def test_run_residues(self, fp_class):
fp_class.run(u.trajectory[0:1],
ligand_ag,
protein_ag,
residues="all",
progress=False)
lig_id = ResidueId.from_string("LIG1.G")
assert hasattr(fp_class, "ifp")
assert len(fp_class.ifp) == 1
res = ResidueId.from_string("LYS387.B")
assert (lig_id, res) in fp_class.ifp[0].keys()
fp_class.run(u.trajectory[1:2],
ligand_ag,
protein_ag,
residues=["ASP129.A"],
progress=False)
assert hasattr(fp_class, "ifp")
assert len(fp_class.ifp) == 1
res = ResidueId.from_string("ASP129.A")
assert (lig_id, res) in fp_class.ifp[0].keys()
fp_class.run(u.trajectory[:3],
ligand_ag,
protein_ag,
residues=None,
progress=False)
assert hasattr(fp_class, "ifp")
assert len(fp_class.ifp) == 3
assert len(fp_class.ifp[0]) > 1
res = ResidueId.from_string("VAL201.A")
assert (lig_id, res) in fp_class.ifp[0].keys()
u.trajectory[0]
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")
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()
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(self, name, number, chain):
atom = Chem.Atom(1)
mi = Chem.AtomPDBResidueInfo()
if name:
mi.SetResidueName(name)
if number:
mi.SetResidueNumber(number)
if chain:
mi.SetChainId(chain)
atom.SetMonomerInfo(mi)
resid = ResidueId.from_atom(atom)
assert resid.name == name
assert resid.number == number
assert resid.chain == chain
def test_pocket_residues():
resids = get_residues_near_ligand(ligand_mol, protein_mol)
residues = [
"TYR38.A", "TYR40.A", "GLN41.A", "VAL102.A", "SER106.A", "TYR109.A",
"THR110.A", "TRP115.A", "TRP125.A", "LEU126.A", "ASP129.A", "ILE130.A",
"THR131.A", "CYS133.A", "THR134.A", "ILE137.A", "ILE180.A", "GLU198.A",
"CYS199.A", "VAL200.A", "VAL201.A", "ASN202.A", "THR203.A", "TYR208.A",
"THR209.A", "VAL210.A", "TYR211.A", "SER212.A", "THR213.A", "VAL214.A",
"GLY215.A", "ALA216.A", "PHE217.A", "TRP327.B", "PHE330.B", "PHE331.B",
"ILE333.B", "SER334.B", "LEU335.B", "MET337.B", "PRO338.B", "LEU348.B",
"ALA349.B", "ILE350.B", "PHE351.B", "ASP352.B", "PHE353.B", "PHE354.B",
"THR355.B", "TRP356.B", "GLY358.B", "TYR359.B"
]
for res in residues:
r = ResidueId.from_string(res)
assert r in resids
def test_from_atom(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)
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_string_methods(self, resid_str, expected):
resid = ResidueId.from_string(resid_str)
assert resid == ResidueId(*expected)
assert str(resid) == resid_str
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_init(self, mol):
resid = ResidueId.from_atom(mol.GetAtomWithIdx(0))
assert mol.resid == resid
def test_repr(self, resid_str):
resid = ResidueId.from_string(resid_str)
expected = f"ResidueId({resid.name}, {resid.number}, {resid.chain})"
assert repr(resid) == expected
def test_lt(self, res1, res2):
res1 = ResidueId.from_string(res1)
res2 = ResidueId.from_string(res2)
assert res1 < res2
def test_from_string(self, resid_str, expected):
resid = ResidueId.from_string(resid_str)
assert resid == ResidueId(*expected)
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_atom_no_mi(self):
atom = Chem.Atom(1)
resid = ResidueId.from_atom(atom)
assert resid.name is None
assert resid.number is None
assert resid.chain is None
def test_eq(self):
name, number, chain = "ALA", 1, "A"
res1 = ResidueId(name, number, chain)
res2 = ResidueId(name, number, chain)
assert res1 == res2
