def _generate_parameters(self):
"""
It generates the parameters of the molecule (from the input_file) as DataLocal in the output folder.
"""
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
# Forcefield and charges method
forcefield = 'openff_unconstrained-1.2.0.offxml'
charges_method = 'am1bcc'
# Create representation of a particular molecule
PATH_molecule = os.path.join(os.getcwd(), 'output', 'ligand.pdb')
molecule = Molecule(PATH_molecule)
# Saving paths
rotamer_library_output_path, impact_output_path, solvent_output_path = \
handle_output_paths(molecule = molecule, output =os.path.join(os.getcwd(),'output'), 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)
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)
def parallel_run(output_path, solvent, charge_method, pele_exec, pele_src,
pele_license, forcefield_name, forcefield, entry):
"""Parallel runner."""
cid, tag, exp_v = entry
try:
molecule = Molecule(smiles=tag, name=cid, tag='LIG')
if forcefield_name is not None:
molecule.parameterize(forcefield_name, charge_method=charge_method)
elif forcefield is not None:
molecule.set_forcefield(forcefield)
molecule.parameterize(charge_method=charge_method)
if ((molecule.forcefield.type == 'OPLS2005')
or (molecule.forcefield.type == 'OpenFF + OPLS2005'
and molecule.forcefield._nonbonding == 'opls2005')):
if solvent == 'OBC':
# Generate OBC parameters for OPLS2005
from peleffy.template import Impact
os.makedirs(os.path.join(output_path, cid), exist_ok=True)
impact = Impact(molecule)
impact.write(os.path.join(output_path, cid, 'ligz'))
os.makedirs(os.path.join(output_path, cid, 'DataLocal/OBC/'),
exist_ok=True)
os.system('python2 {}scripts/solventOBCParamsGenerator.py '.
format(pele_src) +
os.path.join(output_path, cid, 'ligz') +
' >> /dev/null')
shutil.copy(
'{}Data/OBC/solventParamsHCTOBC.txt'.format(pele_src),
os.path.join(output_path, cid, 'DataLocal/OBC/'))
os.system('cat ' + os.path.join(
output_path, cid, 'ligz_OBCParams.txt >> ' +
os.path.join(output_path, cid,
'DataLocal/OBC/solventParamsHCTOBC.txt')))
os.remove(os.path.join(output_path, cid, 'ligz'))
os.remove(os.path.join(output_path, cid, 'ligz_OBCParams.txt'))
forcefield_tag = 'OPLS2005'
else:
forcefield_tag = 'OpenForceField'
# Minimization
pele_vacuum_min = PELEMinimization(pele_exec,
pele_src,
pele_license,
solvent_type='VACUUM',
output_path=output_path,
forcefield=forcefield_tag)
pele_vacuum_out = pele_vacuum_min.run(molecule,
output_file='vacuum_out.txt')
pele_obc_min = PELEMinimization(pele_exec,
pele_src,
pele_license,
solvent_type=solvent,
output_path=output_path,
forcefield=forcefield_tag)
pele_obc_out = pele_obc_min.run(molecule,
output_file='solvent_out.txt')
# Calculate energetic difference
difference = compute_energies(pele_vacuum_out, pele_obc_out)[2]
return tuple((cid, difference, exp_v))
except Exception as e:
print('Exception found with compound {}: '.format(cid) + str(e))