On Tue, Dec 3, 2019 at 9:58 PM Rasmus "Termo" Lundsgaard < termope...@gmail.com> wrote:
> 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()] > > You're absolutely right, thanks for catching that. I updated the gist. -greg > > 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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