def test_charge_molecule(self):
"""Test case for charge_molecule
Submit a molecule for charging
"""
cur_dir = Path(__file__).parent
test_data = cur_dir.parents[1] / 'charge' / 'test' / 'sample_lgf'
repo = Repository.create_from(str(test_data))
with tempfile.TemporaryDirectory() as tmpdir:
repo_location = str(Path(tmpdir) / 'repo.zip')
repo.write(repo_location)
charge_server.init(repo_location)
test_lgf = ('@nodes\n'
'label\tlabel2\tatomType\tinitColor\t\n'
'1\tC1\t12\t0\t\n'
'2\tH1\t20\t0\t\n'
'3\tH2\t20\t0\t\n'
'4\tH3\t20\t0\t\n'
'5\tH4\t20\t0\t\n'
'@edges\n'
'\t\tlabel\t\n'
'1\t2\t0\t\n'
'1\t3\t1\t\n'
'1\t4\t2\t\n'
'1\t5\t3\t\n')
query_string = [('total_charge', 0)]
response = self.client.open('/charge_assign',
method='POST',
data=test_lgf,
content_type='text/plain',
query_string=query_string)
self.assert200(response,
'Response body is : ' + response.data.decode('utf-8'))
def main() -> None:
args = get_args()
repo = Repository.create_from(args.input,
max_shell=args.max_shell,
traceable=args.traceable)
repo.write(args.repository)
def test_create_traceable_from_dir(lgf_data_dir):
repo = Repository.create_from(str(lgf_data_dir), traceable=True)
assert repo._Repository__min_shell == 1
assert repo._Repository__max_shell == 7
assert repo._Repository__traceable == True
assert repo._Repository__versioning == False
assert len(repo.charges_iacm) == 7
assert len(repo.charges_iacm[1]) == 10
assert len(repo.charges_iacm[2]) == 14
assert len(repo.charges_iacm[3]) == 15
assert repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'] == [
(-0.516, 15610, 2)
]
assert repo.charges_iacm[3]['76198d87470cc1b2f871da60449146bc'] == [
(0.077, 1204, 1), (0.077, 1204, 4), (0.077, 1204, 5)
]
assert len(repo.charges_elem) == 7
assert len(repo.charges_elem[1]) == 9
assert len(repo.charges_elem[2]) == 14
assert len(repo.charges_elem[3]) == 15
assert repo.charges_elem[1]['92ed00c54b2190be94748bee34b22847'] == [
(-0.516, 15610, 2)
]
assert repo.charges_elem[3]['17ac3199bf634022485c145821f358d5'] == [
(0.077, 1204, 1), (0.077, 1204, 4), (0.077, 1204, 5)
]
assert hasattr(repo, 'iso_iacm')
assert hasattr(repo, 'iso_elem')
assert len(repo.iso_iacm) == 2
assert len(repo.iso_elem) == 2
def test_read_write_versioning(lgf_data_dir):
repo0 = Repository.create_from(str(lgf_data_dir), versioning=True)
tmp = BytesIO()
repo0.write(tmp)
repo1 = Repository.read(tmp, versioning=True)
assert repo0._Repository__min_shell == repo1._Repository__min_shell
assert repo0._Repository__max_shell == repo1._Repository__max_shell
assert repo0._Repository__traceable == repo1._Repository__traceable
assert repo0._Repository__versioning == repo1._Repository__versioning
assert repo0.charges_iacm == repo1.charges_iacm
assert repo0.charges_elem == repo1.charges_elem
assert not hasattr(repo0, 'iso_iacm')
assert not hasattr(repo0, 'iso_elem')
assert not hasattr(repo1, 'iso_iacm')
assert not hasattr(repo1, 'iso_elem')
assert isinstance(
repo1.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'],
_VersioningList)
assert isinstance(
repo1.charges_iacm[3]['76198d87470cc1b2f871da60449146bc'],
_VersioningList)
assert isinstance(
repo1.charges_elem[1]['92ed00c54b2190be94748bee34b22847'],
_VersioningList)
assert isinstance(
repo1.charges_elem[3]['17ac3199bf634022485c145821f358d5'],
_VersioningList)
def test_read_write_traceable(lgf_data_dir):
repo0 = Repository.create_from(str(lgf_data_dir), traceable=True)
tmp = BytesIO()
repo0.write(tmp)
repo1 = Repository.read(tmp)
assert repo0._Repository__min_shell == repo1._Repository__min_shell
assert repo0._Repository__max_shell == repo1._Repository__max_shell
assert repo0._Repository__traceable == repo1._Repository__traceable
assert repo0._Repository__versioning == repo1._Repository__versioning
# msgpack writes tuples as lists. this is ok for our purposes, but we need to take care of that in testing!
assert repo0.charges_iacm.keys() == repo1.charges_iacm.keys()
for shell_size in repo0.charges_iacm.keys():
assert repo0.charges_iacm[shell_size].keys(
) == repo1.charges_iacm[shell_size].keys()
for key in repo0.charges_iacm[shell_size].keys():
assert repo0.charges_iacm[shell_size][key] == [
tuple(x) for x in repo0.charges_iacm[shell_size][key]
]
assert repo0.charges_elem.keys() == repo1.charges_elem.keys()
for shell_size in repo0.charges_elem.keys():
assert repo0.charges_elem[shell_size].keys(
) == repo1.charges_elem[shell_size].keys()
for key in repo0.charges_elem[shell_size].keys():
assert repo0.charges_elem[shell_size][key] == [
tuple(x) for x in repo0.charges_elem[shell_size][key]
]
assert repo0.iso_iacm == repo1.iso_iacm
assert repo0.iso_elem == repo1.iso_elem
def test_create_versioning_from_dir(lgf_data_dir):
repo = Repository.create_from(str(lgf_data_dir), versioning=True)
assert repo._Repository__min_shell == 1
assert repo._Repository__max_shell == 7
assert repo._Repository__traceable == False
assert repo._Repository__versioning == True
assert len(repo.charges_iacm) == 7
assert len(repo.charges_iacm[1]) == 10
assert len(repo.charges_iacm[2]) == 14
assert len(repo.charges_iacm[3]) == 15
assert isinstance(repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'],
_VersioningList)
assert isinstance(repo.charges_iacm[3]['76198d87470cc1b2f871da60449146bc'],
_VersioningList)
assert repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'] == [-0.516]
assert repo.charges_iacm[3]['76198d87470cc1b2f871da60449146bc'] == [
0.077, 0.077, 0.077
]
assert len(repo.charges_elem) == 7
assert len(repo.charges_elem[1]) == 9
assert len(repo.charges_elem[2]) == 14
assert len(repo.charges_elem[3]) == 15
assert isinstance(repo.charges_elem[1]['92ed00c54b2190be94748bee34b22847'],
_VersioningList)
assert isinstance(repo.charges_elem[3]['17ac3199bf634022485c145821f358d5'],
_VersioningList)
assert repo.charges_elem[1]['92ed00c54b2190be94748bee34b22847'] == [-0.516]
assert repo.charges_elem[3]['17ac3199bf634022485c145821f358d5'] == [
0.077, 0.077, 0.077
]
assert not hasattr(repo, 'iso_iacm')
assert not hasattr(repo, 'iso_elem')
ov0 = repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].version
repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].append(1)
ov1 = repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].version
repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'] += [2]
ov2 = repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].version
del repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'][-1]
ov3 = repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].version
repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].remove(1)
ov4 = repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'].version
assert len({ov0, ov1, ov2, ov3, ov4}) == 5
def test_remove_from(lgf_data_dir):
repo = Repository.create_from(str(lgf_data_dir))
repo.remove_from(lgf_data_dir)
assert repo._Repository__min_shell == 1
assert repo._Repository__max_shell == 7
assert repo._Repository__traceable == False
assert repo._Repository__versioning == False
assert len(repo.charges_iacm) == 0
assert len(repo.charges_elem) == 0
assert not hasattr(repo, 'iso_iacm')
assert not hasattr(repo, 'iso_elem')
def test_add_from_versioning(lgf_data_dir):
repo = Repository.create_from(str(lgf_data_dir), versioning=True)
repo.add_from(lgf_data_dir)
assert repo._Repository__min_shell == 1
assert repo._Repository__max_shell == 7
assert repo._Repository__traceable == False
assert repo._Repository__versioning == True
assert len(repo.charges_iacm) == 7
assert len(repo.charges_iacm[1]) == 10
assert len(repo.charges_iacm[2]) == 14
assert len(repo.charges_iacm[3]) == 15
assert repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'] == [
-0.516, -0.516
]
assert repo.charges_iacm[3]['76198d87470cc1b2f871da60449146bc'] == [
0.077, 0.077, 0.077, 0.077, 0.077, 0.077
]
assert len(repo.charges_elem) == 7
assert len(repo.charges_elem[1]) == 9
assert len(repo.charges_elem[2]) == 14
assert len(repo.charges_elem[3]) == 15
assert repo.charges_elem[1]['92ed00c54b2190be94748bee34b22847'] == [
-0.516, -0.516
]
assert repo.charges_elem[3]['17ac3199bf634022485c145821f358d5'] == [
0.077, 0.077, 0.077, 0.077, 0.077, 0.077
]
assert not hasattr(repo, 'iso_iacm')
assert not hasattr(repo, 'iso_elem')
assert isinstance(repo.charges_iacm[1]['c18208da9e290c6faf8a0c58017d24d9'],
_VersioningList)
assert isinstance(repo.charges_iacm[3]['76198d87470cc1b2f871da60449146bc'],
_VersioningList)
assert isinstance(repo.charges_elem[1]['92ed00c54b2190be94748bee34b22847'],
_VersioningList)
assert isinstance(repo.charges_elem[3]['17ac3199bf634022485c145821f358d5'],
_VersioningList)
def test_read_write(lgf_data_dir):
repo0 = Repository.create_from(str(lgf_data_dir))
tmp = BytesIO()
repo0.write(tmp)
repo1 = Repository.read(tmp)
assert repo0._Repository__min_shell == repo1._Repository__min_shell
assert repo0._Repository__max_shell == repo1._Repository__max_shell
assert repo0._Repository__traceable == repo1._Repository__traceable
assert repo0._Repository__versioning == repo1._Repository__versioning
assert repo0.charges_iacm == repo1.charges_iacm
assert repo0.charges_elem == repo1.charges_elem
assert not hasattr(repo0, 'iso_iacm')
assert not hasattr(repo0, 'iso_elem')
assert not hasattr(repo1, 'iso_iacm')
assert not hasattr(repo1, 'iso_elem')
def cross_validate_methods(
data_location: str,
data_type: IOType = IOType.LGF,
min_shell: Optional[int] = None,
max_shell: Optional[int] = None
) -> Tuple[Dict[str, Dict[bool, float]], Dict[str, Dict[bool, float]]]:
"""Cross-validates all methods on the given molecule data.
Args:
data_location: Path to the directory with the molecule data.
data_type: Format of the molecule data to expect.
min_shell: Smallest shell size to use.
max_shell: Largest shell size to use.
Returns:
Dictionaries keyed by charger name and whether IACM atoms were \
used, containing the mean absolute error and the mean \
square error respectively.
"""
repo = Repository.create_from(data_location, data_type, min_shell, max_shell,
traceable=True)
shell = range[max_shell, min_shell-1, -1]
mean_abs_err = dict()
mean_sq_err = dict()
for charger_type in [MeanCharger, MedianCharger, ModeCharger, ILPCharger, DPCharger, CDPCharger, SymmetricILPCharger, SymmetricILPCharger, SymmetricCDPCharger]:
charger_name = charger_type.__name__
mean_abs_err[charger_name] = dict()
mean_sq_err[charger_name] = dict()
for iacm in [True, False]:
mae, mse = (
cross_validate_molecules(
charger_name, iacm, data_location, data_type, shell, repo))
mean_abs_err[charger_name][iacm] = mae
mean_sq_err[charger_name][iacm] = mse
return mean_abs_err, mean_sq_err
import os
from charge.repository import Repository
if __name__ == '__main__':
test_data_dir = os.path.realpath(
os.path.join(__file__, '..', 'cross_validation_data'))
out_file = 'cross_validation_repository.zip'
repo = Repository.create_from(test_data_dir,
min_shell=0,
max_shell=3,
traceable=True)
repo.write(out_file)
def cross_validate_molecules(
charger_type: str,
iacm: bool,
data_location: str,
data_type: IOType = IOType.LGF,
shell: Union[None, int, Iterable[int]] = None,
repo: Optional[Repository] = None,
bucket: int = 0,
num_buckets: int = 1
) -> ValidationReport:
"""Cross-validates a particular method on the given molecule data.
Runs through all the molecules in the repository, and for each, \
predicts charges using the given charger type and from the rest of \
the molecules in the repository.
If iacm is False, the test molecule is stripped of its charge data \
and its IACM atom types, leaving only plain elements. It is then \
matched first against the IACM side of the repository, and if that \
yields no charges, against the plain element side of the repository.
If iacm is True, the test molecule is stripped of charges but keeps \
its IACM atom types. It is then matched against the IACM side of the \
repository, and if no matches are found, its plain elements are \
matched against the plain element side.
If bucket and num_buckets are specified, then this will only run \
the cross-validation if (molid % num_buckets) == bucket.
Args:
charger_type: Name of a Charger-derived class implementing an \
assignment method.
iacm: Whether to use IACM or plain element atoms.
data_location: Path to the directory with the molecule data.
data_type: Format of the molecule data to expect.
shell: (List of) shell size(s) to use.
repo: A Repository with traceable charges.
bucket: Cross-validate for this bucket.
num_buckets: Total number of buckets that will run.
Returns:
A dict containing AtomReports per element category, and a
MoleculeReport. Keyed by category name, and 'Molecule' for
the per-molecule statistics.
"""
if shell is None:
min_shell, max_shell = None, None
wanted_shells = None
else:
if isinstance(shell, int):
shell = [shell]
min_shell, max_shell = min(shell), max(shell)
wanted_shells = sorted(shell, reverse=True)
if repo is None:
if min_shell is not None:
repo = Repository.create_from(data_location, data_type, min_shell,
max_shell, traceable=True)
else:
repo = Repository.create_from(data_location, data_type,
traceable=True)
if wanted_shells is None:
shells = sorted(repo.charges_iacm.keys(), reverse=True)
else:
shells = []
for s in wanted_shells:
if s not in repo.charges_iacm.keys():
msg = 'Shell {} will not be used, as it is not in the repository'
warn(msg.format(s))
else:
shells.append(s)
nauty = Nauty()
extension = data_type.get_extension()
molids = [int(fn.replace(extension, ''))
for fn in os.listdir(data_location)
if fn.endswith(extension)]
report = ValidationReport()
for molid in molids:
if (molid % num_buckets) == bucket:
#print('molid: {}'.format(molid))
mol_path = os.path.join(data_location, '{}{}'.format(molid, extension))
with open(mol_path, 'r') as f:
graph = convert_from(f.read(), data_type)
report += cross_validate_molecule(repo, molid, graph, charger_type, shells, iacm, nauty)
return report
def test_remove_from_traceable(lgf_data_dir):
repo = Repository.create_from(str(lgf_data_dir), traceable=True)
with pytest.raises(ValueError):
repo.remove_from(lgf_data_dir)