Merge branch 'master' of github.com:dkoes/rdkit-scripts

rdconf.py

@@ -92,7 +92,7 @@ def getRMS(mol, c1,c2):
             mol.SetProp("_Name",name);
 
             if options.etkdg:
-                cids = Chem.EmbedMultipleConfs(mol, int(options.sample*options.maxconfs), Chem.ETKDG(),randomSeed=options.seed)
+                cids = Chem.EmbedMultipleConfs(mol, int(options.sample*options.maxconfs), Chem.ETKDG())
             else:
                 cids = Chem.EmbedMultipleConfs(mol, int(options.sample*options.maxconfs),randomSeed=options.seed)
             if options.verbose:
@@ -101,8 +101,8 @@ def getRMS(mol, c1,c2):
             for conf in cids:
                 #not passing confID only minimizes the first conformer
                 if options.nomin:
-                    cenergy.append(cid)
-                if options.mmff:
+                    cenergy.append(conf)
+                elif options.mmff:
                     converged =  Chem.MMFFOptimizeMolecule(mol,confId=conf)
                     mp = Chem.MMFFGetMoleculeProperties(mol)
                     cenergy.append(Chem.MMFFGetMoleculeForceField(mol,mp,confId=conf).CalcEnergy()) 
@@ -143,8 +143,8 @@ def getRMS(mol, c1,c2):
                         sdwriter.write(mol,conf)
         except (KeyboardInterrupt, SystemExit):
             raise                
-        except:
-            print "Exception"
+        except Exception as e:
+            print "Exception",e
     else:
         print "ERROR:",smi