Builders for classical md workflows #1088
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1088 +/- ##
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- Coverage 90.03% 89.93% -0.10%
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Files 147 154 +7
Lines 13460 13883 +423
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+ Hits 12119 12486 +367
- Misses 1341 1397 +56 ☔ View full report in Codecov by Sentry. |
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Superceded by #1135 |
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This PR implements ElectrolyteBuilder and SolventBenchmarkBuilder classes for analysis of trajectories generated by atomate2.openmm.
The core Builder classes are supported by a variety of utility functions that interact with MDAnalysis, SolvationAnalysis, and TransportAnalysis. In addition to the usual get_items, process_items, update_targets workflow, users can also manually create an MDAnalysis.Universe directly from the taskdoc with ElectrolyteBuilder.instantiate_universe. This makes manual analysis of a small number of systems much easier.
Everything is reasonably well tested and once CI passes this will be ready for review.
NOTE: this is essentially a vastly cleaned up version of PR #1010. I linearized the commit history so that this PR is an update of PR #1087, which can be reviewed separately and merged independently of this PR.