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Fix SepTop resume test #2048

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Merged
IAlibay merged 2 commits into from
Jun 29, 2026
Merged

Fix SepTop resume test #2048

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0440eff
fix the test
IAlibay Jun 28, 2026
1408277
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 28, 2026
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13 changes: 13 additions & 0 deletions src/openfe/tests/protocols/openmm_septop/test_septop_resume.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import shutil

import gufe
import numpy as np
import openmm
import pytest
from gufe.protocols.errors import ProtocolUnitExecutionError
Expand Down Expand Up @@ -233,9 +234,21 @@ def test_resume(
)

# Finally we analyze the results
# First we get some inputs
selection_indices = np.array(setup_results["selection_indices"])
ligand_A_full_indices = np.array(setup_results["ligand_A_indices"])
ligand_B_full_indices = np.array(setup_results["ligand_B_indices"])
ligand_A_indices = np.where(np.isin(selection_indices, ligand_A_full_indices))[0].tolist()
ligand_B_indices = np.where(np.isin(selection_indices, ligand_B_full_indices))[0].tolist()

_ = analysis_unit.run(
trajectory=sim_results["trajectory"],
checkpoint=sim_results["checkpoint"],
pdb_file=setup_results["subsampled_pdb_structure"],
ligand_A_indices=ligand_A_indices,
ligand_B_indices=ligand_B_indices,
smc_A=analysis_unit._inputs["alchemical_components"]["stateA"][0],
smc_B=analysis_unit._inputs["alchemical_components"]["stateB"][0],
scratch_basepath=tmp_path,
shared_basepath=tmp_path,
)
Expand Down
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