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| /* Copyright (C) 2005-2006 Ideaconsult Ltd. | ||
| * 2012 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. | ||
| * 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.annotations.TestClass; | ||
| import org.openscience.cdk.annotations.TestMethod; | ||
| 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.<p> | ||
| * | ||
| * Parameters: "NO. OF FILLED LEVELS", "TOTAL ENERGY","FINAL HEAT OF FORMATION", | ||
| * "IONIZATION POTENTIAL", "ELECTRONIC ENERGY","CORE-CORE REPULSION","MOLECULAR WEIGHT".<p> | ||
| * Doesn't update structure coordinates ! (TODO fix) | ||
| * | ||
| * @author Nina Jeliazkova <nina@acad.bg> | ||
| * @cdk.githash | ||
| * @cdk.module io | ||
| */ | ||
| @TestClass("org.openscience.cdk.io.Mopac7ReaderTest") | ||
| 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 in 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} */ | ||
| @TestMethod("testRead_IChemObject") | ||
| public <T extends IChemObject> 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} */ | ||
| @TestMethod("testSetReader_Reader") | ||
| public void setReader(Reader input) throws CDKException { | ||
| if (input instanceof BufferedReader) { | ||
| this.input = (BufferedReader)input; | ||
| } else { | ||
| this.input = new BufferedReader(input); | ||
| } | ||
| } | ||
|
|
||
| @Override /** {@inheritDoc} */ | ||
| @TestMethod("testSetReader_InputStream") | ||
| public void setReader(InputStream input) throws CDKException { | ||
| this.input = new BufferedReader(new InputStreamReader(input)); | ||
| } | ||
|
|
||
| @Override /** {@inheritDoc} */ | ||
| @TestMethod("testClose") | ||
| public void close() throws IOException { | ||
| input.close(); | ||
|
|
||
| } | ||
|
|
||
| @Override /** {@inheritDoc} */ | ||
| @TestMethod("testAccepts") | ||
| public boolean accepts(Class classObject) { | ||
| Class[] interfaces = classObject.getInterfaces(); | ||
| for (int i=0; i<interfaces.length; i++) { | ||
| if (IAtomContainer.class.equals(interfaces[i])) return true; | ||
| } | ||
| Class superClass = classObject.getSuperclass(); | ||
| if (superClass != null) return this.accepts(superClass); | ||
| return false; | ||
| } | ||
|
|
||
| @Override /** {@inheritDoc} */ | ||
| @TestMethod("testGetFormat") | ||
| public IResourceFormat getFormat() { | ||
| return MOPAC7Format.getInstance(); | ||
| } | ||
| } |
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