writeBonds(IAtomContainer molecule) throws Exception {
Iterator<IBond> bonds = molecule.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
writeBond(bond);
writer.write(" mol.addBond(" + bond.getID() + ");");
writer.newLine();
}
}
public void writeMolecule(IMolecule molecule) throws Exception {
writer.write("{");
writer.newLine();
writer.write(" IMolecule mol = new Molecule();");
writer.newLine();
IDCreator.createIDs(molecule);
writeAtoms(molecule);
writeBonds(molecule);
writer.write("}");
writer.newLine();
}
public void writeAtomContainer(IAtomContainer molecule) throws Exception {
writer.write("{");
writer.newLine();
writer.write(" IAtomContainer mol = new AtomContainer();");
writer.newLine();
IDCreator.createIDs(molecule);
writeAtoms(molecule);
writeBonds(molecule);
writer.write("}");
writer.newLine();
}
public void writeAtom(IAtom atom) throws Exception {
if (atom instanceof IPseudoAtom) {
writer.write(" IPseudoAtom " + atom.getID() + " = mol.getBuilder().newPseudoAtom();");
writer.newLine();
writer.write(" atom.setLabel(\"" + ((IPseudoAtom)atom).getLabel() + "\");");
writer.newLine();
} else {
writer.write(" IAtom " + atom.getID() + " = mol.getBuilder().newAtom(\"" + atom.getSymbol() +
"\");");
writer.newLine();
}
if (atom.getFormalCharge() != null) {
writer.write(" " + atom.getID() + ".setFormalCharge(" + atom.getFormalCharge() + ");");
writer.newLine();
}
if (write2DCoordinates.isSet() &&
atom.getPoint2d() != null) {
Point2d p2d = atom.getPoint2d();
writer.write(" " + atom.getID() + ".setPoint2d(new Point2d(" +
p2d.x + ", " + p2d.y + "));");
writer.newLine();
}
if (write3DCoordinates.isSet() &&
atom.getPoint3d() != null) {
Point3d p3d = atom.getPoint3d();
writer.write(" " + atom.getID() + ".setPoint3d(new Point3d(" +
p3d.x + ", " + p3d.y + ", " + p3d.z + "));");
writer.newLine();
}
}
public void writeBond(IBond bond) throws Exception {
writer.write(" IBond " + bond.getID() + " = mol.getBuilder().newBond(" +
bond.getAtom(0).getID() + ", " +
bond.getAtom(1).getID() + ", IBond.Order." +
bond.getOrder() + ");");
writer.newLine();
}
public int getSupportedDataFeatures() {
return DataFeatures.HAS_2D_COORDINATES |
DataFeatures.HAS_3D_COORDINATES |
DataFeatures.HAS_GRAPH_REPRESENTATION |
DataFeatures.HAS_ATOM_ELEMENT_SYMBOL;
}
public int getRequiredDataFeatures() {
return DataFeatures.HAS_GRAPH_REPRESENTATION |
DataFeatures.HAS_ATOM_ELEMENT_SYMBOL;
}
private void initIOSettings() {
write2DCoordinates = new BooleanIOSetting("write2DCoordinates", IOSetting.LOW,
"Should 2D coordinates be added?",
"true");
write3DCoordinates = new BooleanIOSetting("write3DCoordinates", IOSetting.LOW,
"Should 3D coordinates be added?",
"true");
}
private void customizeJob() {
fireIOSettingQuestion(write2DCoordinates);
fireIOSettingQuestion(write3DCoordinates);
}
public IOSetting[] getIOSettings() {
IOSetting[] settings = new IOSetting[2];
settings[0] = write2DCoordinates;
settings[1] = write3DCoordinates;
return settings;
}
}