def test_Impact_writable_parameters(self):
"""
It checks the Impact writable representation for angles.
"""
# Load benzene ring
molecule = Molecule(smiles='CC=O')
# Parameterize
molecule.parameterize('openff_unconstrained-1.2.0.offxml',
charges_method='gasteiger')
expected_parameters = list(
[[1, 2, 3, 78.67881492645, 128.2771922378],
[1, 2, 7, 34.202963712735, 133.1339832262],
[2, 1, 4, 50.00415699765, 110.81136453],
[2, 1, 5, 50.00415699765, 110.81136453],
[2, 1, 6, 50.00415699765, 110.81136453],
[3, 2, 7, 34.202963712735, 133.1339832262],
[4, 1, 5, 33.78875634641, 110.2468561538],
[4, 1, 6, 33.78875634641, 110.2468561538],
[5, 1, 6, 33.78875634641, 110.2468561538]])
# Check resulting parameters
for angle in molecule.angles:
w_angle = WritableAngle(angle)
w_parameters = [attr[1] for attr in list(w_angle)]
assert w_parameters in expected_parameters, \
'Invalid writable angle parameters {}'.format(w_parameters)
def test_gasteiger_method(self):
"""It tests the gasteiger method"""
ligand_path = get_data_file_path(self.LIGAND_PATH)
molecule = Molecule(ligand_path)
molecule.parameterize(FORCEFIELD_NAME, charges_method='gasteiger')
check_CHO_charges_in_molecule(molecule)
def test_OPLS_method(self):
"""It tests the OPLS method"""
ligand_path = get_data_file_path(self.LIGAND_PATH)
molecule = Molecule(ligand_path)
# To avoid the use of Schrodinger Toolkit
charges = [-0.22, 0.7, -0.12, -0.8, -0.8, -0.12, -0.12, -0.12,
-0.12, -0.12, -0.115, -0.115, -0.12, -0.12, -0.12,
-0.12, -0.12, -0.12, -0.12, -0.18, 0.06, 0.06, 0.06,
0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06,
0.06, 0.06, 0.115, 0.115, 0.06, 0.06, 0.06, 0.06, 0.06,
0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06,
0.06, 0.06, 0.06]
molecule._OPLS_parameters = SchrodingerToolkitWrapper.OPLSParameters(
{'charges': [unit.Quantity(charge, unit.elementary_charge)
for charge in charges]})
molecule.parameterize(FORCEFIELD_NAME, charges_method='OPLS')
assert len(molecule.off_molecule.partial_charges) == len(charges), \
'Size of Molecule\'s partial charges is expected to match ' \
+ 'with size of reference charges list'
for charge, expected_charge in zip(
molecule.off_molecule.partial_charges, charges):
assert charge == unit.Quantity(expected_charge,
unit.elementary_charge), \
'Unexpected charge {}'.format(charge)
def test_Impact_writable_parameters(self):
"""
It checks the Impact writable representation for bonds.
"""
# Load benzene ring
molecule = Molecule(smiles='CC=O')
# Parameterize
molecule.parameterize('openff_unconstrained-1.2.0.offxml',
charges_method='gasteiger')
expected_parameters = list([[1, 2, 332.5750972667, 1.523640340452],
[1, 4, 376.8940758588, 1.094223427522],
[1, 5, 376.8940758588, 1.094223427522],
[1, 6, 376.8940758588, 1.094223427522],
[2, 3, 608.3286693405, 1.225108345696],
[2, 7, 404.20804685, 1.085503378387]])
# Check resulting parameters
for bond in molecule.bonds:
w_bond = WritableBond(bond)
w_parameters = [attr[1] for attr in list(w_bond)]
assert w_parameters in expected_parameters, \
'Invalid writable bond parameters {}'.format(w_parameters)
def test_molecule_tag_assignment(self):
"""
It tests the molecule tag assignment.
"""
# Look for UNK tag when dummy Molecule is loaded
molecule = Molecule()
assert molecule.tag == 'UNK', 'Unexpected atom tag'
# Look for the PDB residue name as a tag when a Molecule is loaded
# from a PDB file
ligand_path = get_data_file_path('ligands/BNZ.pdb')
molecule = Molecule(ligand_path)
assert molecule.tag == 'BNZ', 'Unexpected atom tag'
# Look for BEN tag when a Molecule is loaded from a PDB file with
# a custom name
ligand_path = get_data_file_path('ligands/BNZ.pdb')
molecule = Molecule(ligand_path, tag='BEN')
assert molecule.tag == 'BEN', 'Unexpected atom tag'
# Look for UNK tag when a Molecule is loaded from a SMILES tag
molecule = Molecule(smiles='c1ccccc1')
assert molecule.tag == 'UNK', 'Unexpected atom tag'
# Look for BNZ tag when a Molecule is loaded from a SMILES tag with
# a custom tag
molecule = Molecule(smiles='c1ccccc1', tag='BNZ')
assert molecule.tag == 'BNZ', 'Unexpected atom tag'
def test_molecule_name_assignment(self):
"""
It tests the molecule name assignment.
"""
# Look for an empty name when dummy Molecule is loaded
molecule = Molecule()
assert molecule.name == '', 'Unexpected atom name'
# Look for the PDB name when a Molecule is loaded from a PDB file
ligand_path = get_data_file_path('ligands/BNZ.pdb')
molecule = Molecule(ligand_path)
assert molecule.name == 'BNZ', 'Unexpected atom name'
# Look for benzene name when a Molecule is loaded from a PDB file
# with a custom name
ligand_path = get_data_file_path('ligands/BNZ.pdb')
molecule = Molecule(ligand_path, name='benzene')
assert molecule.name == 'benzene', 'Unexpected atom name'
# Look for the SMILES name when a Molecule is loaded from a SMILES tag
molecule = Molecule(smiles='c1ccccc1')
assert molecule.name == 'c1ccccc1', 'Unexpected atom name'
# Look for benzene name when a Molecule is loaded from a SMILES tag
# with a custom name
molecule = Molecule(smiles='c1ccccc1', name='benzene')
assert molecule.name == 'benzene', 'Unexpected atom name'
def test_OFF_parameters(self):
"""
It checks the standard Open Force Field parameterization for
bonds.
"""
MAX_THRESHOLD = 1e-3
# Load benzene ring
molecule = Molecule(smiles='c1ccccc1')
# Parameterize
molecule.parameterize('openff_unconstrained-1.2.0.offxml',
charges_method='gasteiger')
# Check resulting parameters
expected_lengths = {(0, 1): 1.389761064076,
(0, 5): 1.389761064076,
(0, 6): 1.085503378387,
(1, 2): 1.389761064076,
(1, 7): 1.085503378387,
(2, 3): 1.389761064076,
(2, 8): 1.085503378387,
(3, 4): 1.389761064076,
(3, 9): 1.085503378387,
(4, 5): 1.389761064076,
(4, 10): 1.085503378387,
(5, 11): 1.085503378387}
expected_ks = {(0, 1): 672.0064645264,
(0, 5): 672.0064645264,
(0, 6): 808.4160937,
(1, 2): 672.0064645264,
(1, 7): 808.4160937,
(2, 3): 672.0064645264,
(2, 8): 808.4160937,
(3, 4): 672.0064645264,
(3, 9): 808.4160937,
(4, 5): 672.0064645264,
(4, 10): 808.4160937,
(5, 11): 808.4160937}
for indexes, properties in dict(molecule.parameters['Bonds']).items():
expected_length = unit.Quantity(expected_lengths[indexes],
unit.angstrom)
expected_k = unit.Quantity(expected_ks[indexes],
unit.kilocalorie
/ (unit.angstrom ** 2 * unit.mole))
assert properties.length - expected_length \
< unit.Quantity(MAX_THRESHOLD, unit.angstrom), \
'Invalid length for bond {} {}'.format(indexes, properties)
assert properties.k - expected_k \
< unit.Quantity(MAX_THRESHOLD, unit.kilocalorie
/ (unit.angstrom ** 2 * unit.mole)), \
'Invalid k for bond {} {}'.format(indexes, properties)
def test_good_init_parameterization(self):
"""
It checks that a call to the parameterize function with a Molecule
successfully initialized does not raise any Exception.
"""
FORCEFIELD_NAME = 'openff_unconstrained-1.1.1.offxml'
LIGAND_PATH = SET_OF_LIGAND_PATHS[0]
ligand_path = get_data_file_path(LIGAND_PATH)
molecule = Molecule(ligand_path)
molecule.parameterize(FORCEFIELD_NAME)
def test_Impact_writable_parameters(self):
"""
It checks the Impact writable representation for dihedrals.
"""
# Load benzene ring
molecule = Molecule(smiles='CC=O')
# Parameterize
molecule.parameterize('openff_unconstrained-1.2.0.offxml',
charges_method='gasteiger')
expected_parameters = list(
[[3, 2, 1, 4, 0.5107183999341, 1, 1],
[3, 2, 1, 5, 0.5107183999341, 1, 1],
[3, 2, 1, 6, 0.5107183999341, 1, 1],
[4, 1, 2, 7, 0.1493988458474, 1, 3],
[5, 1, 2, 7, 0.1493988458474, 1, 3],
[6, 1, 2, 7, 0.1493988458474, 1, 3],
[3, 2, 1, 4, -0.0275194074427, 1, 2],
[3, 2, 1, 5, -0.0275194074427, 1, 2],
[3, 2, 1, 6, -0.0275194074427, 1, 2],
[3, 2, 1, 4, -0.1057540923121, -1, 3],
[3, 2, 1, 5, -0.1057540923121, -1, 3],
[3, 2, 1, 6, -0.1057540923121, -1, 3]])
# Check resulting parameters
for proper in molecule.propers:
w_proper = WritableProper(proper)
w_parameters = [attr[1] for attr in list(w_proper)]
assert w_parameters in expected_parameters, \
'Invalid writable proper parameters {}'.format(w_parameters)
expected_parameters = list([[1, 2, 3, 7, 1.1, -1, 2]])
# Check resulting parameters
for improper in molecule.impropers:
w_improper = WritableImproper(improper)
w_parameters = [attr[1] for attr in list(w_improper)]
assert w_parameters in expected_parameters, \
'Invalid writable improper parameters {}'.format(w_parameters)
def test_OFF_to_PELE_conversion(self):
"""
It checks the difference between dihedral equations from PELE and
Open Force Field. Their values should match throughout all the domain.
"""
MAX_THRESHOLD = 1e-10
for ligand_path in SET_OF_LIGAND_PATHS:
ligand_path = get_data_file_path(ligand_path)
molecule = Molecule(ligand_path)
molecule.parameterize(FORCEFIELD_NAME, charges_method='gasteiger')
x = unit.Quantity(np.arange(0, np.pi, 0.1), unit=unit.radians)
for PELE_proper, OFF_proper in zip(molecule.propers,
molecule._OFF_propers):
PELE_y = apply_PELE_dihedral_equation(PELE_proper, x)
OFF_y = apply_OFF_dihedral_equation(OFF_proper, x)
y_diff = PELE_y - OFF_y
assert np.linalg.norm(y_diff) < MAX_THRESHOLD
def test_get_Schrodinger_parameters(self):
"""
It tests the standard methods to obtain Schrodinger parameters
from an offpele's Molecule.
"""
# Load benzene ring
molecule = Molecule(smiles='c1ccccc1')
molecule.parameterize(FORCEFIELD_NAME, charges_method='gasteiger')
with pytest.raises(ToolkitUnavailableException):
molecule.get_OPLS_parameters()
molecule._OPLS_parameters = METHANE_OPLS_PARAMETERS
_ = molecule.get_OPLS_parameters()
molecule.add_OPLS_nonbonding_params()
molecule.add_OPLS_bonds_and_angles()
def test_excluded_dihedrals_handler(self):
"""
It checks the exclusion of dihedrals when generating 1-4 lists
for PELE. This process is done internally in PELE but we
need to mark previously those dihedrals to exclude from 1-4
lists.
"""
molecule = Molecule()
# Add several dummy propers
molecule._add_proper(
Proper(atom1_idx=0, atom2_idx=1, atom3_idx=2, atom4_idx=3,
periodicity=1, prefactor=1, index=0,
constant=unit.Quantity(1.0, unit.kilocalorie / unit.mole)))
molecule._add_proper(
Proper(atom1_idx=0, atom2_idx=1, atom3_idx=2, atom4_idx=3,
periodicity=2, prefactor=1, index=1,
constant=unit.Quantity(1.0, unit.kilocalorie / unit.mole)))
molecule._add_proper(
Proper(atom1_idx=0, atom2_idx=1, atom3_idx=5, atom4_idx=3,
periodicity=2, prefactor=1, index=2,
constant=unit.Quantity(1.0, unit.kilocalorie / unit.mole)))
molecule._add_proper(
Proper(atom1_idx=0, atom2_idx=1, atom3_idx=2, atom4_idx=4,
periodicity=1, prefactor=1, index=3,
constant=unit.Quantity(1.0, unit.kilocalorie / unit.mole)))
molecule._add_proper(
Proper(atom1_idx=0, atom2_idx=1, atom3_idx=2, atom4_idx=5,
periodicity=1, prefactor=1, index=4,
constant=unit.Quantity(1.0, unit.kilocalorie / unit.mole)))
molecule._add_proper(
Proper(atom1_idx=0, atom2_idx=1, atom3_idx=2, atom4_idx=6,
periodicity=1, prefactor=1, index=5,
constant=unit.Quantity(1.0, unit.kilocalorie / unit.mole)))
# Add one bond
molecule._add_bond(
Bond(atom1_idx=0, atom2_idx=4,
spring_constant=unit.Quantity(1.0, unit.kilocalorie
/ (unit.angstrom ** 2
* unit.mole)),
eq_dist=unit.Quantity(1.0, unit.angstrom)))
# Add one angle
molecule._add_angle(
Angle(atom1_idx=0, atom2_idx=1, atom3_idx=5,
spring_constant=unit.Quantity(1.0, unit.kilocalorie
/ (unit.radian ** 2
* unit.mole)),
eq_angle=unit.Quantity(1.0, unit.degrees)))
molecule._handle_excluded_propers()
# Assertions
for proper in molecule.propers:
if proper.index == 0:
assert proper.exclude is False, \
'Proper 0 must be INCLUDED in 1-4 list'
elif proper.index == 1:
assert proper.exclude is False, \
'Proper 1 must be INCLUDED in 1-4 list'
elif proper.index == 2:
assert proper.exclude is True, \
'Proper 2 must be EXCLUDED in 1-4 list'
elif proper.index == 3:
assert proper.exclude is True, \
'Proper 3 must be EXCLUDED in 1-4 list'
elif proper.index == 4:
assert proper.exclude is True, \
'Proper 4 must be EXCLUDED in 1-4 list'
elif proper.index == 5:
assert proper.exclude is False, \
'Proper 5 must be INCLUDED in 1-4 list'
def test_bad_init_parameterization(self):
"""
It checks that a call to the parameterize function with a Molecule
unsuccessfully initialized raises an Exception.
"""
FORCEFIELD_NAME = 'openff_unconstrained-1.1.1.offxml'
LIGAND_PATH = SET_OF_LIGAND_PATHS[0]
ligand_path = get_data_file_path(LIGAND_PATH)
molecule = Molecule()
with pytest.raises(Exception):
molecule.parameterize(FORCEFIELD_NAME)
rdkit_toolkit = RDKitToolkitWrapper()
molecule._rdkit_molecule = rdkit_toolkit.from_pdb(ligand_path)
molecule._off_molecule = None
with pytest.raises(Exception):
molecule.parameterize(FORCEFIELD_NAME)
openforcefield_toolkit = OpenForceFieldToolkitWrapper()
molecule._off_molecule = openforcefield_toolkit.from_rdkit(molecule)
molecule._rdkit_molecule = None
with pytest.raises(Exception):
molecule.parameterize(FORCEFIELD_NAME)
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_PDB_connectivity_template(self):
"""
It tests the initialization of an offpele's Molecule representation
from a PDB file without connectivity and a connectivity template.
"""
# Initialize an empty Molecule object
molecule = Molecule()
assert molecule.connectivity_template is None, \
'Unexpected connectivity template'
# Initialize a Molecule from a PDB without connectivity and
# without a connectivity template
ligand_path = get_data_file_path(
'ligands/BNZ_without_connectivity.pdb')
molecule = Molecule(ligand_path)
expected_bond_ids = [(1, 0, False), (2, 1, False), (3, 2, False),
(4, 3, False), (5, 4, False), (5, 0, False),
(6, 0, False), (7, 1, False), (8, 2, False),
(9, 3, False), (10, 4, False), (11, 5, False)]
for bond in molecule.rdkit_molecule.GetBonds():
bond_id = (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
bond.GetIsAromatic())
assert bond_id in expected_bond_ids, 'Unexpected bond id ' \
+ '{}'.format(bond_id)
# Initialize a Molecule from a PDB without connectivity but with
# a connectivity template
template_path = get_data_file_path('ligands/BNZ.pdb')
template = Molecule(template_path)
ligand_path = get_data_file_path(
'ligands/BNZ_without_connectivity.pdb')
molecule = Molecule(ligand_path,
connectivity_template=template.rdkit_molecule)
expected_bond_ids = [(1, 0, True), (2, 1, True), (3, 2, True),
(4, 3, True), (5, 4, True), (5, 0, True),
(6, 0, False), (7, 1, False), (8, 2, False),
(9, 3, False), (10, 4, False), (11, 5, False)]
for bond in molecule.rdkit_molecule.GetBonds():
bond_id = (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
bond.GetIsAromatic())
assert bond_id in expected_bond_ids, 'Unexpected bond id ' \
+ '{}'.format(bond_id)
# Initialize a Molecule from a PDB with connectivity and with
# a connectivity template
template_path = get_data_file_path('ligands/BNZ.pdb')
template = Molecule(template_path)
ligand_path = get_data_file_path('ligands/BNZ.pdb')
molecule = Molecule(ligand_path,
connectivity_template=template.rdkit_molecule)
expected_bond_ids = [(0, 1, True), (1, 2, True), (2, 3, True),
(3, 4, True), (4, 5, True), (0, 5, True),
(0, 6, False), (1, 7, False), (2, 8, False),
(3, 9, False), (4, 10, False), (5, 11, False)]
for bond in molecule.rdkit_molecule.GetBonds():
bond_id = (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
bond.GetIsAromatic())
assert bond_id in expected_bond_ids, 'Unexpected bond id ' \
+ '{}'.format(bond_id)
def test_assign_Schrodinger_parameters(self):
"""
It tests the assignment of Schrodinger parameters to offpele's
Molecule.
"""
def check_parameters():
""" It checks the current parameters of the molecule. """
for atom in molecule.atoms:
w_atom = WritableAtom(atom)
w_parameters = [
w_atom.index, w_atom.parent.index, w_atom.core,
w_atom.OPLS_type, w_atom.PDB_name, w_atom.unknown,
w_atom.sigma, w_atom.epsilon, w_atom.charge,
w_atom.born_radius, w_atom.SASA_radius,
w_atom.nonpolar_gamma, w_atom.nonpolar_alpha
]
assert w_parameters in expected_nonbonding, \
'Invalid writable nonbonding parameters {}'.format(w_parameters)
for bond in molecule.bonds:
w_bond = WritableBond(bond)
w_parameters = [attr[1] for attr in list(w_bond)]
assert w_parameters in expected_bonds, \
'Invalid writable bond parameters {}'.format(w_parameters)
for angle in molecule.angles:
w_angle = WritableAngle(angle)
w_parameters = [attr[1] for attr in list(w_angle)]
assert w_parameters in expected_angles, \
'Invalid writable angle parameters {}'.format(w_parameters)
# Load benzene ring
molecule = Molecule(smiles='C')
molecule.parameterize(FORCEFIELD_NAME)
# Load OPLS parameters
molecule._OPLS_parameters = METHANE_OPLS_PARAMETERS
# Check parameters
# First check
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_parameters()
# Second check
molecule.add_OPLS_nonbonding_params()
expected_nonbonding = [[
1, 0, 'M', 'CT', '_C1_', 0, 3.5, 0.066, -0.1088, 1.975, 1.75,
0.005, -0.74168571
],
[
2, 1, 'M', 'HC', '_H1_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
],
[
3, 1, 'M', 'HC', '_H2_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
],
[
4, 1, 'M', 'HC', '_H3_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
],
[
5, 1, 'M', 'HC', '_H4_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
]]
check_parameters()
# Third check
molecule.add_OPLS_bonds_and_angles()
expected_bonds = [[1, 2, 340.0, 1.09], [1, 3, 340.0, 1.09],
[1, 4, 340.0, 1.09], [1, 5, 340.0, 1.09]]
expected_angles = [[2, 1, 3, 33.0, 107.8], [2, 1, 4, 33.0, 107.8],
[2, 1, 5, 33.0, 107.8], [3, 1, 4, 33.0, 107.8],
[3, 1, 5, 33.0, 107.8], [4, 1, 5, 33.0, 107.8]]
check_parameters()
def test_OFF_parameters(self):
"""
It checks the standard Open Force Field parameterization for
angles.
"""
MAX_THRESHOLD = 1e-3
# Load benzene ring
molecule = Molecule(smiles='c1ccccc1')
# Parameterize
molecule.parameterize('openff_unconstrained-1.2.0.offxml',
charges_method='gasteiger')
# Check resulting parameters
expected_angles = {(0, 1, 2): 128.2771922378,
(0, 1, 7): 133.1339832262,
(0, 5, 4): 128.2771922378,
(0, 5, 11): 133.1339832262,
(1, 0, 5): 128.2771922378,
(1, 0, 6): 133.1339832262,
(1, 2, 3): 128.2771922378,
(1, 2, 8): 133.1339832262,
(2, 1, 7): 133.1339832262,
(2, 3, 4): 128.2771922378,
(2, 3, 9): 133.1339832262,
(3, 2, 8): 133.1339832262,
(3, 4, 5): 128.2771922378,
(3, 4, 10): 133.1339832262,
(4, 3, 9): 133.1339832262,
(4, 5, 11): 133.1339832262,
(5, 0, 6): 133.1339832262,
(5, 4, 10): 133.1339832262}
expected_ks = {(0, 1, 2): 157.3576298529,
(0, 1, 7): 68.40592742547,
(0, 5, 4): 157.3576298529,
(0, 5, 11): 68.40592742547,
(1, 0, 5): 157.3576298529,
(1, 0, 6): 68.40592742547,
(1, 2, 3): 157.3576298529,
(1, 2, 8): 68.40592742547,
(2, 1, 7): 68.40592742547,
(2, 3, 4): 157.3576298529,
(2, 3, 9): 68.40592742547,
(3, 2, 8): 68.40592742547,
(3, 4, 5): 157.3576298529,
(3, 4, 10): 68.40592742547,
(4, 3, 9): 68.40592742547,
(4, 5, 11): 68.40592742547,
(5, 0, 6): 68.40592742547,
(5, 4, 10): 68.40592742547}
for indexes, properties in dict(molecule.parameters['Angles']).items():
expected_angle = unit.Quantity(expected_angles[indexes],
unit.degree)
expected_k = unit.Quantity(expected_ks[indexes],
unit.kilocalorie
/ (unit.radian ** 2 * unit.mole))
assert properties.angle - expected_angle \
< unit.Quantity(MAX_THRESHOLD, unit.degree), \
'Invalid length for angle {} {}'.format(indexes, properties)
assert properties.k - expected_k \
< unit.Quantity(MAX_THRESHOLD, unit.kilocalorie
/ (unit.radian ** 2 * unit.mole)), \
'Invalid k for angle {} {}'.format(indexes, properties)
def test_OFF_parameters(self):
"""
It checks the standard Open Force Field parameterization for
dihedrals.
"""
MAX_THRESHOLD = 1e-3
# Load molecule
molecule = Molecule(smiles='C=CC(=O)O')
# Parameterize
molecule.parameterize('openff_unconstrained-1.2.0.offxml',
charges_method='gasteiger')
# Check resulting parameters for proper torsions
expected_ks = {(0, 1, 2, 3): [0.603518062312, 0.5248455212365],
(0, 1, 2, 4): [0.9350453896311],
(1, 2, 4, 8): [2.529110648699],
(2, 1, 0, 5): [5.376019778605],
(2, 1, 0, 6): [5.376019778605],
(3, 2, 1, 7): [0.9350453896311],
(3, 2, 4, 8): [2.237928151469, 1.23728649144],
(4, 2, 1, 7): [0.9350453896311],
(5, 0, 1, 7): [5.376019778605],
(6, 0, 1, 7): [5.376019778605]}
expected_phases = {(0, 1, 2, 3): [180.0, 0.0],
(0, 1, 2, 4): [180.0],
(1, 2, 4, 8): [180.0],
(2, 1, 0, 5): [180.0],
(2, 1, 0, 6): [180.0],
(3, 2, 1, 7): [180.0],
(3, 2, 4, 8): [180.0, 0.0],
(4, 2, 1, 7): [180.0],
(5, 0, 1, 7): [180.0],
(6, 0, 1, 7): [180.0]}
expected_periodicities = {(0, 1, 2, 3): [2, 3],
(0, 1, 2, 4): [2],
(1, 2, 4, 8): [2],
(2, 1, 0, 5): [2],
(2, 1, 0, 6): [2],
(3, 2, 1, 7): [2],
(3, 2, 4, 8): [2, 1],
(4, 2, 1, 7): [2],
(5, 0, 1, 7): [2],
(6, 0, 1, 7): [2]}
expected_idivfs = {(0, 1, 2, 3): [1.0, 1.0],
(0, 1, 2, 4): [1.0],
(1, 2, 4, 8): [1.0],
(2, 1, 0, 5): [1.0],
(2, 1, 0, 6): [1.0],
(3, 2, 1, 7): [1.0],
(3, 2, 4, 8): [1.0, 1.0],
(4, 2, 1, 7): [1.0],
(5, 0, 1, 7): [1.0],
(6, 0, 1, 7): [1.0]}
for indexes, properties in dict(
molecule.parameters['ProperTorsions']).items():
for i, (k, phase, periodicity, idivf) in enumerate(
zip(properties.k, properties.phase,
properties.periodicity, properties.idivf)):
expected_k = unit.Quantity(expected_ks[indexes][i],
unit.kilocalorie / unit.mole)
expected_phase = unit.Quantity(expected_phases[indexes][i],
unit.degree)
expected_periodicity = expected_periodicities[indexes][i]
expected_idivf = expected_idivfs[indexes][i]
assert k - expected_k < \
unit.Quantity(MAX_THRESHOLD,
unit.kilocalorie / unit.mole), \
'Invalid k for proper torsion ' \
+ '{} {}'.format(indexes, properties)
assert phase - expected_phase < \
unit.Quantity(MAX_THRESHOLD, unit.degree), \
'Invalid phase for proper torsion ' \
+ '{} {}'.format(indexes, properties)
assert periodicity - expected_periodicity < MAX_THRESHOLD, \
'Invalid periodicity for proper torsion ' \
+ '{} {}'.format(indexes, properties)
assert idivf - expected_idivf < MAX_THRESHOLD, \
'Invalid idivf for proper torsion ' \
+ '{} {}'.format(indexes, properties)
# Check resulting parameters for improper torsions
expected_ks = {(0, 1, 2, 7): [1.1],
(1, 0, 5, 6): [1.1],
(1, 2, 3, 4): [10.5]}
expected_phases = {(0, 1, 2, 7): [180.0],
(1, 0, 5, 6): [180.0],
(1, 2, 3, 4): [180.0]}
expected_periodicities = {(0, 1, 2, 7): [2],
(1, 0, 5, 6): [2],
(1, 2, 3, 4): [2]}
for indexes, properties in dict(
molecule.parameters['ImproperTorsions']).items():
for i, (k, phase, periodicity) in enumerate(
zip(properties.k, properties.phase,
properties.periodicity)):
expected_k = unit.Quantity(expected_ks[indexes][i],
unit.kilocalorie / unit.mole)
expected_phase = unit.Quantity(expected_phases[indexes][i],
unit.degree)
expected_periodicity = expected_periodicities[indexes][i]
assert k - expected_k < \
unit.Quantity(MAX_THRESHOLD,
unit.kilocalorie / unit.mole), \
'Invalid k for improper torsion ' \
+ '{} {}'.format(indexes, properties)
assert phase - expected_phase < \
unit.Quantity(MAX_THRESHOLD, unit.degree), \
'Invalid phase for improper torsion ' \
+ '{} {}'.format(indexes, properties)
assert periodicity - expected_periodicity < MAX_THRESHOLD, \
'Invalid periodicity for improper torsion ' \
+ '{} {}'.format(indexes, properties)
assert properties.idivf is None, \
'Invalid idivf for improper torsion ' \
+ '{} {}'.format(indexes, properties)
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'
def run_offpele(pdb_file,
forcefield=DEFAULT_OFF_FORCEFIELD,
resolution=DEFAULT_RESOLUTION,
charges_method=DEFAULT_CHARGES_METHOD,
use_OPLS_nb_params=False,
use_OPLS_bonds_and_angles=False,
exclude_terminal_rotamers=True,
output=None,
with_solvent=False,
as_datalocal=False):
"""
It runs offpele.
Parameters
----------
pdb_file : str
The path to the pdb_file to parameterize with offpele
forcefield : str
The name of an OpenForceField's forcefield
resolution : float
The resolution in degrees for the rotamer library. Default is 30
charges_method : str
The name of the method to use to compute partial charges. Default
is 'am1bcc'
use_OPLS_nb_params : bool
Whether to use Open Force Field or OPLS to obtain the
nonbonding parameters. Please, note that this option is only
available if a valid Schrodinger installation is found in the
current machine. Default is False
use_OPLS_bonds_and_angles : bool
Whether to use OPLS to obtain the bond and angle parameters
or not. Please, note that this option is only
available if a valid Schrodinger installation is found in the
current machine. Default is False
exclude_terminal_rotamers : bool
Whether to exclude terminal rotamers or not
output : str
Path where output files will be saved
with_solvent : bool
Whether to generate and save the solvent parameters for the input
molecule or not
as_datalocal : bool
Whether to save output files following PELE's DataLocal hierarchy or
not
"""
print('-' * 60)
print('Open Force Field parameterizer for PELE', offpele.__version__)
print('-' * 60)
print(' - General:')
print(' - Input PDB:', pdb_file)
print(' - Output path:', output)
print(' - Write solvent parameters:', with_solvent)
print(' - DataLocal-like output:', as_datalocal)
print(' - Parameterization:')
print(' - Force field:', forcefield)
print(' - Charges method:', charges_method)
print(' - Use OPLS nonbonding parameters:', use_OPLS_nb_params)
print(' - Use OPLS bonds and angles:', use_OPLS_bonds_and_angles)
print(' - Rotamer library:')
print(' - Resolution:', resolution)
print(' - Exclude terminal rotamers:', exclude_terminal_rotamers)
print('-' * 60)
# Supress OpenForceField toolkit warnings
import logging
logging.getLogger().setLevel(logging.ERROR)
from offpele.topology import Molecule
from offpele.template import Impact
from offpele.solvent import OBC2
if not output:
output = os.getcwd()
molecule = Molecule(pdb_file,
rotamer_resolution=resolution,
exclude_terminal_rotamers=exclude_terminal_rotamers)
rotlib_out, impact_out, solvent_out = handle_output_paths(
molecule, output, as_datalocal)
rotamer_library = offpele.topology.RotamerLibrary(molecule)
rotamer_library.to_file(rotlib_out)
molecule.parameterize(forcefield,
charges_method=charges_method,
use_OPLS_nonbonding_params=use_OPLS_nb_params,
use_OPLS_bonds_and_angles=use_OPLS_bonds_and_angles)
impact = Impact(molecule)
impact.write(impact_out)
if with_solvent:
solvent = OBC2(molecule)
solvent.to_json_file(solvent_out)
print(' - All files were generated successfully')
print('-' * 60)
def test_terminal_rotamer_filtering(self):
"""
It tests the rotamer library builder when the terminal rotatable bonds
are ignored.
"""
LIGAND_PATH = 'ligands/OLC.pdb'
ligand_path = get_data_file_path(LIGAND_PATH)
molecule = Molecule(ligand_path, exclude_terminal_rotamers=True)
rotamers_per_branch = molecule.rotamers
assert len(rotamers_per_branch) == 2, "Found an invalid number " + \
"of branches: {}".format(len(rotamers_per_branch))
atom_list_1 = list()
atom_list_2 = list()
rotamers = rotamers_per_branch[0]
for rotamer in rotamers:
atom_list_1.append(set([rotamer.index1, rotamer.index2]))
rotamers = rotamers_per_branch[1]
for rotamer in rotamers:
atom_list_2.append(set([rotamer.index1, rotamer.index2]))
EXPECTED_INDICES_1 = [
set([9, 10]),
set([8, 9]),
set([7, 8]),
set([6, 7]),
set([5, 6]),
set([2, 5]),
set([0, 2]),
set([0, 1])
]
EXPECTED_INDICES_2 = [
set([12, 11]),
set([12, 13]),
set([13, 14]),
set([14, 15]),
set([15, 16]),
set([16, 17]),
set([17, 18])
]
where_1 = list()
for atom_pair in atom_list_1:
if atom_pair in EXPECTED_INDICES_1:
where_1.append(1)
elif atom_pair in EXPECTED_INDICES_2:
where_1.append(2)
else:
where_1.append(0)
where_2 = list()
for atom_pair in atom_list_2:
if atom_pair in EXPECTED_INDICES_1:
where_2.append(1)
elif atom_pair in EXPECTED_INDICES_2:
where_2.append(2)
else:
where_2.append(0)
assert (all(i == 1 for i in where_1)
and all(i == 2 for i in where_2)) or \
(all(i == 2 for i in where_1)
and all(i == 1 for i in where_2)), "Invalid rotamer library " + \
"{}, {}".format(where_1, where_2)
assert (all(i == 1 for i in where_1)
and all(i == 2 for i in where_2)
and len(where_1) == len(EXPECTED_INDICES_1)
and len(where_2) == len(EXPECTED_INDICES_2)) or \
(all(i == 2 for i in where_1)
and all(i == 1 for i in where_2)
and len(where_1) == len(EXPECTED_INDICES_2)
and len(where_2) == len(EXPECTED_INDICES_1)), "Unexpected " + \
"number of rotamers"