diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py index 1546ae688068a378eba223a694e3d6261a85b0ed..1b2d1b2447a20a4fc9ccba9c517784175da4fdee 100644 --- a/modules/mol/alg/tests/test_ligand_scoring.py +++ b/modules/mol/alg/tests/test_ligand_scoring.py @@ -7,7 +7,7 @@ from ost import io, mol, geom # check if we can import: fails if numpy or scipy not available try: from ost.mol.alg.ligand_scoring import * - import ost.mol.alg.ligand_scoring + from ost.mol.alg import ligand_scoring except ImportError: print("Failed to import ligand_scoring.py. Happens when numpy, scipy or " "networkx is missing. Ignoring test_ligand_scoring.py tests.") @@ -132,18 +132,18 @@ class TestLigandScoring(unittest.TestCase): with self.assertRaises(RuntimeError): sc = LigandScorer(mdl, trg, mdl_ligs, [lig0, lig1]) - def test_ResidueToGraph(self): - """Test that ResidueToGraph works as expected + def test__ResidueToGraph(self): + """Test that _ResidueToGraph works as expected """ mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf")) - graph = ResidueToGraph(mdl_lig.residues[0]) + graph = _ResidueToGraph(mdl_lig.residues[0]) assert len(graph.edges) == 34 assert len(graph.nodes) == 32 # Check an arbitrary node assert [a for a in graph.adj["14"].keys()] == ["13", "29"] - graph = ResidueToGraph(mdl_lig.residues[0], by_atom_index=True) + graph = _ResidueToGraph(mdl_lig.residues[0], by_atom_index=True) assert len(graph.edges) == 34 assert len(graph.nodes) == 32 # Check an arbitrary node @@ -161,15 +161,15 @@ class TestLigandScoring(unittest.TestCase): trg_g3d2 = trg.FindResidue("J", 1) mdl_g3d = mdl.FindResidue("L_2", 1) - sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1) + sym = ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1) assert len(sym) == 72 - sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1, by_atom_index=True) + sym = ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1, by_atom_index=True) assert len(sym) == 72 # Test that we can match ions read from SDF sdf_lig = io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_0.sdf")) - sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(trg_mg1, sdf_lig.residues[0], by_atom_index=True) + sym = ligand_scoring._ComputeSymmetries(trg_mg1, sdf_lig.residues[0], by_atom_index=True) assert len(sym) == 1 # Test that it works with views and only consider atoms in the view @@ -178,19 +178,19 @@ class TestLigandScoring(unittest.TestCase): trg_g3d1_sub = trg_g3d1.Select("aindex>6019").residues[0] mdl_g3d_sub = mdl_g3d.Select("aindex>1447").residues[0] - sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1_sub) + sym = ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1_sub) assert len(sym) == 6 - sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1_sub, by_atom_index=True) + sym = ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1_sub, by_atom_index=True) assert len(sym) == 6 # Substructure matches - sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1_sub, substructure_match=True) + sym = ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1_sub, substructure_match=True) assert len(sym) == 6 # Missing atoms only allowed in target, not in model with self.assertRaises(NoSymmetryError): - ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1, substructure_match=True) + ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1, substructure_match=True) def test_SCRMSD(self): """Test that SCRMSD works.