+1 for Symmetrizer too, A must!

De : Michal Krompiec
Date : jeudi, 18 janvier 2018 à 08:18
À : Jason Biggs
Cc : RDKit Discuss, Greg Landrum
Objet : Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+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 
<jasondbi...@gmail.com<mailto:jasondbi...@gmail.com>> 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 
<greg.land...@gmail.com<mailto: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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