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mojaie / MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics
MIT License
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Coulomb matrices calculation #99

Closed DoktorMike closed 11 months ago

DoktorMike commented 11 months ago

I was recently looking into Coulomb matrices and their calculation. I was wondering if such a thing is within the scope of this package? It requires inter-atom distances in, I would assume, 3D. After that the calculation is done per conformer. So to do this we would have to:

  1. Go from SMILES to 3D coordinates
  2. Get the charges for each atom
  3. Generate a set of conformers for each molecule

Currently I think we are lacking 1 and 3. Step 1 could be done by reading SDF files instead of SMILES I would presume.

mojaie commented 11 months ago

Thank you very much. I'm not sure but 1 and 3 maybe requires force fields like MMFF. One of opensource implementation is included in RDKit under BSD license. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-014-0037-3 For now I prefer molecular mechanics/dynamics would be provided as separate package, and MolecularGraph.jl should provide compatible interfaces for them.

DoktorMike commented 11 months ago

Thank you very much. I'm not sure but 1 and 3 maybe requires force fields like MMFF. One of opensource implementation is included in RDKit under BSD license. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-014-0037-3 For now I prefer molecular mechanics/dynamics would be provided as separate package, and MolecularGraph.jl should provide compatible interfaces for them.

Thanks for the clarification. If I manage to implement the coulomb matrices I'll look into interfacing with this project. :) I'll close this for now.