def test_PDB_residue_name(self):
"""
It tests the PDB residue name and checks for consistency with
Molecule tag.
"""
def check_residue_name(name):
"""Check if residue names are valid in the output PDB file"""
with open('molecule.pdb') as f:
for line in f:
if line.startswith('HETATM'):
assert line[17:20] == name, 'Unexpected residue name'
ligand_path = get_data_file_path('ligands/BNZ.pdb')
# Checking tag assignation from PDB
molecule = Molecule(ligand_path)
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
assert molecule.tag == 'BNZ', 'Unexpected molecule tag'
molecule.to_pdb_file('molecule.pdb')
check_residue_name('BNZ')
# Checking set_tag() function
molecule = Molecule(ligand_path)
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
molecule.set_tag('TAG')
assert molecule.tag == 'TAG', 'Unexpected molecule tag'
molecule.to_pdb_file('molecule.pdb')
check_residue_name('TAG')
# Checking default tag assignment from SMILES
molecule = Molecule(smiles='c1ccccc1')
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
assert molecule.tag == 'UNK', 'Unexpected molecule tag'
molecule.to_pdb_file('molecule.pdb')
check_residue_name('UNK')
# Checking custom tag assignment from SMILES
molecule = Molecule(smiles='c1ccccc1', tag='BEN')
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
assert molecule.tag == 'BEN', 'Unexpected molecule tag'
molecule.to_pdb_file('molecule.pdb')
check_residue_name('BEN')
# Checking second custom tag assignment from SMILES
molecule = Molecule(smiles='c1ccccc1')
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
molecule.set_tag('BNZ')
assert molecule.tag == 'BNZ', 'Unexpected molecule tag'
molecule.to_pdb_file('molecule.pdb')
check_residue_name('BNZ')
def test_offpele_default_call(self):
LIGAND_PATH = 'ligands/BNZ.pdb'
ligand_path = get_data_file_path(LIGAND_PATH)
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
run_offpele(ligand_path, output=tmpdir)
def test_offpele_default_call(self):
"""
It checks the default call of offpele's main function.
"""
LIGAND_PATH = 'ligands/BNZ.pdb'
ligand_path = get_data_file_path(LIGAND_PATH)
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
run_offpele(ligand_path, output=tmpdir)
def test_offpele_custom_call(self):
LIGAND_PATH = 'ligands/BNZ.pdb'
ligand_path = get_data_file_path(LIGAND_PATH)
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
run_offpele(ligand_path,
forcefield=FORCEFIELD_NAME,
resolution=10,
charges_method='gasteiger',
output=tmpdir,
with_solvent=True,
as_datalocal=True)
def get_OPLS_parameters(self, molecule):
"""
It calls Schrodinger's ffld_server to parameterize a molecule
with OPLS.
.. todo ::
* Review PlopRotTemp's atom type fixes. Should we apply them here?
Parameters
----------
molecule : an offpele.topology.Molecule
The offpele's Molecule object
Returns
-------
OPLS_params : an OPLSParameters object
The set of lists of parameters grouped by parameter type.
Thus, the dictionary has the following keys: atom_names,
atom_types, charges, sigmas, epsilons, SGB_radii, vdW_radii,
gammas, and alphas
"""
ffld_server_exec = self.path_to_ffld_server()
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
self._rdkit_toolkit_wrapper.to_pdb_file(
molecule, tmpdir + '/molecule.pdb')
subprocess.check_output([
ffld_server_exec, "-ipdb", "molecule.pdb", "-version",
"14", "-print_parameters", "-out_file", "parameters.txt"
])
OPLS_params = self._parse_parameters('parameters.txt')
self._add_solvent_parameters(OPLS_params)
return OPLS_params
def compute_partial_charges(self, molecule, method='am1bcc'):
"""
It computes the partial charges using antechamber.
Parameters
----------
molecule : an offpele.topology.Molecule
The offpele's Molecule object
method : str
The name of the method to use. One of ['gasteiger', 'am1bcc'].
If None, 'am1bcc' will be used
Returns
-------
charges : simtk.unit.Quantity
The array of partial charges
Raises
------
ChargeMethodUnavailableError if the requested charge method can not
be handled by this toolkit
ChargeCalculationError if the charge method is supported by this
toolkit, but fails
"""
SUPPORTED_CHARGE_METHODS = {
'am1bcc': {
'antechamber_keyword': 'bcc'
},
'gasteiger': {
'antechamber_keyword': 'gas'
}
}
if method not in SUPPORTED_CHARGE_METHODS:
raise ChargeMethodUnavailableError(
'partial_charge_method ' +
'{} is not available from '.format(method) +
'AmberToolsToolkitWrapper. Available charge methods are ' +
list(SUPPORTED_CHARGE_METHODS.keys()))
off_molecule = molecule.off_molecule
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
net_charge = off_molecule.total_charge / \
unit.elementary_charge
self._rdkit_toolkit_wrapper.to_sdf_file(
molecule, tmpdir + '/molecule.sdf')
subprocess.check_output([
"antechamber", "-i", "molecule.sdf", "-fi", "sdf", "-o",
"charged.ac", "-fo", "ac", "-pf", "yes", "-dr", "n", "-c",
SUPPORTED_CHARGE_METHODS[method]['antechamber_keyword'],
"-nc",
str(net_charge)
])
# Write out just charges
subprocess.check_output([
"antechamber", "-dr", "n", "-i", "charged.ac", "-fi", "ac",
"-o", "charged2.ac", "-fo", "ac", "-c", "wc", "-cf",
"charges.txt", "-pf", "yes"
])
if not os.path.exists('charges.txt'):
# TODO: copy files into local directory to aid debugging?
raise ChargeCalculationError(
"Antechamber/sqm partial charge calculation failed on "
"molecule {} (SMILES {})".format(
off_molecule.name, off_molecule.to_smiles()))
# Read the charges
with open('charges.txt', 'r') as infile:
contents = infile.read()
text_charges = contents.split()
charges = np.zeros([off_molecule.n_atoms], np.float64)
for index, token in enumerate(text_charges):
charges[index] = float(token)
charges = unit.Quantity(charges, unit.elementary_charge)
assert len(charges) == len(molecule.rdkit_molecule.GetAtoms()), \
'Partial charge computation failed as the length of ' \
+ 'resulting partial charges does not match with the ' \
+ 'number of atoms in molecule'
return charges
def test_default_output_paths(self):
"""
It checks the default output paths that are used for each parameter
file from offpele.
"""
def from_PosixPath_to_string(paths):
"""
Convert PosixPaths to strings
"""
return map(str, paths)
molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
rotlib_path, impact_path, solvent_path = \
handle_output_paths(molecule, '', False)
# Convert PosixPaths to strings
rotlib_path, impact_path, solvent_path = map(
str, [rotlib_path, impact_path, solvent_path])
assert rotlib_path == 'BNZ.rot.assign', 'Unexpected default ' \
+ 'rotamer library path'
assert impact_path == 'bnzz', 'Unexpected default Impact ' \
+ 'template path'
assert solvent_path == 'ligandParams.txt', 'Unexpected default ' \
+ 'solvent parameters path'
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
# To avoid the complain about unexistent folder
os.mkdir('output')
rotlib_path, impact_path, solvent_path = \
handle_output_paths(molecule, 'output', False)
# Convert PosixPaths to strings
rotlib_path, impact_path, solvent_path = map(
str, [rotlib_path, impact_path, solvent_path])
assert rotlib_path == 'output/BNZ.rot.assign', 'Unexpected default ' \
+ 'rotamer library path'
assert impact_path == 'output/bnzz', 'Unexpected default Impact ' \
+ 'template path'
assert solvent_path == 'output/ligandParams.txt', 'Unexpected ' \
+ 'default solvent parameters path'
rotlib_path, impact_path, solvent_path = \
handle_output_paths(molecule, '', True)
# Convert PosixPaths to strings
rotlib_path, impact_path, solvent_path = map(
str, [rotlib_path, impact_path, solvent_path])
assert rotlib_path == 'DataLocal/LigandRotamerLibs/' \
+ 'BNZ.rot.assign', 'Unexpected default rotamer library path'
assert impact_path == 'DataLocal/Templates/OFF/Parsley/' \
+ 'HeteroAtoms/bnzz', 'Unexpected default Impact template'
assert solvent_path == 'DataLocal/OBC/ligandParams.txt', \
'Unexpected default solvent parameters path'
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
# To avoid the complain about unexistent folder
os.mkdir('output')
rotlib_path, impact_path, solvent_path = \
handle_output_paths(molecule, 'output', True)
# Convert PosixPaths to strings
rotlib_path, impact_path, solvent_path = map(
str, [rotlib_path, impact_path, solvent_path])
assert rotlib_path == 'output/DataLocal/LigandRotamerLibs/' \
+ 'BNZ.rot.assign', 'Unexpected default rotamer library path'
assert impact_path == 'output/DataLocal/Templates/OFF/Parsley/' \
+ 'HeteroAtoms/bnzz', 'Unexpected default Impact template path'
assert solvent_path == 'output/DataLocal/OBC/ligandParams.txt', \
'Unexpected default solvent parameters path'