Re: [Rdkit-discuss] chirality assignment

Hi Greg, Thanks for your quick response. I look forward to more flexible version of the command. For the second point, atoms 6 and 8 can be inverted by RDKit_2015_03_1. RDKit_2015_03_1 - >>>

Re: [Rdkit-discuss] isotopic SMILES

On Feb 7, 2017, at 19:02, Curt Fischer wrote: > My ultimate goal is an easy way to create rdkit molecules that have isotopic > substitutions but which are otherwise exactly the same as non-substituted > variants. What's the best approach? Is it to directly call

Re: [Rdkit-discuss] isotopic SMILES

I think you've persuaded me that .SetIsotope() is the way to go... I don't understand how that avoids any problem. How do you specify the > target atom for that case? > In any case, won't the InChI normalization affect some of your structures > (e.g., detaching metals) and make it even harder to

Re: [Rdkit-discuss] isotopic SMILES

On Feb 7, 2017, at 22:26, Curt Fischer wrote: > def same_implicit_valence(mol_1, mol_2, atom_idx=1): > """Returns True if mol_1 and mol_2 have the same implicit valence for the > indexed atom""" > mol_1_implicitH =

[Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

Dear All, I have hit what I think is a problem with stereochemistry perception/handling for certain types of pseudochiral and/or spirocyclic systems. Basically I am observing that some types of input tetrahedral stereochemical information gets lost when an RDKit molecule is generated. But I

Re: [Rdkit-discuss] chirality assignment

Rintarou, On Tue, Feb 7, 2017 at 9:25 AM, Suzuki, Rintarou wrote: > > For the second point, atoms 6 and 8 can be inverted by RDKit_2015_03_1. > > RDKit_2015_03_1 > - > >>>

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

Hi James, This is definitely a bug. The problem seems to be connected to the way what the RDKit calls "ring stereochemistry" is handled when there are spiro linkages. Here's the github issue: https://github.com/rdkit/rdkit/issues/1294 I'll take a look. Best, -greg On Tue, Feb 7, 2017 at

Re: [Rdkit-discuss] isotopic SMILES

I replied to Andrew's very nice discussion of implicit hydrogens in SMILES but forgot to include the whole list. Wow, thank you, that was very useful. I didn't realize those nuances of > SMILES. > > On the rdkit "side", the distinction made in Smiles between implicit and > explicit hydrogens