/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2001-2007 Egon Willighagen <egonw@users.sf.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.
* 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.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.util.Iterator;
import java.util.List;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.openscience.cdk.CDKConstants;
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.IChemObject;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.ShelXFormat;
import org.openscience.cdk.tools.FormatStringBuffer;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
/**
* <p>Serializes a MoleculeSet or a Molecule object to ShelX code.
* The output can be read with Platon.
*
* @cdk.module extra
* @cdk.githash
*
* @author Egon Willighagen
*
* @cdk.keyword file format, ShelX
*/
@TestClass("org.openscience.cdk.io.ShelXWriterTest")
public class ShelXWriter extends DefaultChemObjectWriter {
private BufferedWriter writer;
/**
* Constructs a new ShelXWriter class. Output will be stored in the Writer
* class given as parameter.
*
* @param out Writer to redirect the output to.
*/
public ShelXWriter(Writer out) {
try {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter)out;
} else {
writer = new BufferedWriter(out);
}
} catch (Exception exc) {
}
}
public ShelXWriter(OutputStream output) {
this(new OutputStreamWriter(output));
}
public ShelXWriter() {
this(new StringWriter());
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return ShelXFormat.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));
}
/**
* Flushes the output and closes this object
*/
@TestMethod("testClose")
public void close() throws IOException {
writer.close();
}
@TestMethod("testAccepts")
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (int i=0; i<interfaces.length; i++) {
if (ICrystal.class.equals(interfaces[i])) return true;
}
return false;
}
/**
* Serializes the IChemObject to ShelX and redirects it to the output Writer.
*
* @param object A Molecule of MoleculeSet object
*/
public void write(IChemObject object) throws CDKException {
if (object instanceof ICrystal) {
writeCrystal((ICrystal)object);
} else {
throw new CDKException("Only Crystal objects can be read.");
}
};
// Private procedures
private void writeCrystal(ICrystal crystal) {
Object title = crystal.getProperty(CDKConstants.TITLE);
if (title != null && title.toString().trim().length() > 0) {
writeln("TITL " + title.toString().trim());
} else {
writeln("TITL Produced with CDK (http://cdk.sf.net/)");
}
Vector3d a = crystal.getA();
Vector3d b = crystal.getB();
Vector3d c = crystal.getC();
double alength = a.length();
double blength = b.length();
double clength = c.length();
double alpha = Math.toDegrees(b.angle(c));
double beta = Math.toDegrees(a.angle(c));
double gamma = Math.toDegrees(a.angle(b));
FormatStringBuffer format = new FormatStringBuffer("%7.5lf");
write("CELL " + format.reset("%7.5f").format(1.54184).toString() + " ");
write(format.reset("%8.5f").format(alength) + " ");
write(format.reset("%8.5f").format(blength) + " ");
write(format.reset("%8.5f").format(clength) + " ");
write(format.reset("%8.4f").format(alpha) + " ");
write(format.reset("%8.4f").format(beta) + " ");
writeln(format.reset("%8.4f").format(gamma) + "");
writeln("ZERR " + format.reset("%1.5f").format((double)crystal.getZ()) +
" 0.01000 0.01000 0.01000 0.0100 0.0100 0.0100");
String spaceGroup = crystal.getSpaceGroup();
if ("P1".equals(spaceGroup)) {
writeln("LATT -1");
} else if ("P 2_1 2_1 2_1".equals(spaceGroup)) {
writeln("LATT -1");
writeln("SYMM 1/2+X , 1/2-Y , -Z");
writeln("SYMM -X , 1/2+Y , 1/2-Z");
writeln("SYMM 1/2-X , -Y , 1/2+Z");
}
// MFAnalyser mfa = new MFAnalyser(crystal);
String elemNames = "";
String elemCounts = "";
IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(crystal);
List<IElement> asortedElements = MolecularFormulaManipulator.elements(formula);
Iterator<IElement> elements = asortedElements.iterator();
while (elements.hasNext()) {
IElement element = elements.next();
String symbol = element.getSymbol();
elemNames += symbol + " ".substring(symbol.length());
String countS = Integer.valueOf(MolecularFormulaManipulator.getElementCount(formula, element)).toString();
elemCounts += countS + " ".substring(countS.length());
}
writeln("SFAC " + elemNames);
writeln("UNIT " + elemCounts);
/* write atoms */
for (int i = 0; i < crystal.getAtomCount(); i++) {
IAtom atom = crystal.getAtom(i);
Point3d cartCoord = atom.getPoint3d();
Point3d fracCoord = CrystalGeometryTools.cartesianToFractional(a, b, c, cartCoord);
String symbol = atom.getSymbol();
String output = symbol + (i+1);
write(output);
for (int j=1; j<5 - output.length(); j++) {
write(" ");
}
write(" ");
String elemID = Integer.valueOf(asortedElements.indexOf(symbol)+1).toString();
write(elemID);
write(" ".substring(elemID.length()));
write(format.reset("%7.5f").format(fracCoord.x) + " ");
write(format.reset("%7.5f").format(fracCoord.y) + " ");
writeln(format.reset("%7.5f").format(fracCoord.z) + " 11.00000 0.05000");
}
writeln("END");
}
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());
}
}
}