def test_xmls(ff_file):
file_name = os.path.split(ff_file)[1]
if 'error' in file_name:
error_type = ERRORS[file_name.split('_')[0]]
with pytest.raises(error_type):
Validator(ff_file)
elif file_name.startswith('warning'):
with pytest.warns(ValidationWarning):
Validator(ff_file)
else:
Validator(ff_file)
def test_xmls(self, ff_file):
file_name = os.path.split(ff_file)[1]
if "error" in file_name:
error_type = ERRORS[file_name.split("_")[0]]
with pytest.raises(error_type):
Validator(ff_file)
elif file_name.startswith("warning"):
with pytest.warns(ValidationWarning):
Validator(ff_file)
else:
Validator(ff_file)
def __init__(self, forcefield_files=None, name=None, validation=True, debug=False):
self.atomTypeDefinitions = dict()
self.atomTypeOverrides = dict()
self.atomTypeDesc = dict()
self.atomTypeRefs = dict()
self._included_forcefields = dict()
self.non_element_types = dict()
all_files_to_load = []
if forcefield_files is not None:
if isinstance(forcefield_files, (list, tuple, set)):
for file in forcefield_files:
all_files_to_load.append(file)
else:
all_files_to_load.append(forcefield_files)
if name is not None:
try:
file = self.included_forcefields[name]
except KeyError:
raise IOError('Forcefield {} cannot be found'.format(name))
else:
all_files_to_load.append(file)
preprocessed_files = preprocess_forcefield_files(all_files_to_load)
if validation:
for ff_file_name in preprocessed_files:
Validator(ff_file_name, debug)
super(Forcefield, self).__init__(*preprocessed_files)
self.parser = smarts.SMARTS(self.non_element_types)
def preprocess_forcefield_files(forcefield_files=None, backend="gmso"):
"""Pre-process foyer Forcefield XML files."""
if forcefield_files is None:
return None
tmp_processed_files = list()
if backend == "gmso":
# Run through the forcefield XML conversion
from gmso.external.convert_foyer_xml import from_foyer_xml
for idx, file in enumerate(forcefield_files):
_, suffix = os.path.split(file)
tempfile = NamedTemporaryFile(suffix=suffix, delete=False)
try:
Validator(ff_file_name=file, debug=False)
from_foyer_xml(
foyer_xml=str(file),
gmso_xml=str(tempfile.name),
overwrite=True,
)
except:
warnings.warn(f"Could not convert {str(file)} as a foyer XML,"
f"attempt to read in as a GMSO XML.")
shutil.copyfile(file, tempfile.name)
tmp_processed_files.append(tempfile.name)
else:
raise FoyerError("Backend not supported." 'Supports backend: "gmso".')
return tmp_processed_files
def _validate_foyer(xml_path):
import warnings
from gmso.utils.io import has_foyer
if not has_foyer:
warnings.warn(
'Cannot validate the xml using foyer, since foyer is not installed.'
'Please install foyer using conda install -c conda-forge foyer.'
)
else:
from foyer.validator import Validator
Validator(xml_path)
def test_forcefields(ff_file):
Validator(ff_file)
