search

EPiCs-group / epic-mace

Python package for the automated screening and discovery of octahedral and square-planar mononuclear metal complexes.
GNU General Public License v3.0
0 stars 0 forks source link

Solve "cyclohexane" problem #14

Open IvanChernyshov opened 3 years ago

IvanChernyshov commented 3 years ago

RDKit embeds structures containing several cyclohexanes dreadfully. The easiest way to avoid this is to prepare the library containing SMILES-geometry data (in terms of BoundMatrix). However, this is not an easy-going problem, thus it's a good idea to think about it for more than five minutes.

IvanChernyshov commented 3 years ago

The strongest solution is to get {'smiles': geometry} dictionary for various fragments to modify BoundsMatrix. However, that's a too complex task. It should be enough just to find all cyclohexanes (isolated?) and set the corresponding distances with high precision. I guess it should work in simple cases.

IvanChernyshov commented 3 years ago

It does not work: resulting cyclo-hexanes are twisted even without optimization. Maybe it's a good idea to add tethers between atoms?..

IvanChernyshov commented 3 years ago

Maybe it's a good idea to add tethers between atoms?..

Also does not work. The only way is to set distances between all atoms of cHex, not only 6 Cs. It's a difficult task, not for this milestone