def test_undefined_stereo(self):
"""
It checks the behaviour when ignoring the stereochemistry
in the Molecule initialization.
"""
from openff.toolkit.utils.toolkits import UndefinedStereochemistryError
from peleffy.forcefield import OpenForceField
# This should crash due to an undefined stereochemistry error
with pytest.raises(UndefinedStereochemistryError):
mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
hydrogens_are_explicit=False)
# This now should work
mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
allow_undefined_stereo=True,
hydrogens_are_explicit=False)
# And we can parameterize it
ff = OpenForceField('openff_unconstrained-1.2.1.offxml')
ff.parameterize(mol, charge_method='gasteiger')
# Save it
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
mol.to_pdb_file('molecule.pdb')
def test_writer_OFF(self):
"""
It tests the writer attribute of the Impact class using OFF
to parameterize.
"""
TEMPLATE_METZ = get_data_file_path('tests/metz')
TEMPLATE_MATZ = get_data_file_path('tests/malz')
TEMPLATE_ETLZ = get_data_file_path('tests/etlz')
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
# Generates the template for methane
pdb_path = get_data_file_path('ligands/methane.pdb')
molecule = Molecule(pdb_path)
openff = OpenForceField(self.OPENFF_FORCEFIELD)
parameters = openff.parameterize(molecule)
topology = Topology(molecule, parameters)
# Generates the impact template for methane
impact = Impact(topology)
impact.to_file('metz')
# Compare the reference template and the generated template
compare_files(file1=TEMPLATE_METZ, file2='metz')
# Generates the template for malonate
pdb_path = get_data_file_path('ligands/malonate.pdb')
molecule = Molecule(pdb_path)
openff = OpenForceField(self.OPENFF_FORCEFIELD)
parameters = openff.parameterize(molecule)
topology = Topology(molecule, parameters)
# Generates the impact template for malonate
impact = Impact(topology)
impact.to_file('malz')
# Compare the reference template and the generated template
compare_files(file1=TEMPLATE_MATZ, file2='malz')
# Generates the template for ethylene
pdb_path = get_data_file_path('ligands/ethylene.pdb')
molecule = Molecule(
pdb_path, tag='ETL'
) # Note that in this case we are assigning a tag to the molecule which will be used in the Impact template
openff = OpenForceField(self.OPENFF_FORCEFIELD)
parameters = openff.parameterize(molecule)
topology = Topology(molecule, parameters)
# Generates the impact template for ethylene
impact = Impact(topology)
impact.to_file('etlz')
# Compare the reference template and the generated template
compare_files(file1=TEMPLATE_ETLZ, file2='etlz')
def test_get_all_childs_of_atom(self):
"""
It tests the _get_all_childs_of_atom method used in the building
process of the Impact template.
"""
LIGAND_PATH = get_data_file_path('ligands/malonate.pdb')
FORCEFIELD_NAME = 'openff_unconstrained-1.2.1.offxml'
molecule = Molecule(LIGAND_PATH)
openff = OpenForceField(FORCEFIELD_NAME)
parameters = openff.parameterize(molecule, charge_method='dummy')
topology = Topology(molecule, parameters)
impact = Impact(topology)
absolute_parent = impact._get_absolute_parent_atom()
childs = impact._get_all_childs_of_atom(absolute_parent, 'side chain')
assert [a.PDB_name for a in childs] == \
['_C1_', '_C3_'], \
'Unexpected side-chain-child atoms: {}'.format(childs)
childs = impact._get_all_childs_of_atom(absolute_parent, 'core')
assert [a.PDB_name for a in childs] == \
['_H1_', '_H2_'], \
'Unexpected core-child atoms: {}'.format(childs)
def _initialize_from_topology(self):
"""
Initializes a SolventWrapper object using a peleffy's
molecular Topology.
"""
logger = Logger()
logger.info(' - Generating solvent parameters')
from peleffy.utils.toolkits import OpenForceFieldToolkitWrapper
off_toolkit = OpenForceFieldToolkitWrapper()
GBSA_handler = off_toolkit.get_parameter_handler_from_forcefield(
'GBSA', self._ff_file)
self._solvent_dielectric = GBSA_handler.solvent_dielectric
self._solute_dielectric = GBSA_handler.solute_dielectric
self._surface_area_penalty = GBSA_handler.surface_area_penalty
self._solvent_radius = GBSA_handler.solvent_radius
from peleffy.forcefield import OpenForceField
forcefield = OpenForceField(self._ff_file)
for idx, topology in enumerate(self.topologies):
parameters = forcefield.parameterize(topology.molecule,
charge_method='dummy')
self._radii[idx] = parameters['GBSA_radii']
self._scales[idx] = parameters['GBSA_scales']
def test_single_topology(self):
"""
It tests the class that generates a OpenFFCompatibleSolvent object for
a single topology.
"""
from .utils import compare_dicts
import json
TEMPLATE_PARAMS_MAL = get_data_file_path('tests/ligandParams_MAL.txt')
# Loads the molecule
molecule = Molecule(path=get_data_file_path('ligands/malonate.pdb'),
tag='MAL')
# Sets forcefield and parameterizes it
ff = OpenForceField('openff_unconstrained-1.2.1.offxml')
parameters = ff.parameterize(molecule, charge_method='gasteiger')
# Initializes topology
topology = Topology(molecule, parameters)
# Initializes solvent and gets parameters file
solvent = OBC2(topology)
solvent_dict = solvent.to_dict()
# Loads reference dict from template
with open(TEMPLATE_PARAMS_MAL, 'r') as f:
reference_dict = json.load(f)
# Compare the output parameters dict with the reference parameters
compare_dicts(reference_dict, solvent_dict)
def test_parameterizer(self):
"""It checks the parameterized method."""
from peleffy.topology import Molecule
from peleffy.forcefield import OpenForceField
from peleffy.utils import (get_data_file_path,
convert_all_quantities_to_string)
from .utils import compare_dicts
import json
# Load molecule 1
molecule = Molecule(get_data_file_path('ligands/methane.pdb'))
openff = OpenForceField(self.FORCE_FIELD_NAME)
# Obtain force field parameters
parameters = openff.parameterize(molecule)
writable_parameters = convert_all_quantities_to_string(parameters)
reference_file = get_data_file_path(
'tests/MET_openff-1.2.1_parameters.json')
with open(reference_file) as f:
compare_dicts(writable_parameters, json.load(f))
# Load molecule
molecule = Molecule(get_data_file_path('ligands/ethylene.pdb'))
openff = OpenForceField(self.FORCE_FIELD_NAME)
# Obtain force field parameters
parameters = openff.parameterize(molecule)
writable_parameters = convert_all_quantities_to_string(parameters)
reference_file = get_data_file_path(
'tests/ETL_openff-1.2.1_parameters.json')
with open(reference_file) as f:
compare_dicts(writable_parameters, json.load(f))
def test_multiple_topologies(self):
"""
It tests the class that generates a OpenFFCompatibleSolvent object for
multiple topologies.
"""
from .utils import compare_dicts, merge_dicts
# Path to multiple non standard residues
pdb_path_MAL = get_data_file_path('ligands/malonate.pdb')
pdb_path_MET = get_data_file_path('ligands/methane.pdb')
# Force Field to parameterize the molecules
ff = OpenForceField('openff_unconstrained-1.2.1.offxml')
# Topology of malonate
mol_MAL = Molecule(path=pdb_path_MAL, tag='MAL')
parameters_MAL = ff.parameterize(mol_MAL, charge_method='gasteiger')
topology_MAL = Topology(mol_MAL, parameters_MAL)
# Topology of methane
mol_MET = Molecule(path=pdb_path_MET, tag='MET')
parameters_MET = ff.parameterize(mol_MET, charge_method='gasteiger')
topology_MET = Topology(mol_MET, parameters_MET)
# List containing both topologies
topologies = [topology_MAL, topology_MET]
# Generate the Solvent parameters dictionaries
solvent_MAL_dict = OBC2(topology_MAL).to_dict()
solvent_MET_dict = OBC2(topology_MET).to_dict()
solvent_dict = OBC2(topologies).to_dict()
# Check that merging both single topology dicitionaries we obtain the
# same dictionary that using multiple topologies
compare_dicts(merge_dicts(solvent_MAL_dict['SolventParameters'],
solvent_MET_dict['SolventParameters']),
solvent_dict['SolventParameters'])
def test_add_topological_elements(self):
"""
It tests the addition of topological elements to an empty
topology.
"""
from peleffy.topology import Molecule
from peleffy.forcefield import OpenForceField
from peleffy.forcefield.parameters import BaseParameterWrapper
from peleffy.topology import Topology
from peleffy.utils import get_data_file_path
# Define molecule1 and its topology
pdb_path = get_data_file_path('ligands/ethylene.pdb')
molecule1 = Molecule(pdb_path)
openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
parameters1 = openff.parameterize(molecule1)
topology1 = Topology(molecule1, parameters1)
# Define empty topology2
molecule2 = Molecule()
parameters2 = BaseParameterWrapper()
topology2 = Topology(molecule2, parameters2)
# Add parameters to topology2
for atom in topology1.atoms:
topology2.add_atom(atom)
for bond in topology1.bonds:
topology2.add_bond(bond)
for angle in topology1.angles:
topology2.add_angle(angle)
for proper in topology1.propers:
topology2.add_proper(proper)
for improper in topology1.impropers:
topology2.add_improper(improper)
# Verify content of both topologies
assert topology1.atoms == topology2.atoms, \
'The atoms of boths topologies should match'
assert topology1.bonds == topology2.bonds, \
'The bonds of boths topologies should match'
assert topology1.angles == topology2.angles, \
'The angles of boths topologies should match'
assert topology1.propers == topology2.propers, \
'The propers of boths topologies should match'
assert topology1.impropers == topology2.impropers, \
'The impropers of boths topologies should match'
def test_multiple_topologies_writer(self):
"""
It tests the class that generates a OpenFFCompatibleSolvent object for multiple topologies. It compares the outcome of the Solvent writer with
a reference file.
"""
from .utils import compare_dicts, parameterize_opls2005
import json
TEMPLATE_PARAMS = get_data_file_path('tests/ligandParams.txt')
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
path_OXO = get_data_file_path('tests/MRO_oleic/OXO.pdb')
path_OLC = get_data_file_path('tests/MRO_oleic/OLC.pdb')
ff = OpenForceField('openff_unconstrained-1.2.1.offxml')
opls2005 = OPLS2005ForceField()
# Group OXO
m_OXO = Molecule(path_OXO)
ffld_file = get_data_file_path('tests/OXO_ffld_output.txt')
parameters_OXO = parameterize_opls2005(opls2005, m_OXO,
ffld_file)
topology_OXO = Topology(m_OXO, parameters_OXO)
# Acid oleic
m_OLC = Molecule(path_OLC)
parameters_OLC = ff.parameterize(m_OLC,
charge_method='gasteiger')
topology_OLC = Topology(m_OLC, parameters_OLC)
# Multiple topologies
topologies = [topology_OXO, topology_OLC]
solvent = OBC2(topologies)
solvent.to_file('OBC_parameters.txt')
# Loads reference dict from template
with open(TEMPLATE_PARAMS, 'r') as f:
reference_dict = json.load(f)
# Loads the generated template into a dict
with open('OBC_parameters.txt', 'r') as f:
solvent_dict = json.load(f)
# Compare the output parameters dict with the reference parameters
compare_dicts(reference_dict, solvent_dict)
def __get_template_and_rot(self, template_path='grw', rot_path='GRW.rot.assign', rot_res=30):
os.environ['SCHRODINGER'] = self.sch_path
m = Molecule(self.ligand_pdb,
core_constraints=[' CA ', ' C ', ' N '],
rotamer_resolution=rot_res)
if self.__forcefield == 'OPLS2005':
ff = OPLS2005ForceField()
if self.__forcefield == 'OpenForceField': # Not tested yet
ff = OpenForceField('openff_unconstrained-1.2.0.offxml')
parameters = ff.parameterize(m)
topology = Topology(m, parameters)
impact = Impact(topology)
impact.to_file(template_path)
aa_template = self.__create_aa_template_path()
cov.correct_template(template_path, aa_template)
print("Template modified in {}.".format(template_path))
rotamer_library = RotamerLibrary(m)
rotamer_library.to_file(rot_path)
print("Rotamer library stored in {}".format(rot_path))
def test_get_absolute_parent_atom(self):
"""
It tests the _get_absolute_parent_atom method used in the building
process of the Impact template.
"""
LIGAND_PATH = get_data_file_path('ligands/malonate.pdb')
FORCEFIELD_NAME = 'openff_unconstrained-1.2.1.offxml'
molecule = Molecule(LIGAND_PATH)
openff = OpenForceField(FORCEFIELD_NAME)
parameters = openff.parameterize(molecule, charge_method='dummy')
topology = Topology(molecule, parameters)
impact = Impact(topology)
absolute_parent = impact._get_absolute_parent_atom()
assert absolute_parent.PDB_name == '_C2_', \
'Unexpected absolute parent atom: {}'.format(absolute_parent)
def test_get_core_atoms(self):
"""
It tests the _get_core_atoms method used in the building
process of the Impact template.
"""
LIGAND_PATH = get_data_file_path('ligands/malonate.pdb')
FORCEFIELD_NAME = 'openff_unconstrained-1.2.1.offxml'
molecule = Molecule(LIGAND_PATH)
openff = OpenForceField(FORCEFIELD_NAME)
parameters = openff.parameterize(molecule, charge_method='dummy')
topology = Topology(molecule, parameters)
impact = Impact(topology)
core_atoms = impact._get_core_atoms()
assert [a.PDB_name for a in core_atoms] == \
['_C2_', '_H1_', '_H2_'], \
'Unexpected core atoms: {}'.format(core_atoms)
def test_openff_parameterizer(self):
"""
It checks the behaviour of the Topology with the OpenFF
parameters.
"""
from peleffy.topology import Molecule
from peleffy.forcefield import OpenForceField
from peleffy.topology import Topology
from peleffy.utils import get_data_file_path
from .utils import check_parameters
FORCE_FIELD_NAME = 'openff_unconstrained-1.2.1.offxml'
# Load molecule
molecule = Molecule(get_data_file_path('ligands/methane.pdb'))
openff = OpenForceField(FORCE_FIELD_NAME)
# Obtain force field parameters
parameters = openff.parameterize(molecule)
# Generate molecular topology
topology = Topology(molecule, parameters)
# Define expected parameters
expected_nonbonding = [[
1, 0, 'M', 'OFFT', '_C1_', 0, 3.3996695084235347, 0.1094, -0.1088,
0, 1.6998347542117673, 0, 0
],
[
2, 1, 'M', 'OFFT', '_H1_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
],
[
3, 1, 'M', 'OFFT', '_H2_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
],
[
4, 1, 'M', 'OFFT', '_H3_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
],
[
5, 1, 'M', 'OFFT', '_H4_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
]]
expected_bonds = [[1, 2, 376.8940758588, 1.094223427522],
[1, 3, 376.8940758588, 1.094223427522],
[1, 4, 376.8940758588, 1.094223427522],
[1, 5, 376.8940758588, 1.094223427522]]
expected_angles = [[2, 1, 3, 33.78875634641, 110.2468561538],
[2, 1, 4, 33.78875634641, 110.2468561538],
[2, 1, 5, 33.78875634641, 110.2468561538],
[3, 1, 4, 33.78875634641, 110.2468561538],
[3, 1, 5, 33.78875634641, 110.2468561538],
[4, 1, 5, 33.78875634641, 110.2468561538]]
# Check it up
check_parameters(topology,
expected_nonbonding=expected_nonbonding,
expected_bonds=expected_bonds,
expected_angles=expected_angles)
# Load molecule
molecule = Molecule(get_data_file_path('ligands/ethylene.pdb'))
openff = OpenForceField(FORCE_FIELD_NAME)
# Obtain force field parameters
parameters = openff.parameterize(molecule)
# Generate molecular topology
topology = Topology(molecule, parameters)
# Define expected parameters
expected_propers = [[3, 1, 2, 5, 5.376019778605, -1, 2, 0.0],
[3, 1, 2, 6, 5.376019778605, -1, 2, 0.0],
[4, 1, 2, 5, 5.376019778605, -1, 2, 0.0],
[4, 1, 2, 6, 5.376019778605, -1, 2, 0.0]]
expected_impropers = [[1, 2, 5, 6, 1.1, -1, 2],
[2, 1, 3, 4, 1.1, -1, 2]]
# Check it up
check_parameters(topology,
expected_propers=expected_propers,
expected_impropers=expected_impropers)
def test_parse_charges_from_mae(self):
"""
It tests the MAE parser for assigning partial charges from an external
file.
"""
from peleffy.utils import get_data_file_path, parse_charges_from_mae
from peleffy.topology import Molecule
from peleffy.forcefield import OpenForceField
FORCEFIELD = 'openff_unconstrained-1.2.0.offxml'
PATH_MAE_MAT = get_data_file_path('tests/MAT.mae')
PATH_PDB_MAT = get_data_file_path('tests/MAT.pdb')
PATH_MAE_BHP = get_data_file_path('ligands/BHP.mae')
PATH_PDB_BHP = get_data_file_path('ligands/BHP.pdb')
PATH_MAE_ETL = get_data_file_path('ligands/ethylene.mae')
PATH_PDB_ETL = get_data_file_path('ligands/ethylene.pdb')
PATH_PDB_MAL = get_data_file_path('ligands/malonate.pdb')
CHARGES_REFERENCE_BHP = [[-0.35703, 'O1'],
[-0.59535, 'O2'],
[-0.50292, 'O3'],
[-0.25243, 'C1'],
[0.30438, 'C2'],
[0.22092, 'C3'],
[0.54336, 'C4'],
[-0.20569, 'C5'],
[-0.20192, 'C6'],
[0.16631, 'C7'],
[0.02422, 'C8'],
[-0.09115, 'C9'],
[-0.09904, 'C10'],
[-0.15673, 'C11'],
[-0.13245, 'C12'],
[-0.17806, 'C13'],
[-0.12489, 'C14'],
[-0.09307, 'C15'],
[-0.08973, 'C16'],
[0.05397, 'H1'],
[0.07338, 'H2'],
[0.04514, 'H3'],
[0.12979, 'H4'],
[0.11025, 'H5'],
[0.04054, 'H6'],
[0.04581, 'H7'],
[0.11444, 'H8'],
[0.11761, 'H9'],
[0.37274, 'H10'],
[0.11825, 'H11'],
[0.12584, 'H12'],
[0.1381, 'H13'],
[0.11696, 'H14'],
[0.11148, 'H15'],
[0.10697, 'H16']]
CHARGES_REFERENCE_MAT = [[-0.18938, 'F1'],
[-0.21715, 'F2'],
[-0.21234, 'F3'],
[-0.39736, 'O1'],
[-0.58890, 'O2'],
[-1.00825, 'N1'],
[0.72066, 'C1'],
[-0.06281, 'C2'],
[-0.67474, 'C3'],
[0.10391, 'C4'],
[0.16293, 'C5'],
[-0.61076, 'C6'],
[0.78183, 'C7'],
[0.27041, 'C8'],
[-0.48769, 'C9'],
[0.15704, 'C10'],
[-0.02646, 'H1'],
[-0.08394, 'H2'],
[-0.01308, 'H3'],
[0.14006, 'H4'],
[0.12960, 'H5'],
[0.31245, 'H6'],
[0.30268, 'H7'],
[0.17026, 'H8'],
[0.15782, 'H9'],
[0.03175, 'C11'],
[0.03894, 'H10'],
[0.07509, 'H11'],
[0.01743, 'H12']]
# Check up correct charges for malonate
m = Molecule(PATH_PDB_MAT)
openff = OpenForceField(FORCEFIELD)
parameters = openff.parameterize(m, charge_method='dummy')
parameters = parse_charges_from_mae(PATH_MAE_MAT, parameters)
for charge, atom_name in zip(parameters['charges'],
parameters['atom_names']):
assert [charge._value, atom_name.replace('_', '')] in \
CHARGES_REFERENCE_MAT, \
'Incorrect charge value for {}.'.format(atom_name)
# Check up correct charges for BHP
m = Molecule(PATH_PDB_BHP)
openff = OpenForceField(FORCEFIELD)
parameters = openff.parameterize(m, charge_method='dummy')
parameters = parse_charges_from_mae(PATH_MAE_BHP, parameters)
for charge, atom_name in zip(parameters['charges'],
parameters['atom_names']):
assert [charge._value, atom_name.replace('_', '')] in \
CHARGES_REFERENCE_BHP, \
'Incorrect charge value for {}.'.format(atom_name)
# Error: MAE file without charges information
m = Molecule(PATH_PDB_ETL)
openff = OpenForceField(FORCEFIELD)
parameters = openff.parameterize(m, charge_method='dummy')
with pytest.raises(ValueError):
_ = parse_charges_from_mae(PATH_MAE_ETL, parameters)
# Error: Inconsistency between Moelcule atom names and MAE atom names
m = Molecule(PATH_PDB_MAL)
openff = OpenForceField(FORCEFIELD)
parameters = openff.parameterize(m, charge_method='dummy')
with pytest.raises(ValueError):
_ = parse_charges_from_mae(PATH_PDB_BHP, parameters)