Enumerate input molecule with tautomers #1780
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I think the same issue as in enumerate_protomers (#1779) pops up here (see suggestions), though I haven't actually found a molecule that doesn't return itself. Also need to remove the +1 from max states in OpenEye and update a docstring here or there.
Does tautomer have a different meaning in cheminformatics than in ochem? I couldn't come up with any keto-enol tautomerisation with this, which I thought was, like, THE tautomerisation.
Notebook I messed around in for posterity: tautomers.zip
| @@ -945,16 +949,13 @@ def enumerate_tautomers( | |||
| tautomer_options.SetCarbonHybridization(False) | |||
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- tautomer_options.SetMaxTautomersGenerated(max_states + 1)
+ tautomer_options.SetMaxTautomersGenerated(max_states)No longer need to generate an extra state so we can drop the input.
| self, | ||
| molecule: "Molecule", | ||
| max_states: int = 20, | ||
| ) -> list["Molecule"]: | ||
| """ | ||
| Enumerate the possible tautomers of the current molecule |
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| Enumerate the possible tautomers of the current molecule | |
| Enumerate some possible tautomers of the current molecule |
| molecules: List[openff.toolkit.topology.Molecule] | ||
| A list of openff.toolkit.topology.Molecule instances excluding the input molecule. | ||
| molecules: list[openff.toolkit.Molecule] | ||
| A list of openff.toolkit.Molecule instances excluding the input molecule. |
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| A list of openff.toolkit.Molecule instances excluding the input molecule. | |
| A list of openff.toolkit.Molecule instances, including the input molecule unless it is pruned by the ``max_states`` argument. |
| ) -> List["Molecule"]: | ||
| self, | ||
| molecule: "Molecule", | ||
| max_states: int = 20, |
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I think we could go bigger than 20 if we wanted!
| molecules: List[openff.toolkit.topology.Molecule] | ||
| A list of openff.toolkit.topology.Molecule instances not including the input molecule. | ||
| molecules: list[openff.toolkit.Molecule] | ||
| A list of openff.toolkit.Molecule instances including the input molecule. |
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| A list of openff.toolkit.Molecule instances including the input molecule. | |
| A list of openff.toolkit.Molecule instances including the input molecule unless it has been pruned by the ``max_states`` argument. |
| self, | ||
| molecule: "Molecule", | ||
| max_states: int = 20, | ||
| ) -> list["Molecule"]: | ||
| """ | ||
| Enumerate the possible tautomers of the current molecule. |
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| Enumerate the possible tautomers of the current molecule. | |
| Enumerate some possible tautomers of the current molecule. |
| @@ -12,6 +12,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w | |||
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| ### Behavior changes | |||
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| - [PR #17XX](https://github.com/openforcefield/openff-toolkit/pull/17XX): `Molecule.enumerate_tautomers` now includes the input molecule in the returned list. | |||
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| - [PR #17XX](https://github.com/openforcefield/openff-toolkit/pull/17XX): `Molecule.enumerate_tautomers` now includes the input molecule in the returned list. | |
| - [PR #1780](https://github.com/openforcefield/openff-toolkit/pull/1780): `Molecule.enumerate_tautomers` now includes the input molecule in the returned list. |
Suggestion #2 in #1464 (comment)