org.openscience.cdk.io.CDKSourceCodeWriter Maven / Gradle / Ivy
/* Copyright (C) 2003-2007,2010 Egon Willighagen
*
* Contact: [email protected]
*
* 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.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.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.io.setting.StringIOSetting;
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:
*
* StringWriter stringWriter = new StringWriter();
* ChemObjectWriter writer = new CDKSourceCodeWriter(stringWriter);
* writer.write((Molecule)molecule);
* writer.close();
* System.out.print(stringWriter.toString());
*
*
* @cdk.module io
* @cdk.githash
*
* @author Egon Willighagen
* @cdk.created 2003-10-01
*
* @cdk.keyword file format, CDK source code
* @cdk.iooptions
*/
public class CDKSourceCodeWriter extends DefaultChemObjectWriter {
private BufferedWriter writer;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(CDKSourceCodeWriter.class);
private BooleanIOSetting write2DCoordinates;
private BooleanIOSetting write3DCoordinates;
private StringIOSetting builder;
/**
* 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());
}
@Override
public IResourceFormat getFormat() {
return CDKSourceCodeFormat.getInstance();
}
@Override
public void setWriter(Writer out) throws CDKException {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
}
@Override
public void setWriter(OutputStream output) throws CDKException {
setWriter(new OutputStreamWriter(output));
}
/**
* Flushes the output and closes this object.
*/
@Override
public void close() throws IOException {
writer.flush();
writer.close();
}
@Override
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 (IAtomContainer.class.equals(classObject)) return true;
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
@Override
public void write(IChemObject object) throws CDKException {
customizeJob();
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 IAtomContainer objects.");
}
}
private void writeAtoms(IAtomContainer molecule) throws Exception {
Iterator 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 bonds = molecule.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
writeBond(bond);
writer.write(" mol.addBond(" + bond.getID() + ");");
writer.newLine();
}
}
private void writeAtomContainer(IAtomContainer molecule) throws Exception {
writer.write("{");
writer.newLine();
writer.write(" IChemObjectBuilder builder = ");
writer.write(builder.getSetting());
writer.write(".getInstance();");
writer.newLine();
writer.write(" IAtomContainer mol = builder.newInstance(IAtomContainer.class);");
writer.newLine();
IDCreator.createIDs(molecule);
writeAtoms(molecule);
writeBonds(molecule);
writer.write("}");
writer.newLine();
}
private void writeAtom(IAtom atom) throws Exception {
if (atom instanceof IPseudoAtom) {
writer.write(" IPseudoAtom " + atom.getID() + " = builder.newInstance(IPseudoAtom.class);");
writer.newLine();
writer.write(" atom.setLabel(\"" + ((IPseudoAtom) atom).getLabel() + "\");");
writer.newLine();
} else {
writer.write(" IAtom " + atom.getID() + " = builder.newInstance(IAtom.class,\"" + 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();
}
}
private void writeBond(IBond bond) throws Exception {
writer.write(" IBond " + bond.getID() + " = builder.newInstance(IBond.class," + 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 = addSetting(new BooleanIOSetting("write2DCoordinates", IOSetting.Importance.LOW,
"Should 2D coordinates be added?", "true"));
write3DCoordinates = addSetting(new BooleanIOSetting("write3DCoordinates", IOSetting.Importance.LOW,
"Should 3D coordinates be added?", "true"));
builder = addSetting(new StringIOSetting("builder", IOSetting.Importance.LOW,
"Which IChemObjectBuilder should be used?", "DefaultChemObjectBuilder"));
}
private void customizeJob() {
fireIOSettingQuestion(write2DCoordinates);
fireIOSettingQuestion(write3DCoordinates);
fireIOSettingQuestion(builder);
}
}
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