Re: [Rdkit-discuss] RDKit - contributing conformational entropy descriptor

Hi Geoff, Congrats to you and co-authors on the paper and thanks for offering to contribute to the RDKit. Given the dependence on py_rdl, this probably isn't currently a good match for the core RDKit (we try to minimize adding additional external dependencies), but it would be great to have it

[Rdkit-discuss] RDKit - contributing conformational entropy descriptor

Hi Greg, We just published a paper with a linear model predicting conformational entropies: https://pubs.acs.org/doi/10.1021/acs.jctc.0c01213 https://github.com/hutchisonlab/molecular-entropies We built the notebooks on top of RDKit - and of course would like to contribute the descriptor back

[Rdkit-discuss] rdMolAlign manual pages

Hello colleagues, Seems like the manual pages for the rdMolAlign package and its functions are empty. Perhaps the pointer did not get updated when the package was updated? e.g. https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html or manual page for "AlignMol". Thank you Greg and all the

Re: [Rdkit-discuss] [Rdkit-announce] 2021.03.1 RDKit Release

Hi Greg, I can confirm the issue is solved here. Cheers ! Drew On Sun, 28 Mar 2021 at 08:32, Greg Landrum wrote: > Hi Drew, > > Thanks for pointing out the problem. I had inadvertently done the conda > builds using freetype, but I forgot to add a freetype dependency. > It should be fixed

Re: [Rdkit-discuss] HasSubstructMatch & GetSubstructMatches hang when useChirality is True

Thanks a lot Paolo. Christos Christos Kannas Research Software Engineer (Cheminformatics) [image: View Christos Kannas's profile on LinkedIn] On Fri, 26 Mar 2021 at 16:01, Paolo Tosco wrote: > Hi Christos, > > this is a possible workaround that

Re: [Rdkit-discuss] atom index changes after embedding

Hi Pablo, You could loop over the atoms and use SetProp to add a relevant property to each one. That should survive the embedding. Cheers, Dave On Mon, 29 Mar 2021 at 11:18, Pablo Ramos wrote: > Dear community, > > > > I want to embed a molecule. For my personal application, I really need

[Rdkit-discuss] atom index changes after embedding

Dear community, I want to embed a molecule. For my personal application, I really need the atom indices to be respected, even if they are indistinguishable. The problem is that, because of symmetry, some atoms may be indistinguishable. This is something you can see by using