Hi Leon, you are right, the Python MMFFOptimizeMolecule and MMFFOptimizeMoleculeConfs functions have a default of 100.0, while their C++ counterparts, (and their UFF counterparts, both C++ and Python) have a default of 10.0. There is no particular reason for that, other than historical. Even though there is definitely an inconsistency there, it is clearly documented; the counter argument is that changing those defaults might suddenly cause unexpected changes in results in existing scripts/workflows.
Cheers, p. On Mon, May 10, 2021 at 10:23 PM topgunhaides <sunzhi....@gmail.com> wrote: > Hi guys, > > I noticed a possible inconsistent default value for one parameter ( > nonBondedThresh ) of the "MMFFOptimizeMoleculeConfs" function between > Python and C++ versions: > > C++: nonBondedThresh = 10.0 (I assume this is the default?) > > https://www.rdkit.org/docs/cppapi/namespaceRDKit_1_1MMFF.html#a5fa45054929e5d4313341973d7df9e7c > > Python: defaults to 100.0 > https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html > > Can anyone help me with this? Thank you! > > Leon > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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