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

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xiaoruiDong opened this issue Jun 27, 2021 · 2 comments
Open

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

xiaoruiDong opened this issue Jun 27, 2021 · 2 comments
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@xiaoruiDong
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xiaoruiDong commented Jun 27, 2021 •
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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
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openbabel/openbabel#2392

@xiaoruiDong xiaoruiDong added the bug Something isn't working label Jun 27, 2021
xiaoruiDong added a commit that referenced this issue Jun 28, 2021
@xiaoruiDong
Temporary workaround for issue #1
b5bc5ab 
OBConversion generated molecules have wrong atom attributes, e.g., all zero multiplicity. There may be another workaround, but currently manually assign spin multiplicities for H, C, and O radical sites.
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xiaoruiDong commented Sep 4, 2021 •
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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.

@xiaoruiDong xiaoruiDong added bugs or issue in dependencies and removed bug Something isn't working labels Mar 28, 2024
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