[continuing to dig out from the email pile]
On Mon, Jan 15, 2018 at 4:20 PM, Jason Biggs <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.
>
>
Forcing things into the xy plane is pretty simple: you just need to add a
force that tries to drive the z coordinate to zero. The embedding code
already does something analogous when you embed chiral molecules: those are
initially embedded in 4D and then refined by adding a forcefield term that
drives the fourth coordinate to zero.
Here's the bit of code that adds that term:
https://github.com/rdkit/rdkit/blob/master/Code/DistGeom/DistGeomUtils.cpp#L230
-greg
> - 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
> <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.
>
>
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