[Cdk-commits] CVS: cdk/src/org/openscience/cdk/applications FileConvertor.java,1.30,1.31

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

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/applications
In directory sc8-pr-cvs1:/tmp/cvs-serv8801/src/org/openscience/cdk/applications

Modified Files:
	FileConvertor.java 
Log Message:
Implemented 2d coord generation for SetOfMolecules

Index: FileConvertor.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/applications/FileConvertor.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- FileConvertor.java	4 Jul 2003 15:11:12 -0000	1.30
+++ FileConvertor.java	4 Jul 2003 15:16:12 -0000	1.31
@@ -459,6 +459,22 @@
 
     private void write(SetOfMolecules som, String outputFilename) throws IOException {
         try {
+	        if (apply2DCleanup) {
+				logger.info("Creating 2D coordinates");
+				Molecule[] mols = som.getMolecules();
+	           	StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+				for (int i=0; i<mols.length; i++) {
+					Molecule molecule = mols[i];
+		            try {
+		                sdg.setMolecule(molecule, false); // false -> don't make clone!
+		                sdg.generateCoordinates(new Vector2d(0, 1));
+		                molecule = sdg.getMolecule();
+		            } catch (Exception exc) {
+		                System.out.println("Could not generate coordinates for this molecule.");
+		                System.exit(1);
+		            }
+				}
+			}
             cow.write(som);
         } catch (CDKException e) {
             int count = som.getMoleculeCount();