8000 Coulomb matrices calculation · Issue #99 · mojaie/MolecularGraph.jl · GitHub
[go: up one dir, main page]
Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Coulomb matrices calculation #99

Closed
DoktorMike opened this issue Jul 15, 2023 · 2 comments
Closed

Coulomb matrices calculation #99

DoktorMike opened this issue Jul 15, 2023 · 2 comments

Comments

@DoktorMike
Copy link

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
Copy link
Owner
mojaie commented Jul 18, 2023

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
Copy link
Author

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@mojaie @DoktorMike
0