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Thanks, this fixes the problem case I reported
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This PR closes #350 by preferentially using
RDKit::determineBondOrders()to infer bond orders when missing, only failing back to the existing (MDAnalysis-baed) inference routine when this fails. A unit test confirms that the problem inputs from the issue thread convert correctly when using SDF or AMBER inputs, i.e. the SMILES strings of the convert RDKit molecules match. All existing RDKit conversion tests pass, as do extended tests in BioSimSpace.develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]