[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io MDLReader.java,1.25,1.26

[Stefan K. <sh...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io
In directory sc8-pr-cvs1:/tmp/cvs-serv1212

Modified Files:
	MDLReader.java 
Log Message:
I corrected the reading of isotopes. This till now set the mass of the standard isotop + mass of actual isotope as atomic number. Now the mass of an isotope is set to the mass given in the mdl file. Plus I added that every atom is configured with isotope factory.


Index: MDLReader.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLReader.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- MDLReader.java	15 Apr 2003 09:35:18 -0000	1.25
+++ MDLReader.java	30 Apr 2003 15:16:36 -0000	1.26
@@ -224,7 +224,7 @@
 				logger.debug("Coordinates: " + x + "; " + y + "; " + z);
                 String element = strTok.nextToken();
                 logger.debug("Atom type: " + element);
-				atom = new Atom(element, new Point3d(x, y, z));
+				atom = isotopeFactory.configure(new Atom(element, new Point3d(x, y, z)));
 				atom.setPoint2D(new Point2d(x, y));
 
                 // parse further fields
@@ -351,8 +351,7 @@
                             int massDiff = Integer.parseInt(st.nextToken().trim());
                             if (massDiff != 0) { 
                                 Atom isotope = molecule.getAtomAt(atomNumber - 1);
-                                Isotope major = isotopeFactory.getMajorIsotope(isotope.getSymbol());
-                                isotope.setAtomicNumber(major.getAtomicMass() + massDiff);
+                                isotope.setAtomicMass(massDiff);
                             }
                         }
                     } catch (NumberFormatException exception) {