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RDKit converter inferring #4305
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Hello @cbouy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-08-26 15:54:51 UTC |
Linter Bot Results:Hi @cbouy! Thanks for making this PR. We linted your code and found the following: Some issues were found with the formatting of your code.
Please have a look at the Please note: The |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #4305 +/- ##
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- Coverage 93.62% 93.61% -0.01%
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Files 173 186 +13
Lines 21419 22575 +1156
Branches 3978 4004 +26
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+ Hits 20053 21134 +1081
- Misses 903 976 +73
- Partials 463 465 +2 ☔ View full report in Codecov by Sentry. |
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@dataclass(frozen=True) | ||
class MDAnalysisInferer: |
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No code changes here apart from refactoring all the different bond order inferring functions under this class, a deprecation warning if specifying max_iter
anywhere else than in __init__
, and some code formatting with black
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template : rdkit.Chem.rdchem.Mol | ||
Molecule containing the bond orders and charges. | ||
adjust_hydrogens: bool, default = True |
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Just checking that the default to True
sounds reasonable to everyone? Otherwise if you have a charged mol you'll need to add explicit hydrogens on the template to have an exact match with your input mol which may be a bit of a pain.
This was originally in ProLIF to read PDBQT files as valid RDKit mols, happy to add it here (and should be fine license-wise)
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def __call__(self, mol: "Chem.Mol") -> "Chem.Mol": | ||
new = Chem.Mol(mol) | ||
DetermineBondOrders(new, charge=self.charge) |
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RDKit now also has a DetermineBonds
which could be interesting to add as an alternative to guess_bonds
? Or at least in the RDKitConverter which requires bonds anyway
Thanks @cbouy ! From a quick look this seems great, I'll try to review it at some point over the next week (unless someone gets to it first). P.S. For others that might review here - codecov seems to be throwing a bunch of "uncovered code" messages (when they seem like they are). Cycling the PR might clear them, but I don't think it's a major necessity right now. |
@cbouy are you still working on the PR or is this ready for review? |
Should be ready for review, I'll just need to update the changelog when ready for merging |
That's great. Can you please add the CHANGELOG update right away, even if it will require resolving a merge conflict later? The summary there tends to be really helpful for assessing a PR.... and typically no reviewer will green-light such a PR without the CHANGELOG in place anyway. |
@richardjgowers do you have capacity to shepherd the PR to completion? If not please let me know and un-assign yourself. Thanks! |
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Sorry for the spam, should be good now! |
@richardjgowers are you able to review this PR yourself or is there someone you could ping? From my very cursory glance, this looks pretty much ready and would be good to get in, given our roadmap towards "better chemistry". |
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Not sure why one of the azure test is timing out, or why the bot removed some of the tags but this is re-ready for review 😅 |
/azp run |
Azure Pipelines successfully started running 1 pipeline(s). |
Fixes part of #3996
Changes made in this Pull Request:
RDKitInferring
module. The bond order and charges inferer has been move to aMDAnalysisInferer
dataclass in there.NoImplicit
parameter toimplicit_hydrogens
and added a separateinferer
argument (defaults toMDAnalysisInferer()
. PassingNoImplicit
to any of the relevant functions will issue a warning and make the necessary arrangements to execute the code in a backwards-compatible way (i.e.implicit_hydrogens=not NoImplicit
andif NoImplicit is False: inferer=None
).TemplateInferer
that wraps around RDKit'sAssignBondOrdersFromTemplate
. There's an additionaladjust_hydrogens
parameter that when set toTrue
allows one to assign bond orders from a template molecule with implicit hydrogens to an input molecule with explicit hydrogens (which won't work with the baseAssignBondOrdersFromTemplate
for charged molecules where the charged atom has a hydrogen). I originally had this code in ProLIF for dealing with PDBQT inputs, figured it would be worth here as well.rdDetermineBonds
inferring wrapper as showcased here.PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4305.org.readthedocs.build/en/4305/