Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

[Michal K. <mic...@gm...>]

+1 vote for Symmetrizer. It would be very useful for preparing input for
computational chemistry codes.
Best,
Michal Krompiec
Merck KGaA

On Mon, 15 Jan 2018 at 15:21, Jason Biggs <jas...@gm...> wrote:

>
>    - I've had this on my to-do list for a few months now, implementing
>    the algorithm described in this paper.  I think the force-field energy
>    minimization routines already present in the RDKit can be utilized for this
>    pretty easily.  The only part that I don't think is set up already would be
>    applying a constant force to all atoms to force them into the xy plane.
>
> Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical
> Structure Diagram Generation of Complex Molecules and Ligand–Protein
> Interactions." J. Chem. Inf. Model. 2016, 56, 2320-2335, DOI:
> 10.1021/acs.jcim.6b00391.
>
>
>
>    - Another idea would be to add in point-group symmetry detection.  I'm
>    using the Symmetrizer java library, described here
>    https://www.ncbi.nlm.nih.gov/pubmed/22549414, and pretty happy with it
>    overall.  One could re-implement it in C++, or include the jar in the
>    External folder and write python wrappers.
>
>
> Jason Biggs
>
>
> On Mon, Jan 15, 2018 at 1:09 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>> Dear all,
>>
>> We've been invited again to participate in the OpenChemistry application
>> for Google Summer of Code.
>>
>> In order to participate we need ideas for projects and mentors to go
>> along with them.
>>
>> The current list of RDKit ideas is being maintained here:
>> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>
>> (Note: at the point that I'm pressing "send", that's still a copy of last
>> year's project ideas).
>>
>> If you're willing to be a mentor (please ask me about the ~5 hours/week
>> required here) or have ideas, please reply to this thread.
>>
>> Best,
>> -greg
>>
>>
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>
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