/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
*
* 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.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.StringTokenizer;
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.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLRXNFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Reads a molecule from an MDL RXN file {@cdk.cite DAL92}.
* This MDL RXN reader uses the MDLV2000 reader to read each mol file
* @cdk.module io
* @cdk.githash
*
* @author Egon Willighagen
* @author Thomas Kuhn
* @cdk.created 2003-07-24
*
* @cdk.keyword file format, MDL RXN
* @cdk.bug 1849923
*/
@TestClass("org.openscience.cdk.io.MDLRXNV2000ReaderTest")
public class MDLRXNV2000Reader extends DefaultChemObjectReader {
BufferedReader input = null;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(MDLRXNV2000Reader.class);
/**
* Contructs a new MDLReader that can read Molecule from a given Reader.
*
* @param in The Reader to read from
*/
public MDLRXNV2000Reader(Reader in) {
this(in, Mode.RELAXED);
}
public MDLRXNV2000Reader(Reader in, Mode mode) {
if (in instanceof BufferedReader) {
input = (BufferedReader)in;
} else {
input = new BufferedReader(in);
}
super.mode = mode;
}
public MDLRXNV2000Reader(InputStream input) {
this(input, Mode.RELAXED);
}
public MDLRXNV2000Reader(InputStream input, Mode mode) {
this(new InputStreamReader(input), mode);
}
public MDLRXNV2000Reader() {
this(new StringReader(""));
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return MDLRXNFormat.getInstance();
}
@TestMethod("testSetReader_Reader")
public void setReader(Reader input) throws CDKException {
if (input instanceof BufferedReader) {
this.input = (BufferedReader)input;
} else {
this.input = new BufferedReader(input);
}
}
@TestMethod("testSetReader_InputStream")
public void setReader(InputStream input) throws CDKException {
setReader(new InputStreamReader(input));
}
@TestMethod("testAccepts")
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (int i=0; i<interfaces.length; i++) {
if (IChemModel.class.equals(interfaces[i])) return true;
if (IChemFile.class.equals(interfaces[i])) return true;
if (IReaction.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Takes an object which subclasses IChemObject, e.g.Molecule, and will read
* this (from file, database, internet etc). If the specific implementation
* does not support a specific IChemObject it will throw an Exception.
*
* @param object The object that subclasses
* IChemObject
* @return The IChemObject read
* @exception CDKException
*/
public IChemObject read(IChemObject object) throws CDKException {
if (object instanceof IReaction) {
return (IChemObject) readReaction(object.getBuilder());
} else if (object instanceof IReactionSet) {
IReactionSet reactionSet = object.getBuilder().newReactionSet();
reactionSet.addReaction(readReaction(object.getBuilder()));
return reactionSet;
} else if (object instanceof IChemModel) {
IChemModel model = object.getBuilder().newChemModel();
IReactionSet reactionSet = object.getBuilder().newReactionSet();
reactionSet.addReaction(readReaction(object.getBuilder()));
model.setReactionSet(reactionSet);
return model;
} else if (object instanceof IChemFile) {
IChemFile chemFile = object.getBuilder().newChemFile();
IChemSequence sequence = object.getBuilder().newChemSequence();
sequence.addChemModel((IChemModel)read(object.getBuilder().newChemModel()));
chemFile.addChemSequence(sequence);
return chemFile;
} else {
throw new CDKException("Only supported are Reaction and ChemModel, and not " +
object.getClass().getName() + "."
);
}
}
@TestMethod("testAccepts")
public boolean accepts(IChemObject object) {
if (object instanceof IReaction) {
return true;
} else if (object instanceof IChemModel) {
return true;
} else if (object instanceof IChemFile) {
return true;
} else if (object instanceof IReactionSet) {
return true;
}
return false;
}
/**
* Read a Reaction from a file in MDL RXN format
*
* @return The Reaction that was read from the MDL file.
*/
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
IReaction reaction = builder.newReaction();
try {
input.readLine(); // first line should be $RXN
input.readLine(); // second line
input.readLine(); // third line
input.readLine(); // fourth line
} catch (IOException exception) {
logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try {
String countsLine = input.readLine();
/* this line contains the number of reactants
and products */
StringTokenizer tokenizer = new StringTokenizer(countsLine);
reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + productCount + " products in file");
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try {
for (int i=1; i<=reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // announceMDLFileLine
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
// Changed this to mdlv2000 reader
MDLV2000Reader reader = new MDLV2000Reader(
new StringReader(molFile.toString()),
super.mode
);
IMolecule reactant = (IMolecule)reader.read(
builder.newMolecule()
);
// add reactant
reaction.addReactant(reactant);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try {
for (int i=1; i<=productCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // String announceMDLFileLine =
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
MDLV2000Reader reader = new MDLV2000Reader(
new StringReader(molFile.toString()));
IMolecule product = (IMolecule)reader.read(
builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
java.util.Iterator molecules = reaction.getReactants().molecules().iterator();
while (molecules.hasNext()) {
reactingSide.add((IMolecule)molecules.next());
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.getProducts().molecules().iterator();
while (molecules.hasNext()) {
producedSide.add((IMolecule)molecules.next());
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.getAtoms();
// IAtom[] producedAtoms = producedSide.getAtoms();
for (int i=0; i<reactingSide.getAtomCount(); i++) {
for (int j=0; j<producedSide.getAtomCount(); j++) {
IAtom eductAtom = reactingSide.getAtom(i);
IAtom productAtom = producedSide.getAtom(j);
if (eductAtom.getID() != null &&
eductAtom.getID().equals(productAtom.getID())) {
reaction.addMapping(
builder.newMapping(eductAtom, productAtom)
);
mappingCount++;
break;
}
}
}
logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
@TestMethod("testClose")
public void close() throws IOException {
input.close();
}
}