[Cdk-commits] CVS: cdk/src/org/openscience/cdk/tools SaturationChecker.java,1.66,1.67

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

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2607/src/org/openscience/cdk/tools

Modified Files:
	SaturationChecker.java 
Log Message:
now ignores unknown atom types (ValencyChecker already behaved like this, so this is unified now)


Index: SaturationChecker.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/SaturationChecker.java,v
retrieving revision 1.66
retrieving revision 1.67
diff -u -r1.66 -r1.67
--- SaturationChecker.java	13 Jan 2005 09:39:57 -0000	1.66
+++ SaturationChecker.java	24 Mar 2005 12:25:14 -0000	1.67
@@ -77,7 +77,7 @@
 		double maxBondOrder = ac.getMaximumBondOrder(atom);
 		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
     if(atomTypes.length==0)
-      throw new CDKException("Missing entry in structgen_atomtypes.xml for "+atom.getSymbol());
+      return true;
 		logger.debug("*** Checking for perfect configuration ***");
 		try
 		{
@@ -159,7 +159,7 @@
 	public boolean isSaturated(Atom atom, AtomContainer ac) throws CDKException {
 		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
         if(atomTypes.length==0)
-            throw new CDKException("Missing entry in structgen_atomtypes.xml for "+ atom.getSymbol());
+          return true;
         double bondOrderSum = ac.getBondOrderSum(atom);
         double maxBondOrder = ac.getMaximumBondOrder(atom);
         int hcount = atom.getHydrogenCount();
@@ -194,7 +194,7 @@
 	{
 		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
     if(atomTypes.length==0)
-      throw new CDKException("Missing entry in structgen_atomtypes.xml for "+atom.getSymbol());
+      return false;
 		double bondOrderSum = ac.getBondOrderSum(atom);
 		double maxBondOrder = ac.getMaximumBondOrder(atom);
 		int hcount = atom.getHydrogenCount();
@@ -231,7 +231,7 @@
 	{
 		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
     if(atomTypes.length==0)
-      throw new CDKException("Missing entry in structgen_atomtypes.xml for "+ atom.getSymbol());
+      return 0;
 		double bondOrderSum = ac.getBondOrderSum(atom);
 		int hcount = atom.getHydrogenCount();
 		double max = 0;
@@ -443,7 +443,7 @@
                 logger.debug("Atom has " + partners.length + " partners");
                 atomTypes2 = structgenATF.getAtomTypes(partner.getSymbol());
                 if(atomTypes2.length==0)
-                  throw new CDKException("Missing entry in structgen_atomtypes.xml for "+ partner.getSymbol());
+                  return;
                 if (atomContainer.getBond(partner,atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].getBondOrderSum() - partner.getHydrogenCount())
                 {
                   logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].getBondOrderSum());
@@ -465,7 +465,7 @@
                 logger.debug("Atom has " + partners.length + " partners");
                 atomTypes2 = structgenATF.getAtomTypes(partner.getSymbol());
                 if(atomTypes2.length==0)
-                  throw new CDKException("Missing entry in structgen_atomtypes.xml for "+partner.getSymbol());
+                  return;
                 if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].getBondOrderSum() - partner.getHydrogenCount())
                 {
                   logger.debug("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].getBondOrderSum());
@@ -612,7 +612,7 @@
             // get default atom
             AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
             if(atomTypes.length==0 && throwExceptionForUnknowAtom)
-              throw new CDKException("Missing entry in structgen_atomtypes.xml for " + atom.getSymbol());
+              return 0;
             logger.debug("Found atomtypes: " + atomTypes.length);
             if (atomTypes.length > 0) {
                 AtomType defaultAtom = atomTypes[0];