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Starting with Mathematica 12, the MoleculeModify function has a "GenerateConformers" option.

What is the algorithm used to perform the conformer generation?

Results can vary for different software packages and algorithm choices, so knowing the specific algorithm used is one step towards replicability by others. (Some of the underlying Molecule calculations make use of RDKit functions; knowing that this is being used here would be sufficient, as the conformer generation algorithm implemented in RDKit does pretty well.)

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The primary method for conformer generation used by Molecule and related functions is the ETKDG method described in "Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation". Versions 12 and 12.1 of the Wolfram Language use versions 1 and 2 of the ETKDG method, respectively.

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