Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-20 Thread Greg Landrum
Paolo's gist includes a vocabulary mistake[1] that I think is confusing things here. In the RDKit the stereochemistry of a double bond can be unspecified, unknown, or known. Unspecified means that you haven't said anything about what the stereo is; unknown means that you've actively provided the

Re: [Rdkit-discuss] How to center atom labels vertically?

2020-10-20 Thread Greg Landrum
Hi Theo, The atom label placement in drawings turns out to be very tricky to do in a cross platform way. You're using the RDKit's old drawing code which we haven't been maintaining for a while now, I'd recommend either switching to using one of the convenience functions likes Draw.MolToImage() or

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-20 Thread Paolo Tosco
Hi Adelene, I have updated the gist https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b to account for your questions. Cheers, p. On Tue, Oct 20, 2020 at 2:08 PM Adelene LAI wrote: > Hi Dave and Pablo, > > > Thanks for your helpful replies. > > > @Dave, issue created:

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-20 Thread Adelene LAI
Hi Dave and Pablo, Thanks for your helpful replies. @Dave, issue created: https://github.com/rdkit/rdkit/issues/3514 @Pablo, your gist shows that the internal representation of the mol does indeed factor in undefined stereo, contrary to the way it is depicted. But why then does this

Re: [Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-20 Thread Paolo Tosco
Hi Adelene, this gist https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b shows how to add stereo annotations to RDKit 2D depictions, and also how to access the double bond stereochemistry programmatically. Cheers, p. On Tue, Oct 20, 2020 at 12:24 PM Adelene LAI wrote: > Hi

[Rdkit-discuss] How to center atom labels vertically?

2020-10-20 Thread theozh
Dear RDKit-ers, this sounds like a simple problem, however, I haven't found a link to the corresponding documentation. When I draw a structure with: from.rdkit.Chem import Draw Draw.MolToQPixmap(mol) The non-Carbon atom labels are not centered to the bonds, but typically shifted downwards.

[Rdkit-discuss] How to preserve undefined stereochemistry?

2020-10-20 Thread Adelene LAI
Hi RDKit Community, Is there a way to preserve undefined stereochemistry aka unspecified stereochemistry when doing MolFromSmiles? I'm working with a bunch of molecules, some with stereochemistry defined, some without. If stereochemistry is undefined in the SMILES, I would like it to stay