org.openscience.cdk.io.MDLRXNReader Maven / Gradle / Ivy
/* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
* 2014 Mark B Vine (orcid:0000-0002-7794-0426)
*
* 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 org.openscience.cdk.CDKConstants;
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.IMapping;
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;
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.Iterator;
import java.util.StringTokenizer;
/**
* Reads a molecule from an MDL RXN file {@cdk.cite DAL92}.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @author Egon Willighagen
* @cdk.created 2003-07-24
*
* @cdk.keyword file format, MDL RXN
*/
public class MDLRXNReader extends DefaultChemObjectReader {
BufferedReader input = null;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLReader.class);
/**
* Constructs a new MDLReader that can read Molecule from a given Reader.
*
* @param in The Reader to read from
*/
public MDLRXNReader(Reader in) {
this(in, Mode.RELAXED);
}
public MDLRXNReader(Reader in, Mode mode) {
if (in instanceof BufferedReader) {
input = (BufferedReader) in;
} else {
input = new BufferedReader(in);
}
super.mode = mode;
}
public MDLRXNReader(InputStream input) {
this(input, Mode.RELAXED);
}
public MDLRXNReader(InputStream input, Mode mode) {
this(new InputStreamReader(input), mode);
}
public MDLRXNReader() {
this(new StringReader(""));
}
@Override
public IResourceFormat getFormat() {
return MDLRXNFormat.getInstance();
}
@Override
public void setReader(Reader input) throws CDKException {
if (input instanceof BufferedReader) {
this.input = (BufferedReader) input;
} else {
this.input = new BufferedReader(input);
}
}
@Override
public void setReader(InputStream input) throws CDKException {
setReader(new InputStreamReader(input));
}
@Override
public boolean accepts(Class classObject) {
if (IChemFile.class.equals(classObject)) return true;
if (IChemModel.class.equals(classObject)) return true;
if (IReaction.class.equals(classObject)) return true;
if (IReactionSet.class.equals(classObject)) return true;
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;
if (IReactionSet.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
*/
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
return (T) readChemFile((IChemFile) object);
} else if (object instanceof IChemModel) {
return (T) readChemModel((IChemModel) object);
} else if (object instanceof IReactionSet) {
return (T) readReactionSet((IReactionSet) object);
} else if (object instanceof IReaction) {
return (T) readReaction(object.getBuilder());
} else {
throw new CDKException("Only supported are Reaction, ReactionSet, ChemModel and ChemFile, and not "
+ object.getClass().getName() + ".");
}
}
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 ChemFile from a file in MDL RDF format.
*
* @param chemFile The IChemFile
* @return The IChemFile that was read from the RDF file.
*/
private IChemFile readChemFile(IChemFile chemFile) throws CDKException {
IChemSequence chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);
IChemModel chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
chemSequence.addChemModel(readChemModel(chemModel));
chemFile.addChemSequence(chemSequence);
return chemFile;
}
/**
* Read a IChemModel from a file in MDL RDF format.
*
* @param chemModel The IChemModel
* @return The IChemModel that was read from the RDF file
*/
private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IReactionSet setOfReactions = chemModel.getReactionSet();
if (setOfReactions == null) {
setOfReactions = chemModel.getBuilder().newInstance(IReactionSet.class);
}
chemModel.setReactionSet(readReactionSet(setOfReactions));
return chemModel;
}
/**
* Read a IReactionSet from a file in MDL RDF format.
*
* @param setOfReactions The IReactionSet
* @return The IReactionSet that was read from the RDF file
*/
private IReactionSet readReactionSet(IReactionSet setOfReactions) throws CDKException {
IReaction r = readReaction(setOfReactions.getBuilder());
if (r != null) {
setOfReactions.addReaction(r);
}
try {
String line;
while ((line = input.readLine()) != null) {
logger.debug("line: ", line);
// apparently, this is a SDF file, continue with
// reading mol files
if (line.equals("$$$$")) {
r = readReaction(setOfReactions.getBuilder());
if (r != null) {
setOfReactions.addReaction(r);
}
} else {
// here the stuff between 'M END' and '$$$$'
if (r != null) {
// ok, the first lines should start with '>'
String fieldName = null;
if (line.startsWith("> ")) {
// ok, should extract the field name
int index = line.indexOf('<');
if (index != -1) {
int index2 = line.substring(index).indexOf('>');
if (index2 != -1) {
fieldName = line.substring(index + 1, index + index2);
}
}
// end skip all other lines
while ((line = input.readLine()) != null && line.startsWith(">")) {
logger.debug("data header line: ", line);
}
}
if (line == null) {
throw new CDKException("Expecting data line here, but found null!");
}
String data = line;
while ((line = input.readLine()) != null && line.trim().length() > 0) {
if (line.equals("$$$$")) {
logger.error("Expecting data line here, but found end of molecule: ", line);
break;
}
logger.debug("data line: ", line);
data += line;
// preserve newlines, unless the line is exactly 80 chars; in that case it
// is assumed to continue on the next line. See MDL documentation.
if (line.length() < 80) data += System.getProperty("line.separator");
}
if (fieldName != null) {
logger.info("fieldName, data: ", fieldName, ", ", data);
r.setProperty(fieldName, data);
}
}
}
}
} catch (CDKException cdkexc) {
throw cdkexc;
} catch (IOException exception) {
String error = "Error while parsing SDF";
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
return setOfReactions;
}
/**
* Read a Reaction from a file in MDL RXN format
*
* @return The Reaction that was read from the MDL file.
*/
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
logger.debug("Reading new reaction");
int linecount = 0;
IReaction reaction = builder.newInstance(IReaction.class);
try {
input.readLine(); // first line should be $RXN
input.readLine(); // second line
input.readLine(); // third line
input.readLine(); // fourth line
} catch (IOException exception) {
logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try {
String countsLine = input.readLine();
linecount++;
if (countsLine == null) {
return null;
}
logger.debug("Line " + linecount + ": " + countsLine);
if (countsLine.startsWith("$$$$")) {
logger.debug("File is empty, returning empty reaction");
return reaction;
}
/*
* 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 (IOException | NumberFormatException 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
MDLReader reader = new MDLReader(new StringReader(molFile.toString()));
IAtomContainer reactant = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
reader.close();
// add reactant
reaction.addReactant(reactant);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (IOException | IllegalArgumentException 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
MDLReader reader = new MDLReader(new StringReader(molFile.toString()), super.mode);
IAtomContainer product = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
reader.close();
// add reactant
reaction.addProduct(product);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (IOException | IllegalArgumentException 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.newInstance(IAtomContainer.class);
Iterator molecules = reaction.getReactants().atomContainers().iterator();
while (molecules.hasNext()) {
reactingSide.add(molecules.next());
}
IAtomContainer producedSide = builder.newInstance(IAtomContainer.class);
molecules = reaction.getProducts().atomContainers().iterator();
while (molecules.hasNext()) {
producedSide.add(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.getProperty(CDKConstants.ATOM_ATOM_MAPPING) != null
&& eductAtom.getProperty(CDKConstants.ATOM_ATOM_MAPPING).equals(
productAtom.getProperty(CDKConstants.ATOM_ATOM_MAPPING))) {
reaction.addMapping(builder.newInstance(IMapping.class, eductAtom, productAtom));
mappingCount++;
break;
}
}
}
logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
@Override
public void close() throws IOException {
input.close();
}
}
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