/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2000-2003 The Jmol Development Team
* Copyright (C) 2003-2007 The CDK Project
*
* Contact: cdk-devel@lists.sf.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.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 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.IAtomContainer;
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.interfaces.IMolecule;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PDBFormat;
import org.openscience.cdk.tools.FormatStringBuffer;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
/**
* Saves small molecules in a rudimentary PDB format. It does not allow
* writing of PDBProtein data structures.
*
* @cdk.module io
* @cdk.githash
*/
@TestClass("org.openscience.cdk.io.PDBWriterTest")
public class PDBWriter extends DefaultChemObjectWriter {
final String SERIAL_FORMAT = "%5d";
final String ATOM_NAME_FORMAT = "%-4s";
final String POSITION_FORMAT = "%8.3f";
private BufferedWriter writer;
public PDBWriter() {
this(new StringWriter());
}
/**
* Creates a PDB writer.
*
* @param out the stream to write the PDB file to.
*/
public PDBWriter(Writer out) {
try {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter)out;
} else {
writer = new BufferedWriter(out);
}
} catch (Exception exc) {
}
}
public PDBWriter(OutputStream output) {
this(new OutputStreamWriter(output));
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return PDBFormat.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 (int i=0; i<interfaces.length; i++) {
if (ICrystal.class.equals(interfaces[i])) return true;
if (IMolecule.class.equals(interfaces[i])) return true;
if (IChemFile.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
public void write(IChemObject object) throws CDKException {
if (object instanceof IMolecule){
writeMolecule((IMolecule)object);
} else if (object instanceof ICrystal){
writeCrystal((ICrystal)object);
} else if (object instanceof IChemFile){
IChemFile chemFile = (IChemFile)object;
IChemSequence sequence = chemFile.getChemSequence(0);
if (sequence != null) {
IChemModel model = sequence.getChemModel(0);
if (model != null) {
ICrystal crystal = model.getCrystal();
if (crystal != null) {
write(crystal);
} else {
Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
while (containers.hasNext()) {
writeMolecule(model.getBuilder().newMolecule(
(IAtomContainer)containers.next()
));
}
}
}
}
} else {
throw new CDKException("Only supported is writing of Molecule, Crystal and ChemFile objects.");
}
}
/**
* Writes a single frame in PDB format to the Writer.
*
* @param molecule the Molecule to write
*/
public void writeMolecule(IMolecule molecule) throws CDKException {
try {
int atomNumber = 1;
String hetatmRecordName = "HETATM";
String terRecordName = "TER";
// Loop through the atoms and write them out:
StringBuffer buffer = new StringBuffer();
java.util.Iterator atoms = molecule.atoms().iterator();
FormatStringBuffer fsb = new FormatStringBuffer("");
while (atoms.hasNext()) {
buffer.setLength(0);
buffer.append(hetatmRecordName);
fsb.reset(SERIAL_FORMAT).format(atomNumber);
buffer.append(fsb.toString());
buffer.append(' ');
IAtom atom = (IAtom)atoms.next();
fsb.reset(ATOM_NAME_FORMAT).format(atom.getSymbol());
buffer.append(fsb.toString());
buffer.append(" MOL ");
Point3d position = atom.getPoint3d();
fsb.reset(POSITION_FORMAT).format(position.x);
buffer.append(fsb.toString());
fsb.reset(POSITION_FORMAT).format(position.y);
buffer.append(fsb.toString());
fsb.reset(POSITION_FORMAT).format(position.z);
buffer.append(fsb.toString());
writer.write(buffer.toString(), 0, buffer.length());
writer.newLine();
++atomNumber;
}
writer.write(terRecordName, 0, terRecordName.length());
writer.newLine();
} catch (IOException exception) {
throw new CDKException("Error while writing file: " + exception.getMessage(), exception);
}
}
public void writeCrystal(ICrystal crystal) throws CDKException {
try {
writer.write("HEADER created with the CDK (http://cdk.sf.net/)");
writer.newLine();
Vector3d a = crystal.getA();
Vector3d b = crystal.getB();
Vector3d c = crystal.getC();
double[] ucParams = CrystalGeometryTools.cartesianToNotional(a,b,c);
final String LENGTH_FORMAT = "%4.3f";
final String ANGLE_FORMAT = "%3.3f";
FormatStringBuffer fsb = new FormatStringBuffer("");
fsb.reset(LENGTH_FORMAT).format(ucParams[0]);
writer.write("CRYST1 " + fsb.toString());
fsb.reset(LENGTH_FORMAT).format(ucParams[1]);
writer.write(fsb.toString());
fsb.reset(LENGTH_FORMAT).format(ucParams[2]);
writer.write(fsb.toString());
fsb.reset(ANGLE_FORMAT).format(ucParams[3]);
writer.write(fsb.toString());
fsb.reset(ANGLE_FORMAT).format(ucParams[4]);
writer.write(fsb.toString());
fsb.reset(ANGLE_FORMAT).format(ucParams[4]);
writer.write(fsb.toString());
writer.newLine();
// before saving the atoms, we need to create cartesian coordinates
java.util.Iterator atoms = crystal.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = (IAtom)atoms.next();
// logger.debug("PDBWriter: atom -> " + atom);
// if it got 3D coordinates, use that. If not, try fractional coordinates
if (atom.getPoint3d() == null && atom.getFractionalPoint3d() != null) {
Point3d frac = new Point3d(atom.getFractionalPoint3d());
Point3d cart = CrystalGeometryTools.fractionalToCartesian(a,b,c, frac);
atom.setPoint3d(cart);
}
}
writeMolecule(crystal.getBuilder().newMolecule(crystal));
} catch (IOException exception) {
throw new CDKException("Error while writing file: " + exception.getMessage(), exception);
}
}
/**
* Flushes the output and closes this object.
*/
@TestMethod("testClose")
public void close() throws IOException {
writer.close();
}
}