def test6_SuCOS(self):
"""Complains if wrong input file format"""
ref_sdf = "test_data/4e3g_lig.sdf"
prb_sdf = "test_data/4e3g_lig.pdb"
with self.assertRaises(ValueError):
calc_SuCOS.main(ref_sdf, prb_sdf)
def test7_SuCOS(self):
"""Prb molecule same as ref but with OH missing"""
ref_sdf = "test_data/4e3g_lig.sdf"
prb_sdf = "test_data/4e3g_lig_OHmissing.sdf"
calc_SuCOS.main(ref_sdf, prb_sdf)
outfile = "%s_SuCOS_score.sdf" % os.path.splitext(prb_sdf)[0]
assert os.path.isfile(outfile)
ms = Chem.SDMolSupplier(outfile)
assert len(ms) == 1
SuCOS_score = float(ms[0].GetProp("SuCOS_score"))
assert SuCOS_score < 1
# More groups missing
prb_sdf = "test_data/benzene.sdf"
calc_SuCOS.main(ref_sdf, prb_sdf)
outfile = "%s_SuCOS_score.sdf" % os.path.splitext(prb_sdf)[0]
assert os.path.isfile(outfile)
ms = Chem.SDMolSupplier(outfile)
assert len(ms) == 1
SuCOS_score2 = float(ms[0].GetProp("SuCOS_score"))
assert SuCOS_score2 < 1
assert SuCOS_score2 < SuCOS_score
def test5_SuCOS(self):
"""Prb molecule is same as ref but with extra group"""
ref_sdf = "test_data/4e3g_lig.sdf"
prb_sdf = "test_data/4e3g_lig_Ph.sdf"
calc_SuCOS.main(ref_sdf, prb_sdf)
outfile = "%s_SuCOS_score.sdf" % os.path.splitext(prb_sdf)[0]
assert os.path.isfile(outfile)
ms = Chem.SDMolSupplier(outfile)
assert len(ms) == 1
SuCOS_score = float(ms[0].GetProp("SuCOS_score"))
assert isclose(SuCOS_score, 1.0, abs_tol=1e-2)
def test4_SuCOS(self):
"""Test rotation of COOH group. NB it lowers score by approx 0.05"""
ref_sdf = "test_data/4e3g_lig.sdf"
prb_sdf = "test_data/4e3g_lig_rotatedCOOH.sdf"
calc_SuCOS.main(ref_sdf, prb_sdf)
outfile = "%s_SuCOS_score.sdf" % os.path.splitext(prb_sdf)[0]
assert os.path.isfile(outfile)
ms = Chem.SDMolSupplier(outfile)
assert len(ms) == 1
SuCOS_score = float(ms[0].GetProp("SuCOS_score"))
assert isclose(SuCOS_score, 0.95, abs_tol=1e-2)
def test2_SuCOS(self):
"""Check Hydrogens don't affect score"""
ref_sdf = "test_data/4e3g_lig.sdf"
prb_sdf = "test_data/4e3g_ligH.sdf"
calc_SuCOS.main(ref_sdf, prb_sdf)
outfile = "%s_SuCOS_score.sdf" % os.path.splitext(prb_sdf)[0]
assert os.path.isfile(outfile)
ms = Chem.SDMolSupplier(outfile)
assert len(ms) == 1
SuCOS_score = float(ms[0].GetProp("SuCOS_score"))
assert isclose(SuCOS_score, 1.0, abs_tol=1e-2)
def test3_SuCOS(self):
"""Test multiple prb molecules"""
ref_sdf = "test_data/4e3g_lig.sdf"
prb_sdf = "test_data/mols.sdf"
calc_SuCOS.main(ref_sdf, prb_sdf)
outfile = "%s_SuCOS_score.sdf" % os.path.splitext(prb_sdf)[0]
assert os.path.isfile(outfile)
ms = Chem.SDMolSupplier(outfile)
assert len(ms) == 6
for m in ms:
SuCOS_score = float(m.GetProp("SuCOS_score"))
assert SuCOS_score != 0
def test8_SuCOS(self):
"""Another test to check Hydrogens don't affect score"""
ref_sdf = "test_data/3adu_lig.sdf"
prb_sdf = "test_data/3ads_lig.sdf"
refH_sdf = "test_data/3adu_ligH.sdf"
prbH_sdf = "test_data/3ads_ligH.sdf"
SuCOS_score1 = calc_SuCOS.main(ref_sdf, prb_sdf)
SuCOS_score2 = calc_SuCOS.main(refH_sdf, prbH_sdf)
SuCOS_score3 = calc_SuCOS.main(refH_sdf, prb_sdf)
SuCOS_score4 = calc_SuCOS.main(ref_sdf, prbH_sdf)
assert SuCOS_score1 == SuCOS_score2
assert SuCOS_score1 == SuCOS_score3
assert SuCOS_score1 == SuCOS_score4
def test10_SuCOS(self):
"""Testing to make sure SuCOS score is not > 1 with a
molecule and itself"""
from rdkit.Chem import rdMolAlign
ref_sdf = "test_data/3ivc_ligand.sdf"
ref_ms = Chem.SDMolSupplier(ref_sdf)
gen_mol = Chem.Mol(ref_ms[0])
ref_mol = Chem.Mol(ref_ms[0])
pyO3A = rdMolAlign.GetO3A(gen_mol, ref_mol).Align()
SuCOS_score = calc_SuCOS.main(gen_mol, ref_mol, write=False)
assert SuCOS_score <= 1
def test9_SuCOS(self):
"""Testing to make sure SuCOS score is not > 1 with a
molecule and itself"""
ref_sdf = "test_data/3ivc_ligand.sdf"
SuCOS_score = calc_SuCOS.main(ref_sdf, ref_sdf)
assert SuCOS_score <= 1
