[ WIP ] Membrane support prototype #1561
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1561 +/- ##
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- Coverage 95.39% 93.23% -2.17%
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Files 189 189
Lines 16646 16922 +276
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- Hits 15880 15777 -103
- Misses 766 1145 +379
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| mapper = openfe.setup.KartografAtomMapper() | ||
| scorer = openfe.lomap_scorers.default_lomap_score | ||
| network_planner = openfe.ligand_network_planning.generate_minimal_spanning_network | ||
| ligand_network = network_planner(ligands=ligands, mappers=[mapper], scorer=scorer) | ||
| # get the first edge; it automatically displays in a Jupyter notebook | ||
| mapping = next(iter(ligand_network.edges)) |
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Consider having the ligand mapping for this edge a fixture and hard coded as we don't want changes in the other tools to cause issues with this test?
| assert isinstance(sampler, MultiStateSampler) | ||
| assert sampler.is_periodic | ||
| assert isinstance(sampler._thermodynamic_states[0].barostat, MonteCarloMembraneBarostat) | ||
| assert sampler._thermodynamic_states[1].pressure == 1 * omm_unit.bar | ||
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| # Check we have the right number of atoms in the PDB | ||
| pdb = mdt.load_pdb("hybrid_system.pdb") | ||
| assert pdb.n_atoms == 4667 |
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Should we be checking the box vectors as well?
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Checking the box vectors now!
| assert pytest.approx(geom[0][0].phi_C0) == -0.745093 * offunit.radian | ||
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| class TestA2AMembraneDryRun: |
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Do the tests here make the test_dry_run_membrane_complex test redundant they seem to be testing similar things on the same system?
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Yes, forgot to remove it, did so now!
jthorton
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This looks great @hannahbaumann great job! A few nits but nothing major!
| # - Frequencey as defined in `thermo_settings` | ||
| # Reference: | ||
| # https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5966 | ||
| if thermo_settings.membrane and not has_solvent: |
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Is this the only time the thermo_settings.membrane flag is used?
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Yes! I think whether we need it or not may depend on if we have a ProteinMembraneComponent that really only does that, or if we want to have a more general ExplicitSoventComponent that can handle all kinds of things and then we need a way to say that this one has a membrane and needs the MonteCarloMembraneBarostat.
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…y/openfe into membrane_prototype
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…y/openfe into membrane_prototype
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No API break detected ✅ |
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