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* new workflows.base.guess_elements() to get elements for RDKit because the MDAnalysis element guesser is not very good: here we use the accurate masses from the TPR file to guess any elements where the MDA guesser has problems (as indicated by mass discrepancy) * rtol in guess_elements() to tune how close masses must match GROMACS masses are not exactly identical to MDAnalysis masses. We need a relative tolerance of at least 1e-3 to reliably match them. * manually set all zero masses to DUMMY (MW is detected as DUMMY, DUMMY as D, so this makes all dummies DUMMY for consistency) * hard coded ATOL=1e-6 for detecting dummies with very small discrepancy from 0 * add tests for known problem cases, no problems, and masses that are slightly off * updated CHANGES * updated docs --------- Co-authored-by: Oliver Beckstein <[email protected]>
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