diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py index 847f548b8e16adb7e3d81145b85547de18885926..b5c62d2763b1fa9954d10c47187225a18916dccb 100644 --- a/modules/mol/alg/pymod/ligand_scoring.py +++ b/modules/mol/alg/pymod/ligand_scoring.py @@ -337,7 +337,7 @@ def ResidueToGraph(residue, by_atom_index=False): return nxg -def LigandRMSD(model_ligand, target_ligand, transformation=geom.Mat4(), +def SCRMSD(model_ligand, target_ligand, transformation=geom.Mat4(), substructure_match=False): """Calculate symmetry-corrected RMSD. @@ -464,4 +464,4 @@ class NoSymmetryError(Exception): """ pass -__all__ = ["LigandScorer", "ResidueToGraph", "LigandRMSD", "NoSymmetryError"] +__all__ = ["LigandScorer", "ResidueToGraph", "SCRMSD", "NoSymmetryError"] diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py index d7cf4ef07a0ed0fe7d1eed5ee4d74b9fd9518081..8ee493364fb41ea512fe0ecc18d647c79c1b3819 100644 --- a/modules/mol/alg/tests/test_ligand_scoring.py +++ b/modules/mol/alg/tests/test_ligand_scoring.py @@ -179,8 +179,8 @@ class TestLigandScoring(unittest.TestCase): with self.assertRaises(NoSymmetryError): ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d_sub, trg_g3d1, substructure_match=True) - def test_LigandRMSD(self): - """Test that LigandRMSD works. + def test_SCRMSD(self): + """Test that SCRMSD works. """ trg, trg_seqres = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True) mdl, mdl_seqres = io.LoadMMCIF(os.path.join('testfiles', "P84080_model_02.cif.gz"), seqres=True) @@ -191,23 +191,23 @@ class TestLigandScoring(unittest.TestCase): trg_g3d2 = trg.FindResidue("J", 1) mdl_g3d = mdl.FindResidue("L_2", 1) - rmsd = LigandRMSD(mdl_g3d, trg_g3d1) + rmsd = SCRMSD(mdl_g3d, trg_g3d1) self.assertAlmostEqual(rmsd, 2.21341e-06, 10) - rmsd = LigandRMSD(mdl_g3d, trg_g3d2) + rmsd = SCRMSD(mdl_g3d, trg_g3d2) self.assertAlmostEqual(rmsd, 61.21325, 4) # Ensure we raise a NoSymmetryError if the ligand is wrong with self.assertRaises(NoSymmetryError): - LigandRMSD(mdl_g3d, trg_mg1) + SCRMSD(mdl_g3d, trg_mg1) with self.assertRaises(NoSymmetryError): - LigandRMSD(mdl_g3d, trg_afb1) + SCRMSD(mdl_g3d, trg_afb1) # Assert that transform works trans = geom.Mat4(-0.999256, 0.00788487, -0.0377333, -15.4397, 0.0380652, 0.0473315, -0.998154, 29.9477, -0.00608426, -0.998848, -0.0475963, 28.8251, 0, 0, 0, 1) - rmsd = LigandRMSD(mdl_g3d, trg_g3d2, transformation=trans) + rmsd = SCRMSD(mdl_g3d, trg_g3d2, transformation=trans) self.assertAlmostEqual(rmsd, 0.293972, 5) # Assert that substructure matches work @@ -215,8 +215,8 @@ class TestLigandScoring(unittest.TestCase): trg_g3d1_sub = trg_g3d1.Select("aindex>6019").residues[0] # Skip PA, PB and O[1-3]A and O[1-3]B. mdl_g3d_sub = mdl_g3d.Select("aindex>1447").residues[0] # Skip PA, PB and O[1-3]A and O[1-3]B. with self.assertRaises(NoSymmetryError): - LigandRMSD(mdl_g3d, trg_g3d1_sub) # no full match - rmsd = LigandRMSD(mdl_g3d, trg_g3d1_sub, substructure_match=True) + SCRMSD(mdl_g3d, trg_g3d1_sub) # no full match + rmsd = SCRMSD(mdl_g3d, trg_g3d1_sub, substructure_match=True) if __name__ == "__main__":