def test_multiple_mutations(pdb3aid):
mol = pdb3aid
mut = mdt.mutate_residues(
mol, ['A.2S', 'B.3S']) # Mutate Chain A res 2 and B 3 to SER
assert [r.resname
for r in mut.chains['A'].get_residues(pdbindex=2)] == ['SER']
assert [r.resname
for r in mut.chains['B'].get_residues(pdbindex=3)] == ['SER']
def test_mutation_nomenclature_string_only(pdb3aid):
mol = pdb3aid
res25 = mol.get_residues(pdbindex=25)
assert len(res25) == 2
assert [r.resname for r in res25] == ['ASP', 'ASP']
mut = mdt.mutate_residues(mol, 'D25M') # Mutate ALA43 to MET43
assert mut.get_residues()
mut25 = mut.get_residues(pdbindex=25)
assert len(mut25) == 2
assert [r.resname for r in mut25] == ['MET', 'MET']
def test_mutation_nomenclature_string_only(pdb3aid):
mol = pdb3aid
res25 = mol.get_residues(pdbindex=25)
assert len(res25) == 2
assert [r.resname for r in res25] == ['ASP', 'ASP']
mut = mdt.mutate_residues(mol, 'D25M') # Mutate ALA43 to MET43
assert mut.get_residues()
mut25 = mut.get_residues(pdbindex=25)
assert len(mut25) == 2
assert [r.resname for r in mut25] == ['MET', 'MET']
def test_mutation_topology(pdb1yu8):
""" Test the topology of the backbone atoms for a mutated molecule. """
molecule = pdb1yu8
mutation_residues = ["X.13G"]
mutated_molecule = mdt.mutate_residues(molecule, mutation_residues)
# Check that the number of bonds for backbone atoms match.
for res, mut_res in zip(molecule.residues, mutated_molecule.residues):
if not res.backbone:
continue
for atom in res.backbone:
bonds = [bond for bond in molecule.bond_graph[atom] if bond.name in res.backbone]
mut_atom = mutated_molecule.chains["X"].residues[mut_res.name].atoms[atom.name]
mut_bonds = mutated_molecule.bond_graph[mut_atom]
mut_bonds = [bond for bond in mutated_molecule.bond_graph[mut_atom] \
if bond.name in mut_res.backbone]
assert len(bonds) == len(mut_bonds)
def test_mutation_topology(pdb1yu8):
""" Test the topology of the backbone atoms for a mutated molecule. """
molecule = pdb1yu8
mutation_residues = ["X.13G"]
mutated_molecule = mdt.mutate_residues(molecule, mutation_residues)
# Check that the number of bonds for backbone atoms match.
for res, mut_res in zip(molecule.residues, mutated_molecule.residues):
if not res.backbone:
continue
for atom in res.backbone:
bonds = [
bond for bond in molecule.bond_graph[atom]
if bond.name in res.backbone
]
mut_atom = mutated_molecule.chains["X"].residues[
mut_res.name].atoms[atom.name]
mut_bonds = mutated_molecule.bond_graph[mut_atom]
mut_bonds = [bond for bond in mutated_molecule.bond_graph[mut_atom] \
if bond.name in mut_res.backbone]
assert len(bonds) == len(mut_bonds)
def _mutate_and_check(mol, residx, resname, allatoms):
newmol = mdt.mutate_residues(mol, {mol.residues[residx]: resname})
assert newmol.num_chains == mol.num_chains
assert mol.num_residues == newmol.num_residues
foundnew = False
for i, (res, newres) in enumerate(zip(mol.residues, newmol.residues)):
if i == residx:
foundnew = True
assert newres.resname == resname
assert newres.name == resname+str(newres.pdbindex)
atomnames = set(atom.name for atom in newres)
assert len(atomnames) == newres.num_atoms
assert atomnames.issubset(allatoms)
else:
assert res.name == newres.name
assert res.num_atoms == newres.num_atoms
for oldatom, newatom in zip(res, newres):
assert oldatom.name == newatom.name
assert oldatom.atnum == newatom.atnum
if not foundnew:
assert oldatom.pdbindex == newatom.pdbindex
def _mutate_and_check(mol, residx, resname, allatoms):
newmol = mdt.mutate_residues(mol, {mol.residues[residx]: resname})
assert newmol.num_chains == mol.num_chains
assert mol.num_residues == newmol.num_residues
foundnew = False
for i, (res, newres) in enumerate(zip(mol.residues, newmol.residues)):
if i == residx:
foundnew = True
assert newres.resname == resname
assert newres.name == resname + str(newres.pdbindex)
atomnames = set(atom.name for atom in newres)
assert len(atomnames) == newres.num_atoms
assert atomnames.issubset(allatoms)
else:
assert res.name == newres.name
assert res.num_atoms == newres.num_atoms
for oldatom, newatom in zip(res, newres):
assert oldatom.name == newatom.name
assert oldatom.atnum == newatom.atnum
if not foundnew:
assert oldatom.pdbindex == newatom.pdbindex
def test_mutate_docstring_dict_example(pdb3aid):
mol = pdb3aid
assert mol.residues[5].resname != 'ALA'
mut = mdt.mutate_residues(mol, {mol.residues[5]: 'ALA'}) # mutate residue 5 to ALA
assert mut.residues[5].resname == 'ALA'
def test_multiple_mutations(pdb3aid):
mol = pdb3aid
mut = mdt.mutate_residues(mol, ['A.2S', 'B.3S']) # Mutate Chain A res 2 and B 3 to SER
assert [r.resname for r in mut.chains['A'].get_residues(pdbindex=2)] == ['SER']
assert [r.resname for r in mut.chains['B'].get_residues(pdbindex=3)] == ['SER']
def test_mutate_docstring_dict_example(pdb3aid):
mol = pdb3aid
assert mol.residues[5].resname != 'ALA'
mut = mdt.mutate_residues(
mol, {mol.residues[5]: 'ALA'}) # mutate residue 5 to ALA
assert mut.residues[5].resname == 'ALA'