/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 Egon Willighagen <egonw@users.sf.net>
*
* 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.
*
* 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.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
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.exception.UnsupportedChemObjectException;
import org.openscience.cdk.interfaces.IAtom;
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.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Rather stupid file format used for storing crystal information.
*
* @author Egon Willighagen
* @cdk.created 2004-01-01
*
* @cdk.module extra
* @cdk.githash
*/
@TestClass("org.openscience.cdk.io.CrystClustWriterTest")
public class CrystClustWriter extends DefaultChemObjectWriter {
private BufferedWriter writer;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(CrystClustWriter.class);
/**
* Constructs a new CrystClustWriter class. Output will be stored in the Writer
* class given as parameter.
*
* @param out Writer to redirect the output to.
*/
public CrystClustWriter(Writer out) {
try {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter)out;
} else {
writer = new BufferedWriter(out);
}
} catch (Exception exc) {
logger.debug(exc.toString());
}
}
public CrystClustWriter(OutputStream output) {
this(new OutputStreamWriter(output));
}
public CrystClustWriter() {
this(new StringWriter());
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return CrystClustFormat.getInstance();
}
public void setWriter(Writer out) throws CDKException {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter)out;
} else {
writer = new BufferedWriter(out);
}
}
public void setWriter(OutputStream output) throws CDKException {
setWriter(new OutputStreamWriter(output));
}
@TestMethod("testAccepts")
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (Class anInterface : interfaces) {
if (ICrystal.class.equals(anInterface)) return true;
if (IChemSequence.class.equals(anInterface)) return true;
}
return false;
}
/**
* Serializes the IChemObject to CrystClust format and redirects it to the output Writer.
*
* @param object A Molecule of MoleculeSet object
*/
public void write(IChemObject object) throws UnsupportedChemObjectException {
if (object instanceof ICrystal) {
writeCrystal((ICrystal)object);
} else if (object instanceof IChemSequence) {
writeChemSequence((IChemSequence)object);
} else {
throw new UnsupportedChemObjectException("This object type is not supported.");
}
}
/**
* Flushes the output and closes this object
*/
@TestMethod("testClose")
public void close() throws IOException {
writer.close();
}
// Private procedures
private void writeChemSequence(IChemSequence cs) throws UnsupportedChemObjectException {
int count = cs.getChemModelCount();
for (int i=0; i < count; i++) {
writeln("frame: " + (i+1));
writeCrystal(cs.getChemModel(i).getCrystal());
}
}
/**
* Writes a single frame to the Writer.
*
* <p>Format:
* <pre>
* line data
* ------- --------------------------
* 1 spacegroup
* 2,3,4 cell parameter: a
* 5,6,7 b
* 8,9,10 c
* 11 number of atoms
* 12 number of asym. units
* 13-16 atomtype: charge, atomcoord x, y, z
* 17-20 idem second atom
* 21-24 idem third atom etc
* </pre>
*
* @param crystal the Crystal to serialize
*/
private void writeCrystal(ICrystal crystal) {
String sg = crystal.getSpaceGroup();
if ("P 2_1 2_1 2_1".equals(sg)) {
writeln("P 21 21 21 (1)");
} else {
writeln("P 1 (1)");
}
// output unit cell axes
writeVector3d(crystal.getA());
writeVector3d(crystal.getB());
writeVector3d(crystal.getC());
// output number of atoms
int noatoms = crystal.getAtomCount();
write(Integer.toString(noatoms));
writeln("");
// output number of asym. units (Z)
if (sg.equals("P1")) {
writeln("1");
} else {
// duno
writeln("1");
}
// output atoms
for (int i = 0; i < noatoms; i++) {
// output atom sumbol
IAtom atom = crystal.getAtom(i);
write(atom.getSymbol());
write(":");
// output atom charge
writeln(Double.toString(atom.getCharge()));
// output coordinates
writeln(Double.toString(atom.getPoint3d().x));
writeln(Double.toString(atom.getPoint3d().y));
writeln(Double.toString(atom.getPoint3d().z));
}
}
private void write(String s) {
try {
writer.write(s);
} catch (IOException e) {
System.err.println("CMLWriter IOException while printing \"" +
s + "\":" + e.toString());
}
}
private void writeln(String s) {
try {
writer.write(s);
writer.newLine();
} catch (IOException e) {
System.err.println("CMLWriter IOException while printing \"" +
s + "\":" + e.toString());
}
}
private void writeVector3d(Vector3d vector) {
write(Double.toString(vector.x));
writeln("");
write(Double.toString(vector.y));
writeln("");
write(Double.toString(vector.z));
writeln("");
}
}