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Add normalization code #1490

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lilyminium opened this issue Dec 11, 2022 · 0 comments
Open

Add normalization code #1490

lilyminium opened this issue Dec 11, 2022 · 0 comments

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@lilyminium
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Is your feature request related to a problem? Please describe.

Add code that "normalizes" unusual SMARTS patterns. This came up recently in both Lorenzo's parameter analysis and at MobleyLab/FreeSolv#51 . The code already exists for NAGL, so upstreaming it into the toolkit might be worthwhile.

Describe the solution you'd like

Normalization support in the toolkit.

Describe alternatives you've considered

This is a one-liner in RDKit -- rdkit.Chem.MolStandardize.rdMolStandardize.Normalize -- so it's not too much of a hassle to leave it separate. OpenEye has reaction support but I don't think has the RDKit normalization transformation catalogue easily usable.

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@lilyminium lilyminium mentioned this issue Dec 11, 2022
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