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_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/benzene.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', hydrogens_are_explicit=False)
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',
hydrogens_are_explicit=False)
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', hydrogens_are_explicit=False)
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_smiles_initialization(self):
"""
It checks the initialization from a SMILES tag.
"""
molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
# Save it
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
molecule.to_pdb_file('molecule.pdb')
def test_pdb_initialization(self):
"""
It checks the initialization from a PDB file.
"""
ligand_path = get_data_file_path('ligands/ethylene.pdb')
molecule = Molecule(ligand_path)
# Save it
with tempfile.TemporaryDirectory() as tmpdir:
with temporary_cd(tmpdir):
molecule.to_pdb_file('molecule.pdb')
def _generate_parameters(self, smiles, mol_id, output_path,
forcefield='openff_unconstrained-1.2.0.offxml',
charges_method='am1bcc'):
"""
It generates the parameters of the molecule (from the input_file)
as DataLocal in the output folder.
Parameters
----------
smiles : str
The smiles tag representing the molecule to minimize
mol_id : str
Unique id to identify the molecule to minimize
output_path : str
The output path where parameters will be saved
forcefield : str
The Open Force Field force field to generate the parameters
with
charges_method : str
The charges method to calculate the partial charges with
"""
import peleffy
from peleffy.topology import Molecule
from peleffy.template import Impact
from peleffy.solvent import OBC2
from peleffy.main import handle_output_paths
import os
# Create representation of a particular molecule
molecule = Molecule(smiles=smiles, name=mol_id, tag='UNL')
# Save molecule to PDB file
molecule.to_pdb_file(os.path.join(output_path, 'ligand.pdb'))
# Saving paths
rotamer_library_output_path, impact_output_path, \
solvent_output_path = handle_output_paths(molecule=molecule,
output=output_path,
as_datalocal=True)
# Generate its rotamer library
rotamer_library = peleffy.topology.RotamerLibrary(molecule)
rotamer_library.to_file(rotamer_library_output_path)
# Generate its parameters and template file
molecule.parameterize(forcefield, charges_method=charges_method)
impact = Impact(molecule)
impact.write(impact_output_path)
# Generate its solvent parameters
solvent = OBC2(molecule)
solvent.to_json_file(solvent_output_path)