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Metal binding data, trajectories, and the start of stereochemistry #706

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merged 85 commits into from
Jun 16, 2023

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espottesmith
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This PR mainly adds a new feature/collection/dataset/etc. to MPcules, one describing the coordination behavior and related thermodynamics of metals.

In addition, I have added an API endpoint for molecules/tasks to grab optimization trajectories, similar to how it's done on the materials side, and I've added InChI strings and InChI-keys to molecule and molecule summary docs. These encode some stereo information, which isn't currently captured by the MPculeID.

Contributor Checklist

  • I have run the tests locally and they passed.
  • I have added tests, or extended existing tests, to cover any new features or bugs fixed in this PR

…. SHE (conversions to other electrodes can happen on front-end)
…etalBindingDoc, one for each metal in the molecule
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codecov-commenter commented May 9, 2023

Codecov Report

Patch coverage: 90.86% and project coverage change: -3.20 ⚠️

Comparison is base (c7ae50e) 90.71% compared to head (dda9686) 87.51%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #706      +/-   ##
==========================================
- Coverage   90.71%   87.51%   -3.20%     
==========================================
  Files         148       50      -98     
  Lines       11446     4246    -7200     
==========================================
- Hits        10383     3716    -6667     
+ Misses       1063      530     -533     
Impacted Files Coverage Δ
emmet-core/emmet/core/qchem/calc_types/utils.py 92.50% <ø> (ø)
emmet-core/emmet/core/structure.py 100.00% <ø> (ø)
emmet-core/emmet/core/task.py 100.00% <ø> (ø)
emmet-core/emmet/core/molecules/bonds.py 86.90% <50.00%> (+10.97%) ⬆️
emmet-core/emmet/core/molecules/thermo.py 84.21% <71.42%> (-3.29%) ⬇️
emmet-core/emmet/core/molecules/metal_binding.py 93.00% <93.00%> (ø)
emmet-core/emmet/core/molecules/summary.py 95.42% <95.65%> (-0.03%) ⬇️
emmet-core/emmet/core/elasticity.py 85.10% <100.00%> (-1.28%) ⬇️
emmet-core/emmet/core/mobility/migrationgraph.py 94.52% <100.00%> (ø)
emmet-core/emmet/core/molecules/redox.py 91.30% <100.00%> (-0.37%) ⬇️
... and 3 more

... and 105 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

@espottesmith
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Hey @munrojm (or anyone else): any idea why test_electronic_structure.py is failing? Seems there's an issue deep up the stack, at the pydash level?

@munrojm
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munrojm commented May 30, 2023

Hm, not too sure. I will take a look.

@espottesmith
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Hey, any update on this?

@munrojm
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munrojm commented Jun 10, 2023

Is it still an issue? FAILED emmet-builders/tests/test_qchem.py::test_molecules_builder appears to be the failing test at the moment. The ES builder tests seem okay.

@espottesmith
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No, seems to have resolved itself.

@munrojm munrojm merged commit 1774f3c into materialsproject:main Jun 16, 2023
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4 participants