org.openscience.cdk.io.Mopac7Reader Maven / Gradle / Ivy
/* Copyright (C) 2005-2006 Ideaconsult Ltd.
* 2012 Egon Willighagen
*
* Contact: [email protected]
*
* 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 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 java.io.StringReader;
import java.util.StringTokenizer;
import javax.vecmath.Point3d;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MOPAC7Format;
/**
* Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule
* properties.
*
* Parameters: "NO. OF FILLED LEVELS", "TOTAL ENERGY","FINAL HEAT OF FORMATION",
* "IONIZATION POTENTIAL", "ELECTRONIC ENERGY","CORE-CORE REPULSION","MOLECULAR WEIGHT".
* Doesn't update structure coordinates ! (TODO fix)
*
* @author Nina Jeliazkova
* @cdk.githash
* @cdk.module io
*/
public class Mopac7Reader extends DefaultChemObjectReader {
BufferedReader input = null;
private static String[] parameters = {"NO. OF FILLED LEVELS", "TOTAL ENERGY", "FINAL HEAT OF FORMATION",
"IONIZATION POTENTIAL", "ELECTRONIC ENERGY", "CORE-CORE REPULSION", "MOLECULAR WEIGHT", "EHOMO", "ELUMO"};
private static String[] units = {"", "EV", "KJ", "", "EV", "EV", "", "EV", "EV"};
private static String eigenvalues = "EIGENVALUES";
private static String filledLevels = "NO. OF FILLED LEVELS";
/**
* Constructs a new Mopac7reader that can read a molecule from a given {@link Reader}.
*
* @param input The {@link Reader} to read from
*/
public Mopac7Reader(Reader input) {
if (input instanceof BufferedReader) {
this.input = (BufferedReader) input;
} else {
this.input = new BufferedReader(input);
}
}
/**
* Constructs a new Mopac7reader that can read a molecule from a given {@link InputStream}.
*
* @param input The {@link InputStream} to read from
*/
public Mopac7Reader(InputStream input) {
this(new InputStreamReader(input));
}
/**
* Constructs a new Mopac7reader that can read a molecule. The reader to read from has
* yet to be set.
*/
public Mopac7Reader() {
this(new StringReader(""));
}
/*
* FINAL HEAT OF FORMATION = -32.90826 KCAL = -137.68818 KJ TOTAL ENERGY =
* -1618.31024 EV ELECTRONIC ENERGY = -6569.42640 EV POINT GROUP: C1
* CORE-CORE REPULSION = 4951.11615 EV IONIZATION POTENTIAL = 10.76839 NO.
* OF FILLED LEVELS = 23 MOLECULAR WEIGHT = 122.123
*/
@Override
/** {@inheritDoc} */
public T read(T object) throws CDKException {
final String[] expected_columns = {"NO.", "ATOM", "X", "Y", "Z"};
StringBuffer eigenvalues = new StringBuffer();
if (object instanceof IAtomContainer) {
IAtomContainer container = (IAtomContainer) object;
try {
String line = input.readLine();
while (line != null) {
if (line.indexOf("**** MAX. NUMBER OF ATOMS ALLOWED") > -1) throw new CDKException(line);
if (line.indexOf("TO CONTINUE CALCULATION SPECIFY \"GEO-OK\"") > -1) throw new CDKException(line);
if ("CARTESIAN COORDINATES".equals(line.trim())) {
IAtomContainer atomcontainer = ((IAtomContainer) object);
input.readLine(); //reads blank line
line = input.readLine();
String[] columns = line.trim().split(" +");
int okCols = 0;
if (columns.length == expected_columns.length)
for (int i = 0; i < expected_columns.length; i++)
okCols += (columns[i].equals(expected_columns[i])) ? 1 : 0;
if (okCols < expected_columns.length) continue;
//if (!" NO. ATOM X Y Z".equals(line)) continue;
input.readLine(); //reads blank line
int atomIndex = 0;
while (!line.trim().isEmpty()) {
line = input.readLine();
StringTokenizer tokenizer = new StringTokenizer(line);
int token = 0;
IAtom atom = null;
double[] point3d = new double[3];
while (tokenizer.hasMoreTokens()) {
String tokenStr = tokenizer.nextToken();
switch (token) {
case 0: {
atomIndex = Integer.parseInt(tokenStr) - 1;
if (atomIndex < atomcontainer.getAtomCount()) {
atom = atomcontainer.getAtom(atomIndex);
} else
atom = null;
break;
}
case 1: {
if ((atom != null) && (!tokenStr.equals(atom.getSymbol()))) atom = null;
break;
}
case 2: {
point3d[0] = Double.parseDouble(tokenStr);
break;
}
case 3: {
point3d[1] = Double.parseDouble(tokenStr);
break;
}
case 4: {
point3d[2] = Double.parseDouble(tokenStr);
if (atom != null) atom.setPoint3d(new Point3d(point3d));
break;
}
}
token++;
if (atom == null) break;
}
if ((atom == null) || ((atomIndex + 1) >= atomcontainer.getAtomCount())) break;
}
} else if (line.indexOf(Mopac7Reader.eigenvalues) >= 0) {
line = input.readLine();
line = input.readLine();
while (!line.trim().equals("")) {
eigenvalues.append(line);
line = input.readLine();
}
container.setProperty(Mopac7Reader.eigenvalues, eigenvalues.toString());
} else
for (int i = 0; i < parameters.length; i++)
if (line.indexOf(parameters[i]) >= 0) {
String value = line.substring(line.lastIndexOf('=') + 1).trim();
/*
* v = v.replaceAll("EV",""); v =
* v.replaceAll("KCAL",""); v =
* v.replaceAll("KJ","");
*/
value = value.replaceAll(Mopac7Reader.units[i], "").trim();
int pos = value.indexOf(' ');
if (pos >= 0) value = value.substring(0, pos - 1);
container.setProperty(parameters[i], value.trim());
break;
}
line = input.readLine();
}
calcHomoLumo(container);
return (T) container;
} catch (IOException exception) {
throw new CDKException(exception.getMessage());
}
} else
return null;
}
private void calcHomoLumo(IAtomContainer mol) {
Object eigenProp = mol.getProperty(eigenvalues);
if (eigenProp == null) return;
//mol.getProperties().remove(eigenvalues);
Object filledLevelsProp = mol.getProperty(filledLevels);
//mol.getProperties().remove(filledLevels);
if (filledLevelsProp == null) return;
int nFilledLevels = 0;
try {
nFilledLevels = Integer.parseInt(filledLevelsProp.toString());
} catch (NumberFormatException exception) {
return;
}
String[] eigenVals = eigenProp.toString().split("\\s");
int levelCounter = 0;
for (int i = 0; i < eigenVals.length; i++) {
if (eigenVals[i].trim().isEmpty())
continue;
else
try {
// check if the value is an proper double:
Double.parseDouble(eigenVals[i]);
levelCounter++;
if (levelCounter == nFilledLevels) {
mol.setProperty("EHOMO", eigenVals[i]);
} else if (levelCounter == (nFilledLevels + 1)) {
mol.setProperty("ELUMO", eigenVals[i]);
}
} catch (NumberFormatException exception) {
return;
}
}
}
@Override
/** {@inheritDoc} */
public void setReader(Reader input) throws CDKException {
if (input instanceof BufferedReader) {
this.input = (BufferedReader) input;
} else {
this.input = new BufferedReader(input);
}
}
@Override
/** {@inheritDoc} */
public void setReader(InputStream input) throws CDKException {
this.input = new BufferedReader(new InputStreamReader(input));
}
@Override
/** {@inheritDoc} */
public void close() throws IOException {
input.close();
}
@Override
/** {@inheritDoc} */
public boolean accepts(Class extends IChemObject> classObject) {
Class>[] interfaces = classObject.getInterfaces();
for (int i = 0; i < interfaces.length; i++) {
if (IAtomContainer.class.equals(interfaces[i])) return true;
}
if (IAtomContainer.class.equals(classObject)) return true;
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
@Override
/** {@inheritDoc} */
public IResourceFormat getFormat() {
return MOPAC7Format.getInstance();
}
}