org.openscience.cdk.io.SDFWriter Maven / Gradle / Ivy
/* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
* 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.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
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.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.SDFFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.smiles.InvPair;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
/**
* Writes MDL SD files ({@cdk.cite DAL92}). A MDL SD file contains one or more molecules,
* complemented by properties.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
* @cdk.keyword file format, MDL SD file
*/
public class SDFWriter extends DefaultChemObjectWriter {
private final static ILoggingTool logger = LoggingToolFactory.createLoggingTool(SDFWriter.class);
private BufferedWriter writer;
private BooleanIOSetting writerProperties;
private Set propertiesToWrite;
/**
* Constructs a new SDFWriter that writes to the given {@link Writer}.
*
* @param out The {@link Writer} to write to
*/
public SDFWriter(Writer out) {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
initIOSettings();
}
/**
* Constructs a new MDLWriter that can write to a given
* {@link OutputStream}.
*
* @param output The {@link OutputStream} to write to
*/
public SDFWriter(OutputStream output) {
this(new OutputStreamWriter(output));
}
public SDFWriter() {
this(new StringWriter());
}
/**
* Constructs a new SDFWriter that writes to the given {@link Writer}.
*
* @param out The {@link Writer} to write to
*/
public SDFWriter(Writer out, Set propertiesToWrite) {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
initIOSettings();
this.propertiesToWrite = propertiesToWrite;
}
/**
* Constructs a new SdfWriter that can write to a given
* {@link OutputStream}.
*
* @param output The {@link OutputStream} to write to
*/
public SDFWriter(OutputStream output, Set propertiesToWrite) {
this(new OutputStreamWriter(output), propertiesToWrite);
}
/**
* Writes SD-File to a String including the given properties
*/
public SDFWriter(Set propertiesToWrite) {
this(new StringWriter(), propertiesToWrite);
}
@Override
public IResourceFormat getFormat() {
return SDFFormat.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.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 (IChemFile.class.equals(interfaces[i])) return true;
if (IChemModel.class.equals(interfaces[i])) return true;
if (IAtomContainerSet.class.equals(interfaces[i])) return true;
}
if (IAtomContainer.class.equals(classObject)) return true;
if (IChemFile.class.equals(classObject)) return true;
if (IChemModel.class.equals(classObject)) return true;
if (IAtomContainerSet.class.equals(classObject)) return true;
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Writes a IChemObject to the MDL SD file formated output. It can only
* output IChemObjects of type {@link IChemFile}, {@link IAtomContainerSet}
* and {@link IAtomContainerSet}.
*
* @param object an acceptable {@link IChemObject}
*
* @see #accepts(Class)
*/
@Override
public void write(IChemObject object) throws CDKException {
try {
if (object instanceof IAtomContainerSet) {
writeMoleculeSet((IAtomContainerSet) object);
return;
} else 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 ChemFile, MoleculeSet, AtomContainer and Molecule objects.");
}
/**
* Writes an {@link IAtomContainerSet}.
*
* @param som the {@link IAtomContainerSet} to serialize
*/
private void writeMoleculeSet(IAtomContainerSet som) throws Exception {
for (IAtomContainer mol : som.atomContainers()) {
writeMolecule(mol);
}
}
private void writeChemFile(IChemFile file) throws Exception {
for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(file)) {
writeMolecule(container);
}
}
private void writeMolecule(IAtomContainer container) throws CDKException {
try {
// write the MDL molfile bits
StringWriter stringWriter = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(stringWriter);
mdlWriter.addSettings(getSettings());
mdlWriter.write(container);
mdlWriter.close();
writer.write(stringWriter.toString());
// write the properties
Map sdFields = container.getProperties();
boolean writeAllProperties = propertiesToWrite == null;
if (sdFields != null) {
for (Object propKey : sdFields.keySet()) {
if (!isCDKInternalProperty(propKey)) {
if (writeAllProperties || propertiesToWrite.contains(propKey)) {
writer.write("> <" + propKey + ">");
writer.newLine();
writer.write("" + sdFields.get(propKey));
writer.newLine();
writer.newLine();
}
}
}
}
writer.write("$$$$\n");
} catch (IOException exception) {
throw new CDKException("Error while writing a SD file entry: " + exception.getMessage(), exception);
}
}
/**
* A list of properties used by CDK algorithms which must never be
* serialized into the SD file format.
*/
private static List cdkInternalProperties = new ArrayList();
static {
cdkInternalProperties.add(InvPair.CANONICAL_LABEL);
cdkInternalProperties.add(InvPair.INVARIANCE_PAIR);
// I think there are a few more, but cannot find them right now
}
private boolean isCDKInternalProperty(Object propKey) {
return cdkInternalProperties.contains(propKey);
}
private void initIOSettings() {
writerProperties = addSetting(new BooleanIOSetting("writeProperties", IOSetting.Importance.LOW,
"Should molecular properties be written?", "true"));
addSettings(new MDLV2000Writer().getSettings());
}
public void customizeJob() {
for (IOSetting setting : getSettings()) {
fireIOSettingQuestion(setting);
}
}
}
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