[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io Gaussian98Reader.java,1.6,1.7 Gaussian03Reader.java,1.3,1.4

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io
In directory sc8-pr-cvs1:/tmp/cvs-serv20256/src/org/openscience/cdk/io

Modified Files:
	Gaussian98Reader.java Gaussian03Reader.java 
Log Message:
Added reading of partial atomic charges

Index: Gaussian98Reader.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/Gaussian98Reader.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- Gaussian98Reader.java	10 Sep 2003 12:42:54 -0000	1.6
+++ Gaussian98Reader.java	22 Sep 2003 13:18:31 -0000	1.7
@@ -176,6 +176,8 @@
                     
                     // Found a set of vibrations
                     // readFrequencies(frame);
+                } else if (line.indexOf("Total atomic charges") >= 0) {
+                    readPartialCharges(model);
                 } else if (line.indexOf("Magnetic shielding") >= 0) {
                     
                     // Found NMR data
@@ -185,6 +187,8 @@
                     
                     // Found calculation level of theory
                     levelOfTheory = parseLevelOfTheory(line);
+                } else {
+                    logger.debug("Skipping line: " + line);
                 }
                 line = input.readLine();
             }
@@ -262,6 +266,42 @@
         }
         moleculeSet.addMolecule(molecule);
         model.setSetOfMolecules(moleculeSet);
+    }
+
+    /**
+     * Reads partial atomic charges and add the to the given ChemModel.
+     */
+    private void readPartialCharges(ChemModel model) throws CDKException, IOException {
+        logger.info("Reading partial atomic charges");
+        SetOfMolecules moleculeSet = model.getSetOfMolecules();
+        Molecule molecule = moleculeSet.getMolecule(0);
+        String line = input.readLine(); // skip first line after "Total atomic charges"
+        while (input.ready()) {
+            line = input.readLine();
+            logger.debug("Read charge block line: " + line);
+            if ((line == null) || (line.indexOf("Sum of Mulliken charges") >= 0)) {
+                logger.debug("End of charge block found");
+                break;
+            }
+            StringReader sr = new StringReader(line);
+            StreamTokenizer tokenizer = new StreamTokenizer(sr);
+            if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
+                int atomCounter = (int) tokenizer.nval;
+
+                tokenizer.nextToken(); // ignore the symbol
+                
+                double charge = 0.0;
+                if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
+                    charge = (double)tokenizer.nval;
+                    logger.debug("Found charge for atom " + atomCounter + 
+                                 ": " + charge);
+                } else {
+                    throw new CDKException("Error while reading charge: expected double.");
+                }
+                Atom atom = molecule.getAtomAt(atomCounter-1);
+                atom.setCharge(charge);
+            }
+        }
     }
 
     /**

Index: Gaussian03Reader.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/Gaussian03Reader.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- Gaussian03Reader.java	3 Sep 2003 07:58:31 -0000	1.3
+++ Gaussian03Reader.java	22 Sep 2003 13:18:31 -0000	1.4
@@ -27,6 +27,7 @@
 
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.ChemFile;
 import org.openscience.cdk.ChemModel;
 import org.openscience.cdk.ChemObject;
 import org.openscience.cdk.ChemSequence;
@@ -34,6 +35,7 @@
 import org.openscience.cdk.SetOfMolecules;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.tools.IsotopeFactory;
+import org.openscience.cdk.tools.LoggingTool;
 import java.io.Reader;
 import java.io.BufferedReader;
 import java.io.StringReader;
@@ -69,9 +71,11 @@
 
     private IsotopeFactory isotopeFactory;
     private BufferedReader input;
+    private LoggingTool logger;
     
     public Gaussian03Reader(Reader reader) {
         input = new BufferedReader(reader);
+        logger = new LoggingTool(this.getClass().getName());
         try {
             isotopeFactory = IsotopeFactory.getInstance();
         } catch (Exception exception) {
@@ -82,6 +86,8 @@
     public boolean accepts(ChemObject object) {
         if (object instanceof ChemSequence) {
             return true;
+        } else if (object instanceof ChemFile) {
+            return true;
         } else {
             return false;
         }
@@ -90,6 +96,8 @@
     public ChemObject read(ChemObject object) throws CDKException {
         if (object instanceof ChemSequence) {
             return readChemSequence();
+        } else if (object instanceof ChemFile) {
+            return readChemFile();
         } else {
             throw new CDKException("Object " + object.getClass().getName() + " is not supported");
         }
@@ -99,6 +107,13 @@
         input.close();
     }
     
+    private ChemFile readChemFile() throws CDKException {
+        ChemFile chemFile = new ChemFile();
+        ChemSequence sequence = readChemSequence();
+        chemFile.addChemSequence(sequence);
+        return chemFile;
+    }
+    
     private ChemSequence readChemSequence() throws CDKException {
         ChemSequence sequence = new ChemSequence();
         ChemModel model = null;
@@ -143,6 +158,8 @@
                         } catch (IOException exception) {
                             throw new CDKException("Error while reading frequencies: " + exception.toString());
                         }
+                    } else if (line.indexOf("Mulliken atomic charges") >= 0) {
+                        readPartialCharges(model);
                     } else if (line.indexOf("Magnetic shielding") >= 0) {
                         // Found NMR data
                         try {
@@ -232,6 +249,42 @@
         SetOfMolecules moleculeSet = new SetOfMolecules();
         moleculeSet.addMolecule(new Molecule(container));
         model.setSetOfMolecules(moleculeSet);
+    }
+
+    /**
+     * Reads partial atomic charges and add the to the given ChemModel.
+     */
+    private void readPartialCharges(ChemModel model) throws CDKException, IOException {
+        logger.info("Reading partial atomic charges");
+        SetOfMolecules moleculeSet = model.getSetOfMolecules();
+        Molecule molecule = moleculeSet.getMolecule(0);
+        String line = input.readLine(); // skip first line after "Total atomic charges"
+        while (input.ready()) {
+            line = input.readLine();
+            logger.debug("Read charge block line: " + line);
+            if ((line == null) || (line.indexOf("Sum of Mulliken charges") >= 0)) {
+                logger.debug("End of charge block found");
+                break;
+            }
+            StringReader sr = new StringReader(line);
+            StreamTokenizer tokenizer = new StreamTokenizer(sr);
+            if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
+                int atomCounter = (int) tokenizer.nval;
+
+                tokenizer.nextToken(); // ignore the symbol
+                
+                double charge = 0.0;
+                if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
+                    charge = (double)tokenizer.nval;
+                    logger.debug("Found charge for atom " + atomCounter + 
+                                 ": " + charge);
+                } else {
+                    throw new CDKException("Error while reading charge: expected double.");
+                }
+                Atom atom = molecule.getAtomAt(atomCounter-1);
+                atom.setCharge(charge);
+            }
+        }
     }
 
     /**