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
# 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'
lj = LennardJones(pro)
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', is_protein=True)
# 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):
printf("starting protein prep, reading pdb file...")
protein = Protein(values)
printf(f"{len(protein.residues)} residues found!")
# TODO find the magic numbers for the box for onetep
protein.write_xyz(name="protein")
printf(f"protein.xyz file made for ONETEP\n Run this file")
sys.exit()
def __call__(self, pars, namespace, values, option_string=None):
"""This function is executed when setup is called."""
printf('starting protein prep, reading pdb file...')
protein = Protein(values)
printf(f'{len(protein.Residues)} residues found!')
# TODO find the magic numbers for the box for onetep
protein.write_xyz(name='protein')
printf(f'protein.xyz file made for ONETEP\n Run this file')
sys.exit()
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 test_from_pdb():
"""
Make sure we can make a protein from a pdb file.
"""
pro = Protein.from_file(file_name=get_data("capped_leu.pdb"))
assert pro.n_atoms == 31
assert pro.coordinates.shape == (pro.n_atoms, 3)
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)
def setUpClass(cls):
"""
Write the big string in test_structures to a file to be used for testing.
Cannot use actual files as pathing causes issues.
"""
with open('aceleunme.pdb', 'w+') as pdb_test_file:
pdb_test_file.write(aceleunme)
cls.molecule = Protein('aceleunme.pdb')
def setUpClass(cls):
"""Create temp working directory and copy across test files."""
cls.files_folder = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'files')
os.mkdir('temp')
os.chdir('temp')
copy(os.path.join(cls.files_folder, 'capped_leu.pdb'), 'capped_leu.pdb')
cls.molecule = Protein('capped_leu.pdb')
cls.molecule.testing = True
def test_pdb_round_trip(tmpdir):
"""
Make sure we can round trip a protein to pdb.
"""
with tmpdir.as_cwd():
pro = Protein.from_file(file_name=get_data("capped_leu.pdb"))
pro.write_pdb(name="test")
pro2 = Protein.from_file("test.pdb")
assert pro.n_atoms == pro2.n_atoms
assert pro.n_bonds == pro.n_bonds
for bond in pro.bonds:
assert bond in pro2.bonds
for angle in pro.angles:
assert angle in pro2.angles
for central_bond, torsions in pro.dihedrals.items():
for d in torsions:
assert d in pro2.dihedrals[central_bond]
def setUp(self):
"""
Set up a protein testing class, make temp folder and copy capped leu file
"""
self.home = os.getcwd()
self.test_folder = os.path.join(os.path.dirname(__file__), 'files')
# Make the temp folder and move there with the required files
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
copy(os.path.join(self.test_folder, 'capped_leu.pdb'),
'capped_leu.pdb')
self.molecule = Protein('capped_leu.pdb')
def setUpClass(cls):
cls.files_folder = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'files')
os.mkdir('temp')
os.chdir('temp')
copy(os.path.join(cls.files_folder, 'capped_leu.pdb'), 'capped_leu.pdb')
cls.molecule = Protein('capped_leu.pdb')
def test_not_pdb():
"""
Make sure an error is raised if we try and make a protein from a non pdb file.
"""
with pytest.raises(FileTypeError):
_ = Protein.from_file(file_name=get_data("bace0.xyz"))
def test_normal_init():
"""
Make sure a pdb file is directed to the from pdb path.
"""
pro = Protein(get_data("capped_leu.pdb"))
assert pro.n_atoms == 31