def __call__(self, pars, namespace, values, option_string=None):
pro = Protein(values)
# print the QUBE general FF to use in the parametrisation
qube_general()
# now we want to add the connections and parametrise the protein
XMLProtein(pro)
# finally we need the non-bonded parameters from onetep
# TODO should we also have the ability to get DDEC6 charges from the cube file?
pro.charge = 0
pro.charges_engine = "onetep"
pro.density_engine = "onetep"
ExtractChargeData(pro).extract_charge_data()
LennardJones(pro).calculate_non_bonded_force()
# Write out the final parameters
printf("Writing pdb file with connections...")
pro.write_pdb(name=f"QUBE_pro_{pro.name}")
printf("Writing XML file for the system...")
pro.write_parameters(name=f"QUBE_pro_{pro.name}")
# now remove the qube general file
os.remove("QUBE_general_pi.xml")
printf("Done")
sys.exit()
def __call__(self, pars, namespace, values, option_string=None):
"""This function is executed when build is called."""
pro = Protein(values)
# print the QUBE general FF to use in the parametrisation
qube_general()
# now we want to add the connections and parametrise the protein
XMLProtein(pro)
# this updates the bonded info that is now in the object
# finally we need the non-bonded parameters from onetep
# fake configs as this will always be true
# TODO should we also have the ability to get DDEC6 charges from the cube file?
configs = [{'charge': 0}, {'charges_engine': 'onetep', 'density_engine': 'onetep'}, {}, {}]
lj = LennardJones(pro, config_dict=configs)
pro.NonbondedForce = lj.calculate_non_bonded_force()
# now we write out the final parameters
# we should also calculate the charges and lj at this point!
printf('Writing pdb file with connections...')
pro.write_pdb(name='QUBE_pro')
printf('Writing XML file for the system...')
pro.write_parameters(name='QUBE_pro', protein=True)
# now remove the qube general file
os.remove('QUBE_general_pi.xml')
printf('Done')
sys.exit()
def test_protein_params(tmpdir):
"""
Load up the small protein and make sure it is parametrised with the general qube forcefield.
"""
with tmpdir.as_cwd():
pro = Protein.from_file(file_name=get_data("capped_leu.pdb"))
shutil.copy(get_data("capped_leu.pdb"), "capped_leu.pdb")
XMLProtein(protein=pro)