def _parameterize(self):
if not self.mol.ff:
params = mdt.create_ff_parameters(
self.mol,
charges=self.params.partial_charges,
baseff=self.params.gaff_version)
params.assign(self.mol)
def test_ff_assignment_doesnt_change_topology(pdb3aid):
m = pdb3aid
protein = mdt.Molecule(m.get_atoms('protein'))
ligand = mdt.Molecule(m.get_atoms('unknown'))
ligff = mdt.create_ff_parameters(ligand, charges='gasteiger')
mdt.guess_histidine_states(protein)
mol = protein.combine(ligand)
ff = mdt.forcefields.DefaultAmber()
ff.add_ff(ligff)
mdready = ff.create_prepped_molecule(mol)
assert mdready.num_residues == mol.num_residues
assert mdready.num_chains == mol.num_chains
for c1, c2 in zip(mdready.chains, mol.chains):
assert c1.name == c2.name
assert c1.num_residues == c2.num_residues
assert c1.index == c2.index
for newr, oldr in zip(mdready.residues, mol.residues):
assert newr.index == oldr.index
if newr.resname == 'HIS':
assert oldr.resname in 'HIS HID HIE HIP'.split()
else:
assert newr.resname == oldr.resname
assert newr.pdbindex == oldr.pdbindex
assert newr.chain.index == oldr.chain.index
for atom in oldr:
assert atom.name in newr
def test_ff_assignment_doesnt_change_topology(pdb3aid):
m = pdb3aid
protein = mdt.Molecule(m.get_atoms('protein'))
ligand = mdt.Molecule(m.get_atoms('unknown'))
ligff = mdt.create_ff_parameters(ligand, charges='gasteiger')
mdt.guess_histidine_states(protein)
mol = protein.combine(ligand)
ff = mdt.forcefields.DefaultAmber()
ff.add_ff(ligff)
mdready = ff.create_prepped_molecule(mol)
assert mdready.num_residues == mol.num_residues
assert mdready.num_chains == mol.num_chains
for c1, c2 in zip(mdready.chains, mol.chains):
assert c1.name == c2.name
assert c1.num_residues == c2.num_residues
assert c1.index == c2.index
for newr, oldr in zip(mdready.residues, mol.residues):
assert newr.index == oldr.index
if newr.resname == 'HIS':
assert oldr.resname in 'HIS HID HIE HIP'.split()
else:
assert newr.resname == oldr.resname
assert newr.pdbindex == oldr.pdbindex
assert newr.chain.index == oldr.chain.index
for atom in oldr:
assert atom.name in newr
def h2params():
mol = mdt.from_smiles('[H][H]')
mol.atoms[0].name = 'HA'
mol.atoms[1].name = 'HB'
mol.residues[0].name = 'H2'
params = mdt.create_ff_parameters(mol, charges='gasteiger')
return mol, params
def h2params():
mol = mdt.from_smiles('[H][H]')
mol.atoms[0].name = 'HA'
mol.atoms[1].name = 'HB'
mol.residues[0].name = 'H2'
params = mdt.create_ff_parameters(mol, charges='gasteiger')
return mol, params
def test_charge_models(ethylene, chargemodel):
mol = ethylene
if chargemodel == 'esp':
pytest.xfail("ESP not yet implemented")
assert not mol.ff
params = mdt.create_ff_parameters(mol, charges=chargemodel)
assert params is not None
_test_succesful_parameterization(mol)
def test_charge_models(ethylene, chargemodel):
mol = ethylene
if chargemodel == 'esp':
pytest.xfail("ESP not yet implemented")
assert not mol.ff
params = mdt.create_ff_parameters(mol, charges=chargemodel)
assert params is not None
_test_succesful_parameterization(mol)
def test_parameterize_multiple_identical_small_molecules():
m1 = mdt.from_smiles('O')
params = mdt.create_ff_parameters(m1, charges='am1-bcc')
assert params is not None
m2 = m1.copy()
m2.translate([4.0, 0.0, 0.0] * mdt.units.angstrom)
mol = m1.combine(m2)
ff = mdt.forcefields.DefaultAmber()
ff.add_ff(params)
ff.assign(mol)
_test_succesful_parameterization(mol)
def test_parameterize_multiple_identical_small_molecules():
m1 = mdt.from_smiles('O')
params = mdt.create_ff_parameters(m1, charges='am1-bcc')
assert params is not None
m2 = m1.copy()
m2.translate([4.0, 0.0, 0.0] * mdt.units.angstrom)
mol = m1.combine(m2)
ff = mdt.forcefields.DefaultAmber()
ff.add_ff(params)
ff.assign(mol)
_test_succesful_parameterization(mol)
def test_numeric_residue_name_1PYN(request, mol):
""" The ligand in this residue is named "941", which causes a little trickiness
"""
import parmed
mol = request.getfixturevalue(mol)
ligand = mdt.Molecule(mol.residues[283])
params = mdt.create_ff_parameters(ligand, charges='gasteiger')
params._file_list['mol.lib'].put('/tmp/tmp.lib')
contents = parmed.load_file('/tmp/tmp.lib')
assert len(contents) == 1
assert list(contents.keys())[0] == '941'
def _param_small_mol(cached_small_molecule, chargemodel):
mol = cached_small_molecule.copy()
params = mdt.create_ff_parameters(mol, charges=chargemodel, baseff='gaff2')
params.assign(mol)
mol.set_energy_model(mdt.models.ForceField)
return mol
def _param_small_mol(cached_small_molecule, chargemodel):
mol = cached_small_molecule.copy()
params = mdt.create_ff_parameters(mol, charges=chargemodel, baseff='gaff2')
params.assign(mol)
mol.set_energy_model(mdt.models.ForceField)
return mol
def test_parameterization_from_formats(objkey, request):
mol = request.getfixturevalue(objkey)
assert not mol.ff
params = mdt.create_ff_parameters(mol, charges='gasteiger')
assert params is not None
_test_succesful_parameterization(mol)
def test_parameterization_from_formats(objkey, request):
mol = request.getfixturevalue(objkey)
assert not mol.ff
params = mdt.create_ff_parameters(mol, charges='gasteiger')
assert params is not None
_test_succesful_parameterization(mol)