Page Comparison

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The YAMMBS benchmarks were calculated as follows. The MoleculeStore object was generated with this commit of the YAMMBS package, which optimizes the molecules using a convergence threshold of 5e-9 kJ/mol/nm^2. The ddE’s, TFD’s, and ICRMSD’s were calculated using this commit of the YAMMBS package, which has revised the ddE definition to be consistent with the old benchmarking script (defined with respect to the lowest energy QM conformer, and ddE’s between the lowest energy conformers are excluded) and uses mapped SMILES to create molecules for TFD analysis. The RMSD’s have been calculated using the same commit as the ddE and TFD, but with a modified RMSD function that uses all atoms to calculate the RMSD, in order to be consistent with the RMSD definition in the old benchmarks. YAMMBS typically uses a heavy-atom-only RMSD, which is much faster to compute.

The code and files used in this are available here

DDE

The overall DDE’s are nearly identical between YAMMBS and the old benchmark (“og” in the figures).

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