def test_atomtyping(self, only_run=None):
resource_dir = resource_filename('foyer', '../opls_validation')
top_files = glob.glob(os.path.join(resource_dir, '*.top'))
# Please update this file if you implement atom typing for a test case.
implemented_tests_path = os.path.join(os.path.dirname(__file__),
'implemented_opls_tests.txt')
correctly_implemented = [
line.strip() for line in open(implemented_tests_path)
]
for top in top_files:
top_name = os.path.split(top)[-1]
system, known_opls_types, mol_name = load_top_opls(top, only_run)
if only_run and only_run != mol_name:
continue
elif mol_name not in correctly_implemented:
continue
print("Typing {} ({})...".format(mol_name, top_name))
prepare_atoms(system)
find_atomtypes(list(system.atoms),
forcefield='OPLS-AA',
debug=False)
generated_opls_types = list()
for i, atom in enumerate(system.atoms):
message = (
'Found multiple or no OPLS types for atom {} in {} ({}): {}\n'
'Should be atomtype: {}'.format(i, mol_name, top_name,
atom.atomtype[0],
known_opls_types[i]))
assert isinstance(atom.atomtype[0], string_types), message
generated_opls_types.append(atom.atomtype[0])
both = zip(generated_opls_types, known_opls_types)
message = "Found inconsistent OPLS types in {} ({}): {}".format(
mol_name, top_name,
list(
zip(range(len(generated_opls_types)), generated_opls_types,
known_opls_types)))
assert all([a == b for a, b in both]), message
print("Passed.\n")
def test_atomtyping(self, only_run=None):
resource_dir = resource_filename('foyer', '../opls_validation')
top_files = glob.glob(os.path.join(resource_dir, '*.top'))
# Please update this file if you implement atom typing for a test case.
implemented_tests_path = os.path.join(os.path.dirname(__file__), 'implemented_opls_tests.txt')
correctly_implemented = [line.strip() for line in open(implemented_tests_path)]
for top in top_files:
top_name = os.path.split(top)[-1]
system, known_opls_types, mol_name = load_top_opls(top, only_run)
if only_run and only_run != mol_name:
continue
elif mol_name not in correctly_implemented:
continue
print("Typing {} ({})...".format(mol_name, top_name))
prepare_atoms(system)
find_atomtypes(list(system.atoms), forcefield='OPLS-AA', debug=False)
generated_opls_types = list()
for i, atom in enumerate(system.atoms):
message = ('Found multiple or no OPLS types for atom {} in {} ({}): {}\n'
'Should be atomtype: {}'.format(
i, mol_name, top_name, atom.atomtype[0], known_opls_types[i]))
assert isinstance(atom.atomtype[0], string_types), message
generated_opls_types.append(atom.atomtype[0])
both = zip(generated_opls_types, known_opls_types)
message = "Found inconsistent OPLS types in {} ({}): {}".format(
mol_name, top_name, list(zip(range(len(generated_opls_types)),
generated_opls_types,
known_opls_types)))
assert all([a == b for a, b in both]), message
print("Passed.\n")
def uff_C_3(atom):
""" """
return True
@Element('H')
@NeighborCount(1)
@NeighborsExactly('C', 1)
@Whitelist('H_')
def uff_H_(atom):
""" """
return True
if __name__ == "__main__":
from foyer.atomtyper import find_atomtypes
from foyer.forcefield import prepare_atoms
from mbuild.examples.methane.methane import Methane
m = Methane()
# m = Ethane()
traj = m.to_trajectory()
prepare_atoms(traj.top)
find_atomtypes(traj.top._atoms, forcefield='UFF')
for atom in traj.top._atoms:
print("Atom name={}, opls_type={}".format(atom.name, atom.atomtype))
def uff_C_3(atom):
""" """
return True
@Element("H")
@NeighborCount(1)
@NeighborsExactly("C", 1)
@Whitelist("H_")
def uff_H_(atom):
""" """
return True
if __name__ == "__main__":
from foyer.atomtyper import find_atomtypes
from foyer.forcefield import prepare_atoms
from mbuild.examples.methane.methane import Methane
m = Methane()
# m = Ethane()
traj = m.to_trajectory()
prepare_atoms(traj.top)
find_atomtypes(traj.top._atoms, forcefield="UFF")
for atom in traj.top._atoms:
print("Atom name={}, opls_type={}".format(atom.name, atom.atomtype))