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matteoferla/rototranslate.py

Created May 9, 2024 16:36
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RDKit fix reference frame of molecule
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rototranslate.py
# I am sure I have pasted this snippet somewhere, but I always forget where —so may be a duplicate.
wrong_ref: Chem.Mol = ... # the reference mol in former frame/location/crystal
right_ref: Chem.Mol = ... # the reference mol in desired frame
wrong: Chem.Mol = ... # the target
affine_matrix = AllChem.GetAlignmentTransform(wrong_ref, right_ref)[1]
AllChem.TransformConformer(wrong.GetConformer(), affine_matrix) # this is in place
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