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
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swails
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Thank you! This is a nice addition!
I actually think the functionality you added should be made the default and people that use it will have to deal with the backwards incompatibility (there are several in the upcoming 4.0 release).
Co-authored-by: Jason Swails <[email protected]>
Co-authored-by: Jason Swails <[email protected]>
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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.