org.openscience.cdk.io.Mol2Writer Maven / Gradle / Ivy
/* Copyright (C) 2005-2007 Egon Willighagen
*
* Contact: [email protected]
*
* 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 org.openscience.cdk.CDKConstants;
import org.openscience.cdk.atomtype.SybylAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.Mol2Format;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* An output Writer that writes molecular data into the
* Tripos Mol2 format.
* Writes the atoms and the bonds only at this moment.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @author Egon Willighagen
*/
public class Mol2Writer extends DefaultChemObjectWriter {
private BufferedWriter writer;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(Mol2Writer.class);
private SybylAtomTypeMatcher matcher;
public Mol2Writer() {
this(new StringWriter());
}
/**
* Constructs a new Mol2 writer.
* @param out the stream to write the Mol2 file to.
*/
public Mol2Writer(Writer out) {
try {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
} catch (Exception exc) {
}
}
public Mol2Writer(OutputStream output) {
this(new OutputStreamWriter(output));
}
@Override
public IResourceFormat getFormat() {
return Mol2Format.getInstance();
}
@Override
public void setWriter(Writer out) throws CDKException {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
}
@Override
public void setWriter(OutputStream output) throws CDKException {
setWriter(new OutputStreamWriter(output));
}
/**
* Flushes the output and closes this object.
*/
@Override
public void close() throws IOException {
writer.close();
}
@Override
public boolean accepts(Class classObject) {
if (IAtomContainer.class.equals(classObject)) return true;
Class[] interfaces = classObject.getInterfaces();
for (Class anInterface : interfaces) {
if (IAtomContainer.class.equals(anInterface)) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
@Override
public void write(IChemObject object) throws CDKException {
if (object instanceof IAtomContainer) {
try {
writeMolecule((IAtomContainer) object);
} catch (Exception ex) {
throw new CDKException("Error while writing Mol2 file: " + ex.getMessage(), ex);
}
} else {
throw new CDKException("Mol2Writer only supports output of Molecule classes.");
}
}
/**
* Writes a single frame in XYZ format to the Writer.
*
* @param mol the Molecule to write
* @throws java.io.IOException if there is an error during writing
*/
public void writeMolecule(IAtomContainer mol) throws IOException {
matcher = SybylAtomTypeMatcher.getInstance(mol.getBuilder());
try {
logger.debug("Writing header...");
if (mol.getProperty(CDKConstants.TITLE) != null) {
writer.write("# Name: " + mol.getProperty(CDKConstants.TITLE));
writer.newLine();
}
// FIXME: add other types of meta data
writer.newLine();
/*
* @MOLECULE benzene 12 12 1 0 0 SMALL NO_CHARGES
*/
logger.debug("Writing molecule block...");
writer.write("@MOLECULE");
writer.newLine();
if (mol.getID() == null) {
writer.write("CDKMolecule");
} else {
writer.write(mol.getID());
}
writer.newLine();
writer.write(mol.getAtomCount() + " " + mol.getBondCount()); // that's the minimum amount of info required the format
writer.newLine();
writer.write("SMALL"); // no biopolymer
writer.newLine();
writer.write("NO CHARGES"); // other options include Gasteiger charges
writer.newLine();
/*
* @ATOM 1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000 2 C2
* 2.414 1.394 0.000 C.ar 1 BENZENE 0.000 3 C3 2.414 0.000 0.000
* C.ar 1 BENZENE 0.000 4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000
* 5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000 6 C6 0.000 1.394
* 0.000 C.ar 1 BENZENE 0.000 7 H1 1.207 3.175 0.000 H 1 BENZENE
* 0.000 8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000 9 H3 3.353 -0.542
* 0.000 H 1 BENZENE 0.000 10 H4 1.207 -1.781 0.000 H 1 BENZENE
* 0.000 11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000 12 H6 -0.939
* 1.936 0.000 H 1 BENZENE 0.000
*/
// write atom block
logger.debug("Writing atom block...");
writer.write("@ATOM");
writer.newLine();
for (int i = 0; i < mol.getAtomCount(); i++) {
IAtom atom = mol.getAtom(i);
writer.write((i + 1) + " " + atom.getSymbol() + (mol.getAtomNumber(atom) + 1) + " ");
if (atom.getPoint3d() != null) {
writer.write(atom.getPoint3d().x + " ");
writer.write(atom.getPoint3d().y + " ");
writer.write(atom.getPoint3d().z + " ");
} else if (atom.getPoint2d() != null) {
writer.write(atom.getPoint2d().x + " ");
writer.write(atom.getPoint2d().y + " ");
writer.write(" 0.000 ");
} else {
writer.write("0.000 0.000 0.000 ");
}
IAtomType sybylType = null;
try {
sybylType = matcher.findMatchingAtomType(mol, atom);
} catch (CDKException e) {
e.printStackTrace();
}
if (sybylType != null) {
writer.write(sybylType.getAtomTypeName());
} else {
writer.write(atom.getSymbol());
}
writer.newLine();
}
/*
* @BOND 1 1 2 ar 2 1 6 ar 3 2 3 ar 4 3 4 ar 5 4 5 ar 6 5 6
* ar 7 1 7 1 8 2 8 1 9 3 9 1 10 4 10 1 11 5 11 1 12 6 12 1
*/
// write bond block
logger.debug("Writing bond block...");
writer.write("@BOND");
writer.newLine();
int counter = 0;
for (IBond bond : mol.bonds()) {
String sybylBondOrder = "-1";
if (bond.getOrder().equals(IBond.Order.SINGLE))
sybylBondOrder = "1";
else if (bond.getOrder().equals(IBond.Order.DOUBLE))
sybylBondOrder = "2";
else if (bond.getOrder().equals(IBond.Order.TRIPLE)) sybylBondOrder = "3";
if (bond.getFlag(CDKConstants.ISAROMATIC)) sybylBondOrder = "ar";
// we need to check the atom types to see if we have an amide bond
// and we're assuming a 2-centered bond
final IAtom bondAtom1 = bond.getAtom(0);
final IAtom bondAtom2 = bond.getAtom(1);
try {
final IAtomType bondAtom1Type = matcher.findMatchingAtomType(mol, bondAtom1);
final IAtomType bondAtom2Type = matcher.findMatchingAtomType(mol, bondAtom2);
if (bondAtom1Type != null && bondAtom2Type != null &&
((bondAtom1Type.getAtomTypeName().equals("N.am") && bondAtom2Type.getAtomTypeName().equals("C.2"))
|| (bondAtom2Type.getAtomTypeName().equals("N.am") && bondAtom1Type.getAtomTypeName().equals("C.2")))) {
sybylBondOrder = "am";
}
} catch (CDKException e) {
e.printStackTrace();
}
writer.write((counter + 1) + " " + (mol.getAtomNumber(bond.getAtom(0)) + 1) + " "
+ (mol.getAtomNumber(bond.getAtom(1)) + 1) + " " + sybylBondOrder);
writer.newLine();
counter++;
}
} catch (IOException e) {
throw e;
}
}
}
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