Re: [Rdkit-discuss] calculation of spherical harmonics coefficients for 3D molecules?
I'm not aware of any open-source implementations of this method or any of the other published approaches for representing/comparing molecular shapes with spherical harmonics, but it is something that would be interesting. -greg On Mon, Aug 3, 2020 at 8:12 PM James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > RDkit Discussion Group, > > Has anyone implemented code to calculate spherical harmonics > coefficients for 3D conformations of molecules? The approach I have > in mind is described in Morris, R.J. et al., Real Spherical Harmonic > expansion coefficients for protein binding pocket and ligand comparisons, > Bioinformatics, 21 (2005) 2347 - 2355. > > Regards, > Jim Metz > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] calculation of spherical harmonics coefficients for 3D molecules?
RDkit Discussion Group, Has anyone implemented code to calculate spherical harmonicscoefficients for 3D conformations of molecules? The approach I havein mind is described in Morris, R.J. et al., Real Spherical Harmonic expansion coefficients for protein binding pocket and ligand comparisons,Bioinformatics, 21 (2005) 2347 - 2355. Regards, Jim Metz ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit installation problem
Hi Sebastian, As far as I can tell, the latest version available in conda is 2020.03.3. As Dave mentioned, I was able to get this version by specifying python 3.7: More information on this method here: http://rdkit.blogspot.com/2019/10/sharing-conda-environments.html You can also specify the rdkit version instead: https://github.com/rdkit/conda-rdkit/issues/84 Vin From: Francois Berenger Sent: Sunday, August 2, 2020 8:32 PM To: Sebastián J. Castro Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] RDKit installation problem Dear Sebastian, Since last week, you should also be able to install rdkit on Linux via linuxbrew: --- sudo apt install linuxbrew-wrapper brew tap rdkit/rdkit brew update brew install rdkit # to test it /home/linuxbrew/.linuxbrew/bin/python3 import rdkit --- Thanks to Nuri Jung on github (@jnooree) for proposing a fix to the brew rdkit install formula. Regards, F. On 02/08/2020 03:03, Sebastián J. Castro wrote: > I have try the installation suggested at > http://www.rdkit.org/docs/Install.html: > > $ conda create -c rdkit -n my-rdkit-env rdkit > > But I get 2017 version instead of 2020 (last released). > > I don't know how to install it. Can you help me? > > I have Ubuntu 20.04 LTS > > Thank you > > Best regards! > > -- > > Dr. Sebastián J. Castro > Departamento de Ciencias Farmacéuticas > Facultad de Ciencias Químicas > Universidad Nacional de Córdoba > UNITEFA-CONICET > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
