from .parser import add_componentSmarts, load_HalogenGroups, load_PFASDefinitions
from .core import HALOGEN_GROUPS_FILE, PFAS_DEFINITIONS_FILE, COMPONENTS_FILE
from .HalogenGroupModel import HalogenGroup
import json
@add_componentSmarts()
def get_compiled_componentSMARTSs(**kwargs):
return kwargs.get('componentSmartss')
[docs]
def get_componentSMARTSs():
with open(COMPONENTS_FILE, 'r') as f:
data = json.load(f)
return data
[docs]
@load_HalogenGroups()
def get_HalogenGroups(**kwargs):
if kwargs.get('json_format',False):
return kwargs.get('pfas_groups',[]).extend(kwargs.get('agg_pfas_groups',[]))
with open(HALOGEN_GROUPS_FILE, 'r') as f:
data = json.load(f)
return data
[docs]
@load_HalogenGroups()
def get_compiled_HalogenGroups(**kwargs):
"""Return compiled HalogenGroup instances (compute=True groups only).
Unlike :func:`get_HalogenGroups` which returns raw JSON dicts, this
function returns ready-to-use :class:`HalogenGroup` instances that can
be directly passed to :func:`parse_smiles` or extended with custom groups.
Returns
-------
list of HalogenGroup
All compiled groups, suitable for passing as *pfas_groups* to
:func:`parse_smiles` or :class:`~PFASGroups.fingerprints.PFASFingerprint`.
Examples
--------
>>> from PFASGroups import get_compiled_HalogenGroups, HalogenGroup, parse_smiles
>>> groups = get_compiled_HalogenGroups()
>>> groups.append(HalogenGroup(
... id=200, name="Perfluoroalkyl nitrates",
... smarts={"[C$(C[ON+](=O)[O-])]": 1},
... componentSaturation="per", componentHalogens="F",
... componentForm="alkyl",
... constraints={"eq": {"N": 1}, "gte": {"F": 1}},
... ))
>>> results = parse_smiles(["FC(F)(F)C(F)(F)ON(=O)=O"], pfas_groups=groups)
"""
return list(kwargs.get('pfas_groups', []))
def get_compiled_PFASGroups() -> list:
"""Return compiled HalogenGroup instances restricted to fluorine (PFAS).
Similar to :func:`get_compiled_HalogenGroups` but every group has
``componentHalogens`` forced to ``'F'``, so the compiled component-SMARTS
patterns are built for fluorine only. Suitable for extending with custom
PFAS-specific groups and passing directly to :func:`parse_smiles` or
:class:`~PFASGroups.fingerprints.PFASFingerprint` when analysing PFAS/fluorinated compounds.
Returns
-------
list of HalogenGroup
All compute=True groups compiled with ``componentHalogens='F'``,
suitable for passing as *pfas_groups* to :func:`parse_smiles` or
:class:`~PFASGroups.fingerprints.PFASFingerprint`.
Examples
--------
>>> from PFASGroups import get_compiled_PFASGroups, HalogenGroup, parse_smiles
>>> groups = get_compiled_PFASGroups()
>>> groups.append(HalogenGroup(
... id=200, name="Perfluoroalkyl nitrates",
... smarts={"[C$(C[ON+](=O)[O-])]": 1},
... componentSmarts="Perfluoroalkyl",
... componentSaturation="per", componentHalogens="F",
... componentForm="alkyl",
... constraints={"eq": {"N": 1}, "gte": {"F": 1}},
... ))
>>> results = parse_smiles(["FC(F)(F)C(F)(F)ON(=O)=O"], pfas_groups=groups)
See Also
--------
get_compiled_HalogenGroups : same but supports all halogens (F, Cl, Br, I).
"""
with open(HALOGEN_GROUPS_FILE, 'r') as f:
_pfg = json.load(f)
return [
HalogenGroup(**{**entry, 'componentHalogens': 'F'})
for entry in _pfg
if entry.get('compute', True)
]
@load_HalogenGroups()
def get_PFASGroups(**kwargs):
if kwargs.get('json_format',False):
return kwargs.get('pfas_groups',[]).extend(kwargs.get('agg_pfas_groups',[]))
with open(HALOGEN_GROUPS_FILE, 'r') as f:
data = json.load(f)
for entry in data:
entry["componentHalogen"] = ['F']
return data
[docs]
@load_PFASDefinitions()
def get_PFASDefinitions(**kwargs):
if kwargs.get('json_format',False):
return kwargs.get('pfas_definitions',[])
with open(PFAS_DEFINITIONS_FILE, 'r') as f:
data = json.load(f)
return data