def __init__(self, forcefield_files=None, name=None):
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)
super(Forcefield, self).__init__(*all_files_to_load)
self.parser = smarts.SMARTS(self.non_element_types)
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.atomTypeClasses = dict()
self.atomTypeElements = dict()
self._included_forcefields = dict()
self.non_element_types = dict()
self._version = None
self._name = None
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)
try:
super(Forcefield, self).__init__(*preprocessed_files)
finally:
for ff_file_name in preprocessed_files:
os.remove(ff_file_name)
if isinstance(forcefield_files, str):
self._version = self._parse_version_number(forcefield_files)
self._name = self._parse_name(forcefield_files)
elif isinstance(forcefield_files, list):
self._version = [
self._parse_version_number(f) for f in forcefield_files
]
self._name = [self._parse_name(f) for f in forcefield_files]
self.parser = smarts.SMARTS(self.non_element_types)
self._SystemData = self._SystemData()
def __init__(self,
forcefield_files=None,
name=None,
backend="gmso",
**kwargs):
self.atomTypeDefinitions = dict()
self.atomTypeOverrides = dict()
self.atomTypeDesc = dict()
self.atomTypeRefs = dict()
self.atomTypeClasses = dict()
self.atomTypeElements = dict()
self._included_forcefields = dict()
self.backend = backend
self.non_element_types = dict()
self._version = None
self._name = None
all_files_to_load = []
if forcefield_files is not None:
if isinstance(forcefield_files, (list, tuple, set)):
all_files_to_load = list(forcefield_files)
else:
all_files_to_load = [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 = [file]
# Preprocessed the input files
preprocessed_files = preprocess_forcefield_files(all_files_to_load,
backend=backend)
# Load in an internal forcefield object depends on given backend
if backend == "gmso":
self._parse_gmso(preprocessed_files, **kwargs)
else:
raise FoyerError("Backend not supported."
'Supoprts backend: "gmso".')
# Remove the temporary files afterward
for ff_file_name in preprocessed_files:
os.remove(ff_file_name)
self.parser = smarts.SMARTS(self.non_element_types)
