Add explicit hydrogens when loading in SMILES #1172
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Previously, if a user decided to use `parmed.rdkit.load_smiles` to generate a `parmed` structure, no explicit hydrogens are added to the structure, this can be an issue if trying to generate hydrocarbon systems. This PR leverages the built-in `rdkit` ability to generate explicit hydrogens for an rdkit mol using `rdkit.Chem.AddHs` by passing a boolean flag `hydrogens=True` to use this method. Since this could break others' workflows, the default value is `False` to comply with current functionality.
swails
reviewed
May 12, 2021
Co-authored-by: Jason Swails <jason@entos.ai>
Co-authored-by: Jason Swails <jason@entos.ai>
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@swails , I went through and made the necessary changes discussed above and the units tests are passing locally for me. There was very little modification of the codebase to support these changes 🎉 . Let me know if there is anything else needed on my end! It seems like for builds to run it needs approval from a maintainer: https://github.com/ParmEd/ParmEd/actions/runs/836655356 |
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Thanks! I approved and will merge when the tests pass. |
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Previously, if a user decided to use
parmed.rdkit.load_smilestogenerate a
parmedstructure, no explicit hydrogens are added to thestructure, this can be an issue if trying to generate hydrocarbon
systems.
This PR leverages the built-in
rdkitmethodrdkit.Chem.AddHsto generate explicithydrogens for an rdkit mol. An additional boolean flag:
hydrogens=Truehas been added to this method. Since this could break others' workflows, the default value isFalseto comply with current functionality.