Witness atom iteration very slow with mol.GetAtoms

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

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Open xiaoruiDong opened 10 months ago

xiaoruiDong commented 10 months ago

Similar to https://github.com/rdkit/rdkit/issues/6208. About 3 - 20x slower according to their benchmark.

This will be fixed in 2023.09 version of RDKit. Using the [mol.GetAtomWithIdx(i) for i in range(mol.GetNumAtoms)] as a replacement for now.