search

xiaoruiDong / RDMC

Reaction Data and Molecular Conformers (RDMC) is a package dealing with reactions, molecules, conformers, majorly in 3D.
https://xiaoruidong.github.io/RDMC/
MIT License
23 stars 1 forks source link

Openbabel 3.1 has a mistake in generating radical molecules from XYZs #1

Open xiaoruiDong opened 3 years ago

xiaoruiDong commented 3 years ago

Openbabel 3.1 has a mistake in generating radical molecules from XYZs. This influences TS-GCN notebook that uses openbabel as the backend to perceive XYZs for radicals. A temporary fix here may be

  1. checking the total spin multiplicity and valence of each atom
  2. manually assign the multiplicity according to 1.
xiaoruiDong commented 3 years ago

https://github.com/openbabel/openbabel/issues/2392

xiaoruiDong commented 3 years ago

This is a bug possibly due to a bad compilation of the anaconda binary (maybe only for macOS). Currently workaround for N, C, H, and O is added.