Re: [Rdkit-discuss] Docs intentionally broken?

Ok, things should be better now: https://rdkit.org/docs/source/rdkit.Geometry.rdGeometry.html#rdkit.Geometry.rdGeometry.Point3D https://rdkit.org/docs/source/rdkit.SimDivFilters.rdSimDivPickers.html#rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker I have no doubt that there are still some things

Re: [Rdkit-discuss] install rdkit with pipenv

Hi Ali, At the moment there are no pypi packages for the RDKit and it can only be installed using conda -greg On Tue, Nov 13, 2018 at 11:40 PM Ali Eftekhari wrote: > This open issue try to > address if rdkit can be installed by pip. I was

Re: [Rdkit-discuss] How to encode atomic contributions to logP (hydrophobicity) in MOL2 formatted charge slot?

On 14/11/2018 02:42, James T. Metz via Rdkit-discuss wrote: RDkit Discussion Group, Given a set of small molecules as a SDF file, I would like to generate a MOL2 file where the atomic contributions to logP (hydrophobicity) from each atom including hydrogens have been calculated and are now

[Rdkit-discuss] install rdkit with pipenv

Hello, This Is it possible to install rdkit with pipenv? Thanks, Ali ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] GetReactingAtoms getting everything

Hi,I have been using rdkit (thank you for creating this!) to get reacting atoms from an rxn but it isn't behaving as I thought it would work. As a test case I have tried this: tsmi='[cH:1]1[cH:2][c:3]([F:4])[n:5][cH:6][cH:7]1>>[cH:1]1[cH:2][c:3]([Cl:4])[n:5][cH:6][cH:7]1' rxn2 =

[Rdkit-discuss] How to encode atomic contributions to logP (hydrophobicity) in MOL2 formatted charge slot?

RDkit Discussion Group,     Given a set of small molecules as a SDF file, I would like to generate a MOL2 file where the atomic contributions to logP (hydrophobicity) from each atom including hydrogens have been calculated and are now encoded in the partial atomic charge"slot" in a MOL2 file. 

Re: [Rdkit-discuss] RDKit and organometallics

Thank you for the tips. In a lng and dumb workflow, I was able to load a sample molecule. * Downloaded a sample .cif structure from CCDC https://www.ccdc.cam.ac.uk/structures/search?id=doi:10.5517/ccdc.csd.cc1m9hgw=DataCite * Used OpenBabel to convert my .cif to .mol V3000 (the

Re: [Rdkit-discuss] RDKit and organometallics

Isn't this patch already incorporated in the master branch? On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner < malgorzata.wer...@molecularhealth.com> wrote: > Hi Henrique, > > You could try using v3000 sd files. > > Here's a blog about this: >

Re: [Rdkit-discuss] RDKit and organometallics

Hi Henrique, You could try using v3000 sd files. Here's a blog about this: https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/ Best, Malgorzata From: Henrique Castro Sent: 13 November 2018 11:57:34

[Rdkit-discuss] RDKit and organometallics

Dear colleagues, I know that this is probably a dumb question, but since my searches showed no clarifying results I'm asking here anyway. I'm planning to use RDKit on my Ph.D. thesis, but my field of research is inorganic chemistry and molecular magnetism. That means that I'm dealing with