org.openscience.cdk.io.XYZReader Maven / Gradle / Ivy
/* Copyright (C) 2001-2007 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.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 javax.vecmath.Point3d;
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.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.XYZFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Reads an object from XYZ formated input.
*
* This class is based on Dan Gezelter's XYZReader from Jmol
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @cdk.keyword file format, XYZ
*/
public class XYZReader extends DefaultChemObjectReader {
private BufferedReader input;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(XYZReader.class);
/**
* Construct a new reader from a Reader type object.
*
* @param input reader from which input is read
*/
public XYZReader(Reader input) {
this.input = new BufferedReader(input);
}
public XYZReader(InputStream input) {
this(new InputStreamReader(input));
}
public XYZReader() {
this(new StringReader(""));
}
@Override
public IResourceFormat getFormat() {
return XYZFormat.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;
Class[] interfaces = classObject.getInterfaces();
for (int i = 0; i < interfaces.length; i++) {
if (IChemFile.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* reads the content from a XYZ input. It can only return a
* IChemObject of type ChemFile
*
* @param object class must be of type ChemFile
*
* @see IChemFile
*/
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
return (T) readChemFile((IChemFile) object);
} else {
throw new CDKException("Only supported is reading of ChemFile objects.");
}
}
// private procedures
/**
* Private method that actually parses the input to read a ChemFile
* object.
*
* @return A ChemFile containing the data parsed from input.
*/
private IChemFile readChemFile(IChemFile file) {
IChemSequence chemSequence = file.getBuilder().newInstance(IChemSequence.class);
int number_of_atoms = 0;
StringTokenizer tokenizer;
try {
String line = input.readLine();
while (input.ready() && line != null) {
// parse frame by frame
tokenizer = new StringTokenizer(line, "\t ,;");
String token = tokenizer.nextToken();
number_of_atoms = Integer.parseInt(token);
String info = input.readLine();
IChemModel chemModel = file.getBuilder().newInstance(IChemModel.class);
IAtomContainerSet setOfMolecules = file.getBuilder().newInstance(IAtomContainerSet.class);
IAtomContainer m = file.getBuilder().newInstance(IAtomContainer.class);
m.setProperty(CDKConstants.TITLE, info);
for (int i = 0; i < number_of_atoms; i++) {
line = input.readLine();
if (line == null) break;
if (line.startsWith("#") && line.length() > 1) {
Object comment = m.getProperty(CDKConstants.COMMENT);
if (comment == null) {
comment = "";
}
comment = comment.toString() + line.substring(1).trim();
m.setProperty(CDKConstants.COMMENT, comment);
logger.debug("Found and set comment: ", comment);
i--; // a comment line does not count as an atom
} else {
double x = 0.0f, y = 0.0f, z = 0.0f;
double charge = 0.0f;
tokenizer = new StringTokenizer(line, "\t ,;");
int fields = tokenizer.countTokens();
if (fields < 4) {
// this is an error but cannot throw exception
} else {
String atomtype = tokenizer.nextToken();
x = (new Double(tokenizer.nextToken())).doubleValue();
y = (new Double(tokenizer.nextToken())).doubleValue();
z = (new Double(tokenizer.nextToken())).doubleValue();
if (fields == 8) charge = (new Double(tokenizer.nextToken())).doubleValue();
IAtom atom = file.getBuilder().newInstance(IAtom.class, atomtype, new Point3d(x, y, z));
atom.setCharge(charge);
m.addAtom(atom);
}
}
}
setOfMolecules.addAtomContainer(m);
chemModel.setMoleculeSet(setOfMolecules);
chemSequence.addChemModel(chemModel);
line = input.readLine();
}
file.addChemSequence(chemSequence);
} catch (IOException e) {
// should make some noise now
file = null;
logger.error("Error while reading file: ", e.getMessage());
logger.debug(e);
}
return file;
}
@Override
public void close() throws IOException {
input.close();
}
}