The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
The aromaticity_model keyword is given as an argument in Topology.chemical_environment_matches, but is not actually used in the function or passed to Molecule.chemical_environment_matches. The default value "MDL" also appears to be unsupported as the only supported value in the toolkit _find_smarts_matches functions is "OEAroModel_MDL". The aromaticity_model keyword is also not available in Molecule.chemical_environment_matches even though it seems like a nice option to have.
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lilyminium
commented
3 years ago
Describe the bug A clear and concise description of what the bug is.
https://github.com/openforcefield/openff-toolkit/blob/b2b76bb457c2a8235f86e887d75ee815030b605e/openff/toolkit/topology/topology.py#L2016-L2018
The
aromaticity_modelkeyword is given as an argument inTopology.chemical_environment_matches, but is not actually used in the function or passed toMolecule.chemical_environment_matches. The default value "MDL" also appears to be unsupported as the only supported value in the toolkit_find_smarts_matchesfunctions is "OEAroModel_MDL". Thearomaticity_modelkeyword is also not available inMolecule.chemical_environment_matcheseven though it seems like a nice option to have.To Reproduce Steps to reproduce the behavior. A minimal reproducing set of python commands is ideal.
If the problem involves a specific molecule or file, please upload that as well.
See https://github.com/openforcefield/openff-toolkit/blob/b2b76bb457c2a8235f86e887d75ee815030b605e/openff/toolkit/topology/topology.py#L2016-L2018
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