fixes

alignmcs.py

@@ -3,7 +3,6 @@
 import argparse, sys, rdkit, collections
 from rdkit.Chem import AllChem as Chem
 from rdkit.Chem import rdMolAlign
-from rdkit.Chem.rdShape import Align
 from rdkit.Chem.rdMolAlign import AlignMol
 from rdkit.Chem import rdMolAlign
 from rdkit.Chem import rdFMCS

rdconf.py

@@ -110,7 +110,7 @@ def getRMS(mol, c1,c2):
                     converged = not Chem.UFFOptimizeMolecule(mol,confId=conf)
                     cenergy.append(Chem.UFFGetMoleculeForceField(mol,confId=conf).CalcEnergy())
                 if options.verbose:
-                    print("Convergence of conformer",conf,converged)
+                    print("Convergence of conformer",conf,converged,cenergy[-1])
 
             mol = Chem.RemoveHs(mol)
             sortedcids = sorted(cids,key = lambda cid: cenergy[cid])

uffminimize.py

@@ -9,7 +9,8 @@
 parser = OptionParser(usage="Usage: %prog [options] <input>.sdf <output>.sdf")
 parser.add_option("-v","--verbose", dest="verbose",action="store_true",default=False,
                   help="verbose output")
-
+parser.add_option("-a","--add_hydrogens", dest="addh",action="store_true",default=False,
+                  help="add hydrogens")
 
 
 (options, args) = parser.parse_args()
@@ -18,31 +19,33 @@
 
 inmols = Chem.SDMolSupplier(input)
 if inmols is None:
-    print "Could not open ".input
+    print("Could not open ".input)
     sys.exit(-1)
 
 sdwriter = Chem.SDWriter(output)
 if sdwriter is None:
-    print "Could not open ".output
+    print("Could not open ".output)
     sys.exit(-1)
 
 for mol in inmols:
     if mol is not None:
         try:
+            if options.addh:
+                mol = Chem.AddHs(mol,addCoords=True)
             orig = Chem.UFFGetMoleculeForceField(mol).CalcEnergy()
             a=Chem.UFFOptimizeMolecule(mol)
 
             #sometimes the UFF Optimization does not converge (returns a 1 instead of 0)
             if a==1:
-              a=Chem.UFFOptimizeMolecule(mol, maxIter=1000)
+              a=Chem.UFFOptimizeMolecule(mol, maxIters=1000)
 
             if options.verbose:
                 e = Chem.UFFGetMoleculeForceField(mol).CalcEnergy()
-                print mol.GetProp('_Name'),orig,"->",e
+                print(mol.GetProp('_Name'),orig,"->",e)
             sdwriter.write(mol)
         except (KeyboardInterrupt, SystemExit):
             raise            
-        except:
-            print "Exception occurred",mol.GetProp('_Name')
+        except:            
+            print("Exception occurred",mol.GetProp('_Name'))
     else:
-        print "ERROR"
+        print("ERROR")