- 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 <greg.land...@gmail.com>
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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