/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Egon Willighagen <egonw@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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 javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.CrystalGeometryTools;
import org.openscience.cdk.interfaces.IAtom;
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.interfaces.ICrystal;
import org.openscience.cdk.io.formats.CrystClustFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.math.FortranFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* @cdk.module extra
* @cdk.githash
*/
@TestClass("org.openscience.cdk.io.CrystClustReaderTest")
public class CrystClustReader extends DefaultChemObjectReader {
private BufferedReader input;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(CrystClustReader.class);
public CrystClustReader() {
}
public CrystClustReader(Reader input) {
this();
if (input instanceof BufferedReader) {
this.input = (BufferedReader)input;
} else {
this.input = new BufferedReader(input);
}
}
public CrystClustReader(InputStream input) {
this(new InputStreamReader(input));
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return CrystClustFormat.getInstance();
}
@TestMethod("testSetReader_Reader")
public void setReader(Reader reader) throws CDKException {
if (reader instanceof BufferedReader) {
this.input = (BufferedReader)reader;
} else {
this.input = new BufferedReader(reader);
}
}
@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 (IChemFile.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
public IChemObject read(IChemObject object) throws CDKException {
if (object instanceof IChemFile) {
IChemFile cf = readChemFile((IChemFile)object);
return cf;
} else {
throw new CDKException("Only supported is reading of ChemFile.");
}
}
private IChemFile readChemFile(IChemFile file) throws CDKException {
IChemSequence seq = file.getBuilder().newChemSequence();
IChemModel model = file.getBuilder().newChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3d a, b, c;
try {
String line = input.readLine();
while (input.ready() && line != null) {
logger.debug((lineNumber++) + ": ", line);
if (line.startsWith("frame:")) {
logger.debug("found new frame");
model = file.getBuilder().newChemModel();
crystal = file.getBuilder().newCrystal();
// assume the file format is correct
logger.debug("reading spacegroup");
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
crystal.setSpaceGroup(line);
logger.debug("reading unit cell axes");
Vector3d axis = new Vector3d();
logger.debug("parsing A: ");
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.setA(axis);
axis = new Vector3d();
logger.debug("parsing B: ");
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.setB(axis);
axis = new Vector3d();
logger.debug("parsing C: ");
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.setC(axis);
logger.debug("Crystal: ", crystal);
a = crystal.getA();
b = crystal.getB();
c = crystal.getC();
logger.debug("Reading number of atoms");
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
int atomsToRead = Integer.parseInt(line);
logger.debug("Reading no molecules in assym unit cell");
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
int Z = Integer.parseInt(line);
crystal.setZ(Z);
String symbol;
double charge;
Point3d cart;
for (int i=1; i<=atomsToRead; i++) {
cart = new Point3d();
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
symbol = line.substring(0, line.indexOf(":"));
charge = Double.parseDouble(line.substring(line.indexOf(":")+1));
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
cart.x = Double.parseDouble(line); // x
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
cart.y = Double.parseDouble(line); // y
line = input.readLine();
logger.debug((lineNumber++) + ": ", line);
cart.z = Double.parseDouble(line); // z
IAtom atom = file.getBuilder().newAtom(symbol);
atom.setCharge(charge);
// convert cartesian coords to fractional
Point3d frac = CrystalGeometryTools.cartesianToFractional(a, b, c, cart);
atom.setFractionalPoint3d(frac);
crystal.addAtom(atom);
logger.debug("Added atom: ", atom);
}
model.setCrystal(crystal);
seq.addChemModel(model);
} else {
logger.debug("Format seems broken. Skipping these lines:");
while (!line.startsWith("frame:") &&
input.ready() && line != null) {
line = input.readLine();
logger.debug(lineNumber++ + ": ", line);
}
logger.debug("Ok, resynched: found new frame");
}
}
file.addChemSequence(seq);
} catch (Exception exception) {
String message = "Error while parsing CrystClust file: " + exception.getMessage();
logger.error(message);
logger.debug(exception);
throw new CDKException(message, exception);
}
return file;
}
@TestMethod("testClose")
public void close() throws IOException {
input.close();
}
}