And here an other example in which a stereocenter is lost. Glicolyc acid C1[C@H](C[C@@H]2[C@](C1)([C@@H]1[C@@H]([C@@H](C2)O)[C@H]2[C@]([C@H](C1)O)([C@@H](CC2)[C@H](C)CCC(=O)NCC(=O)O)C)C)O
You can get this error... Warning Different Chirality!! [(1, 'R'), (3, 'R'), (4, 'S'), (7, 'R'), (8, 'R'), (9, 'S'), (10, 'S'), (11, 'R'), (12, 'S'), (16, 'S'), (22, 'R')] [(1, 'R'), (3, 'R'), (4, 'S'), (7, 'R'), (8, 'R'), (9, 'S'), (10, 'S'), (11, 'R'), (16, 'S'), (22, 'R’)] GMR > On 10 Jan 2015, at 19:30, Giuseppe Marco Randazzo <[email protected]> > wrote: > > Hello Greg, > > and hello to all other developers. > > Thanks for this nice package that i enjoy and i love a lot!!! So.. i’ve > noticed maybe a bug in the stereocenter preservation when more conformer are > generated with “EmbedMultipleConfs” > > Here my example with a simple steroid alpha cortolone. > > Is it normal? or there is something wrong? > > Best regards > GMR > > > > from rdkit import Chem > from rdkit.Chem import AllChem > > m = > Chem.MolFromSmiles("C1C[C@H](C[C@@H]2[C@]1([C@@H]1[C@@H](CC2)[C@H]2[C@](CC1=O)([C@](CC2)([C@@H](O)CO)O)C)C)O") > mchirality = Chem.FindMolChiralCenters(m) > AllChem.EmbedMultipleConfs(m, 300) > > example = Chem.SDWriter("Example.sdf") > for i in range(m.GetNumConformers()): > Chem.AssignAtomChiralTagsFromStructure(m, confId=i) > AllChem.UFFOptimizeMolecule(m,confId=i) > example.write(m, confId=i) > example.flush() > > suppl = Chem.SDMolSupplier("Example.sdf") > for molid in range(len(suppl)): > confchirality = Chem.FindMolChiralCenters(suppl[molid]) > problems = False > for i in range(len(confchirality)): > if mchirality[i] == confchirality[i]: > continue > else: > problems = True > break > if problems == True: > print "Warning Different Chirality in Conformer %d" % molid > print mchirality > print confchirality > print "-"*100 > else: > continue > > > > > > Warning Different Chirality in Conformer 25 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 44 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 67 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 87 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 95 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 100 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'S'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 101 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 102 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'S'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 108 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 114 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 144 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 149 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 166 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 170 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 174 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 196 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 214 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 240 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'R'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 251 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 252 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 260 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 286 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'R'), (15, > 'R'), (18, 'S')] > ---------------------------------------------------------------------------------------------------- > Warning Different Chirality in Conformer 297 > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'R'), (18, 'S')] > [(2, 'R'), (4, 'R'), (5, 'S'), (6, 'S'), (7, 'S'), (10, 'S'), (11, 'S'), (15, > 'S'), (18, 'S')] > > > > <testconf.py> > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming! 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