Fix networks

industry_benchmarks/utils/tests/test_fix_networks.py

@@ -0,0 +1,96 @@
+import pathlib
+import pytest
+from importlib import resources
+import gufe
+import os
+import glob
+from ..fix_networks import (
+ parse_alchemical_network,
+ parse_results,
+ alchemical_network_to_ligand_network,
+ fix_network,
+)
+
+
+@pytest.fixture
+def results():
+ with resources.files("utils.tests.data.bace_results") as d:
+ yield glob.glob(f"{str(d)}/results_*_remove_edges/*json")
+
+
+@pytest.fixture
+def input_alchemical_network():
+ with resources.files("utils.tests.data.bace_results") as d:
+ yield str(d / "alchemicalNetwork/alchemical_network.json")
+
+
+@pytest.fixture
+def output_dir():
+ return pathlib.Path("utils/tests/data/bace_results/newNetwork")
+
+
+@pytest.fixture
+def expected_transformations():
+ return ["complex_spiro10_spiro1.json",
+ "complex_spiro1_spiro15.json",
+ "complex_spiro2_spiro15.json",
+ "complex_spiro5_spiro10.json",
+ "complex_spiro5_spiro6.json",
+ "complex_spiro6_spiro4.json",
+ "solvent_spiro10_spiro1.json",
+ "solvent_spiro1_spiro15.json",
+ "solvent_spiro2_spiro15.json",
+ "solvent_spiro5_spiro10.json",
+ "solvent_spiro5_spiro6.json",
+ "solvent_spiro6_spiro4.json",
+ "complex_spiro1_spiro10.json",
+ "complex_spiro15_spiro1.json",
+ "complex_spiro15_spiro2.json",
+ "complex_spiro10_spiro5.json",
+ "complex_spiro6_spiro5.json",
+ "complex_spiro4_spiro6.json",
+ "solvent_spiro1_spiro10.json",
+ "solvent_spiro15_spiro1.json",
+ "solvent_spiro15_spiro2.json",
+ "solvent_spiro10_spiro5.json",
+ "solvent_spiro6_spiro5.json",
+ "solvent_spiro4_spiro6.json",
+ "complex_spiro4_spiro10.json",
+ "complex_spiro10_spiro4.json",
+ "solvent_spiro4_spiro10.json",
+ "solvent_spiro10_spiro4.json",
+ ]
+
+
+def test_parse_alchemical_network(input_alchemical_network):
+ alchem_network = parse_alchemical_network(input_alchemical_network)
+ assert isinstance(alchem_network, gufe.AlchemicalNetwork)
+ # AlchemicalNetwork with 11 edges, meaning 22 transformations
+ assert len(alchem_network.edges) == 22
+
+
+def test_parse_results(results, input_alchemical_network):
+ result_alchem_network = parse_results(results, input_alchemical_network)
+ assert isinstance(result_alchem_network, gufe.AlchemicalNetwork)
+ # only 6 edges (12 transformations) had completed successfully
+ assert len(result_alchem_network.edges) == 12
+ ligand_network = alchemical_network_to_ligand_network(result_alchem_network)
+ assert isinstance(ligand_network, gufe.LigandNetwork)
+ # The resulting LigandNetwork should have 6 edges
+ assert len(ligand_network.edges) == 6
+
+
+def test_fix_network(results, input_alchemical_network, output_dir, expected_transformations, tmp_path):
+ temp_out_dir = tmp_path / output_dir
+ fix_network(results, input_alchemical_network, temp_out_dir)
+ assert os.path.isdir(temp_out_dir)
+ output_alchemical_network = temp_out_dir / 'alchemical_network.json'
+ assert output_alchemical_network.is_file()
+ new_transformations = glob.glob(f"{temp_out_dir}/transformations/*json")
+ # The direction of the transformation can switch, therefore include both
+ # directions in the expected_transformations
+ # Some of the scores of potential transformations are the same,
+ # therefore the new_transformations will not always be the same
+ assert len(new_transformations) == 12
+ for transform in new_transformations:
+ assert transform.split("/")[-1] in expected_transformations