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divelab / MoleculeX

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Conformer Screening #5

Open hansen7 opened 2 years ago

hansen7 commented 2 years ago

Thanks for sharing!

I can't find the codes for the conformer screening, which is the descried in the arXiv:

We generate mutliple conformers for each molecule with RDKit [Landrum et al., 2006] and prune similar conformers with an RMSD cutoff R = 0.5Å.

neither from here https://github.com/divelab/MoleculeX/blob/29951d711f2923feb60914147feb450e2c0c922f/Molecule3D/preprocess/PubChemQCDataset.py#L195-L197

nor here: https://github.com/divelab/MoleculeX/blob/29951d711f2923feb60914147feb450e2c0c922f/molx/dataset/molecule3d.py#L135-L137

would you mind elaborating a bit more?

floatlazer commented 2 years ago

Hi,

Thanks for your interest. The paper you referred corresponds to our kddcup solution: https://github.com/divelab/MoleculeX/tree/molx/BasicProp/kddcup2021

The code for conformer generation is here: https://github.com/divelab/MoleculeX/blob/29951d711f2923feb60914147feb450e2c0c922f/BasicProp/kddcup2021/conformer/gen_confs.py#L30