def test_basics(self):
fname = os.path.join(os.environ["RDBASE"], "External", "FreeSASA",
"test_data", "1d3z.pdb")
mol = Chem.MolFromPDBFile(fname)
radii = rdFreeSASA.classifyAtoms(mol)
for atom in mol.GetAtoms():
self.assertEqual(expected[atom.GetIdx()][3], radii[atom.GetIdx()])
leeRichards = 5004.79964427
shrakerupley = 5000.340175
sasa = rdFreeSASA.CalcSASA(mol, radii=radii)
self.assertTrue((sasa - leeRichards) < 1e-5)
opts = rdFreeSASA.SASAOpts(rdFreeSASA.ShrakeRupley, rdFreeSASA.Protor)
sasa = rdFreeSASA.CalcSASA(mol, radii=radii, opts=opts)
self.assertTrue((sasa - shrakerupley) < 1e-5)
apolar = rdFreeSASA.CalcSASA(
mol,
radii,
query=rdFreeSASA.MakeFreeSasaAPolarAtomQuery(),
opts=opts)
polar = rdFreeSASA.CalcSASA(
mol,
radii,
query=rdFreeSASA.MakeFreeSasaPolarAtomQuery(),
opts=opts)
self.assertTrue((polar + apolar - 5000.340175) < 1e-5)
def cal_sasa(m):
radii = rdFreeSASA.classifyAtoms(m)
radii = classifyAtoms(m)
# radii = rdFreeSASA.classifyAtoms(m1)
sasa = rdFreeSASA.CalcSASA(m,
radii,
query=rdFreeSASA.MakeFreeSasaAPolarAtomQuery())
return sasa
def test_opts(self):
fname = os.path.join(os.environ["RDBASE"], "External", "FreeSASA",
"test_data", "1d3z.pdb")
mol = Chem.MolFromPDBFile(fname)
radii = rdFreeSASA.classifyAtoms(mol)
for atom in mol.GetAtoms():
self.assertEqual(expected[atom.GetIdx()][3], radii[atom.GetIdx()])
leeRichards = 5004.79964427
shrakerupley = 5000.340175
opts = rdFreeSASA.SASAOpts()
for alg, res in ((rdFreeSASA.ShrakeRupley, shrakerupley),
(rdFreeSASA.LeeRichards, leeRichards)):
opts.algorithm = alg
sasa = rdFreeSASA.CalcSASA(mol, radii=radii, opts=opts)
self.assertTrue(abs(sasa - res) < 1e-5)
leeRichards = 5009.93014166
shrakerupley = 4977.7709106
opts = rdFreeSASA.SASAOpts()
opts.probeRadius = 2.0
for alg, res in ((rdFreeSASA.ShrakeRupley, shrakerupley),
(rdFreeSASA.LeeRichards, leeRichards)):
opts.algorithm = alg
sasa = rdFreeSASA.CalcSASA(mol, radii=radii, opts=opts)
self.assertTrue(abs(sasa - res) < 1e-5)
def _get_sasa(i):
conf = mol.GetConformer(i)
sasa = rdFreeSASA.CalcSASA(mol, radii, confIdx=conf.GetId())
conf.SetDoubleProp("rdkit_free_sasa", sasa)
return sasa