org.openscience.cdk.io.MDLRXNV3000Reader Maven / Gradle / Ivy
/* Copyright (C) 2003-2008 Egon Willighagen
*
* Contact: [email protected]
*
* This library 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.
*
* This library 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 library; 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.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
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.MDLRXNV3000Format;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Class that implements the new MDL mol format introduced in August 2002.
* The overall syntax is compatible with the old format, but I consider
* the format completely different, and thus implemented a separate Reader
* for it.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @author Egon Willighagen
* @cdk.created 2003-10-05
*
* @cdk.keyword MDL V3000
* @cdk.require java1.4+
*/
public class MDLRXNV3000Reader extends DefaultChemObjectReader {
BufferedReader input = null;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLRXNV3000Reader.class);
public MDLRXNV3000Reader(Reader in) {
this(in, Mode.RELAXED);
}
public MDLRXNV3000Reader(Reader in, Mode mode) {
if (in instanceof BufferedReader) {
input = (BufferedReader) in;
} else {
input = new BufferedReader(in);
}
initIOSettings();
super.mode = mode;
}
public MDLRXNV3000Reader(InputStream input) {
this(input, Mode.RELAXED);
}
public MDLRXNV3000Reader(InputStream input, Mode mode) {
this(new InputStreamReader(input), mode);
}
public MDLRXNV3000Reader() {
this(new StringReader(""));
}
@Override
public IResourceFormat getFormat() {
return MDLRXNV3000Format.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 (IChemModel.class.equals(classObject)) return true;
if (IReaction.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 (IReaction.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
@Override
public T read(T object) throws CDKException {
if (object instanceof IReaction) {
return (T) readReaction(object.getBuilder());
} else if (object instanceof IChemModel) {
IChemModel model = object.getBuilder().newInstance(IChemModel.class);
IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
reactionSet.addReaction(readReaction(object.getBuilder()));
model.setReactionSet(reactionSet);
return (T) model;
} else {
throw new CDKException("Only supported are Reaction and ChemModel, and not " + object.getClass().getName()
+ ".");
}
}
/**
* Reads the command on this line. If the line is continued on the next, that
* part is added.
*
* @return Returns the command on this line.
*/
private String readCommand() throws CDKException {
String line = readLine();
if (line.startsWith("M V30 ")) {
String command = line.substring(7);
if (command.endsWith("-")) {
command = command.substring(0, command.length() - 1);
command += readCommand();
}
return command;
} else {
throw new CDKException("Could not read MDL file: unexpected line: " + line);
}
}
private String readLine() throws CDKException {
String line = null;
try {
line = input.readLine();
logger.debug("read line: " + line);
} catch (Exception exception) {
String error = "Unexpected error while reading file: " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
return line;
}
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
IReaction reaction = builder.newInstance(IReaction.class);
readLine(); // first line should be $RXN
readLine(); // second line
readLine(); // third line
readLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
boolean foundCOUNTS = false;
while (isReady() && !foundCOUNTS) {
String command = readCommand();
if (command.startsWith("COUNTS")) {
StringTokenizer tokenizer = new StringTokenizer(command);
try {
tokenizer.nextToken();
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);
}
foundCOUNTS = true;
} else {
logger.warn("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.equals("BEGIN REACTANT")) {
String error = "Excepted start of reactant, but found: " + announceMDLFileLine;
logger.error(error);
throw new CDKException(error);
}
String molFileLine = "";
while (!molFileLine.endsWith("END REACTANT")) {
molFileLine = readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
};
try {
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.toString()), super.mode);
IAtomContainer reactant = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
reader.close();
// add reactant
reaction.addReactant(reactant);
} catch (IllegalArgumentException | CDKException | IOException exception) {
String error = "Error while reading reactant: " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++) {
StringBuffer molFile = new StringBuffer();
String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.equals("BEGIN PRODUCT")) {
String error = "Excepted start of product, but found: " + announceMDLFileLine;
logger.error(error);
throw new CDKException(error);
}
String molFileLine = "";
while (!molFileLine.endsWith("END PRODUCT")) {
molFileLine = readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
};
try {
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StringReader(molFile.toString()));
IAtomContainer product = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
reader.close();
// add product
reaction.addProduct(product);
} catch (IllegalArgumentException | CDKException | IOException exception) {
String error = "Error while reading product: " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
}
return reaction;
}
private boolean isReady() throws CDKException {
try {
return input.ready();
} catch (Exception exception) {
String error = "Unexpected error while reading file: " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
}
public boolean accepts(IChemObject object) {
if (object instanceof IReaction) {
return true;
} else if (object instanceof IChemModel) {
return true;
}
return false;
}
@Override
public void close() throws IOException {
input.close();
}
private void initIOSettings() {}
}
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