Hi Greg. Thks for your gist. I guess the line:
nbrs = [(x.GetOtherAtomIdx(1),x.GetIdx()) for x in atom.GetBonds()] should be: nbrs = [(x.GetOtherAtomIdx(atom.GetIdx()),x.GetIdx()) for x in atom.GetBonds()] On Tue, Dec 3, 2019 at 5:38 PM Greg Landrum <greg.land...@gmail.com> wrote: > What's going on here is that the RDKit defines stereochemistry based on > the ordering of bonds, not atom indices. > This has come up on the list multiple times, a relatively recent instance > is here: > > https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08955.html > > Here's a gist that I have laying around that may help here:[1] > https://gist.github.com/greglandrum/9f0e068e53171174b6797348eca64b3e > > > -greg > [1] Now if only I could find *why* have that gist laying around... > > > On Tue, Dec 3, 2019 at 3:32 PM Rasmus "Termo" Lundsgaard < > termope...@gmail.com> wrote: > >> Hi Pablo, >> >> thank you for the heads up on that removeHs is not honorred when not >> sanitizing (and that removeH has to be done to solve that issue here). >> >> Now I tried with the same molecule but where I also move around on the >> order of the atoms (attached as Ran1_neworder.sdf), and here I still get a >> different isomeric smiles, eventhough the chiral tag is the same: >> for f in ['Ran1.sdf','Ran2.sdf', 'Ran1_neworder.sdf']: >> m = Chem.MolFromMolFile(f, sanitize=False) >> m = Chem.RemoveHs(m, sanitize=False) >> print( Chem.MolToSmiles(set_correct_Chiral_flags(m), >> isomericSmiles=True) ) >> >> >> C[C@@H](N)C(=O)O >> C[C@@H](N)C(=O)O >> C[C@H](N)C(=O)O >> >> >> On Tue, Dec 3, 2019 at 2:58 PM Paolo Tosco <paolo.tosco.m...@gmail.com> >> wrote: >> >>> Hi Rasmus, >>> >>> the problem is that, as stated in the rdmolfiles.MolFromMolFile() docs, >>> the removeHs option is only honored when sanitize is True. >>> >>> So to obtain sensible results without sanitizing you should rather do >>> something like: >>> >>> m1 = Chem.MolFromMolFile('Ran1.sdf', sanitize=False) >>> m1 = Chem.RemoveHs(m1, sanitize=False) >>> print( Chem.MolToSmiles(set_correct_Chiral_flags(m1), >>> isomericSmiles=True) ) >>> m2 = Chem.MolFromMolFile('Ran2.sdf', sanitize=False) >>> m2 = Chem.RemoveHs(m2, sanitize=False) >>> print( Chem.MolToSmiles(set_correct_Chiral_flags(m2), >>> isomericSmiles=True) ) >>> >>> You may check the individual sanitization operations here: >>> >>> https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=rdmolops%20sanitizeflags#rdkit.Chem.rdmolops.SanitizeFlags >>> >>> Cheers, >>> p. >>> >>> On 03/12/2019 12:46, Rasmus "Termo" Lundsgaard wrote: >>> >>> Hi all >>> >>> I would like to avoid sanitizing the sdf files, as information in these >>> files should be seen as the ground truth. >>> >>> I however have some problems in figuring out how to read and set chiral >>> information from the file and also have RDkit behave the same always. >>> Attached are two sdf files with no 3d information and only stereo >>> information in the atoms section for R-Aniline. The only difference as I >>> see it is the order of the lines of the bond information. >>> Even so I get two different smiles back with isomeric information when >>> not sanitizing. >>> >>> Attached is also the minimal python code: which for me at least outputs: >>> >>> not setting chiral flags >>>> CC(N)C(=O)O >>>> CC(N)C(=O)O >>>> >>>> setting chiral flags >>>> [H]OC(=O)[C@]([H])(N([H])[H])C([H])([H])[H] >>>> [H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])[H] >>>> >>>> setting chiral flags and sanitize >>>> C[C@@H](N)C(=O)O >>>> C[C@@H](N)C(=O)O >>>> >>> >>> Any ideas to why this happens and how I can handle it strictly. Also >>> what does the sanitizing exactly do? >>> >>> Regards Rasmus >>> >>> >>> >>> _______________________________________________ >>> Rdkit-discuss mailing >>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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