def test_from_rdkit(self):
rdkit_mol = Molecule(ligand_rdkit)
newmol = Molecule.from_rdkit(ligand_rdkit)
assert rdkit_mol[0].resid == newmol[0].resid
mol = Chem.MolFromSmiles("CCO")
newmol = Molecule.from_rdkit(mol)
assert newmol[0].resid == ResidueId("UNL", 1)
newmol = Molecule.from_rdkit(mol, "FOO", 42, "A")
assert newmol[0].resid == ResidueId("FOO", 42, "A")
class TestMolecule(TestBaseRDKitMol):
@pytest.fixture(scope="class")
def mol(self):
return Molecule(rdkit_mol)
def test_mapindex(self, mol):
for atom in mol.GetAtoms():
assert atom.GetUnsignedProp("mapindex") == atom.GetIdx()
def test_from_mda(self):
rdkit_mol = Molecule(ligand_rdkit)
mda_mol = Molecule.from_mda(u, "resname LIG")
assert rdkit_mol[0].resid == mda_mol[0].resid
assert (rdkit_mol.HasSubstructMatch(mda_mol) and
mda_mol.HasSubstructMatch(rdkit_mol))
@pytest.mark.parametrize("key", [
0,
42,
-1,
"LYS49.A",
ResidueId("LYS", 49, "A")
])
def test_getitem(self, mol, key):
assert mol[key].resid is mol.residues[key].resid
def test_iter(self, mol):
for i, r in enumerate(mol):
assert r.resid == mol[i].resid
def test_n_residues(self, mol):
assert mol.n_residues == mol.residues.n_residues
def test_init(self, name, number, chain):
resid = ResidueId(name, number, chain)
name = name or "UNK"
number = number or 0
chain = chain or None
assert resid.name == name
assert resid.number == number
assert resid.chain == chain
def test_from_atom_empty(self, name, number, chain):
atom = Chem.Atom(1)
mi = Chem.AtomPDBResidueInfo()
if name is not None:
mi.SetResidueName(name)
if number is not None:
mi.SetResidueNumber(number)
if chain is not None:
mi.SetChainId(chain)
atom.SetMonomerInfo(mi)
resid = ResidueId.from_atom(atom)
assert resid == ResidueId()
def test_init_empty(self, name, number, chain):
resid = ResidueId(name, number, chain)
assert resid == ResidueId()
def test_getitem(self, residues, ix, resid, resid_str):
rg = ResidueGroup(residues)
resid = ResidueId(*resid)
assert rg[ix] == rg[resid]
assert rg[ix] == rg[resid_str]
def test_init(self, name, number, chain):
resid = ResidueId(name, number, chain)
assert resid.name == name
assert resid.number == number
assert resid.chain == chain
def test_eq(self):
name, number, chain = "ALA", 1, "A"
res1 = ResidueId(name, number, chain)
res2 = ResidueId(name, number, chain)
assert res1 == res2
def test_string_methods(self, resid_str, expected):
resid = ResidueId.from_string(resid_str)
assert resid == ResidueId(*expected)
assert str(resid) == resid_str
def test_generate(self, fp_class):
ifp = fp_class.generate(ligand_mol, protein_mol)
key = (ResidueId("LIG", 1, "G"), ResidueId("THR", 355, "B"))
bv = ifp[key]
assert isinstance(bv, np.ndarray)
assert bv[0] is np.True_
def test_from_string(self, resid_str, expected):
resid = ResidueId.from_string(resid_str)
assert resid == ResidueId(*expected)
