def from_dict(cls, json_obj):
"""Recreate an object from the JSON representation.
Parameters
----------
json_obj : dict
JSON representation
Returns
-------
StatMech : StatMech object
"""
json_obj = json_pMuTT.remove_class(json_obj)
name = json_obj['name']
trans_model = json_pMuTT.json_to_pMuTT(json_obj['trans_model'])
vib_model = json_pMuTT.json_to_pMuTT(json_obj['vib_model'])
rot_model = json_pMuTT.json_to_pMuTT(json_obj['rot_model'])
elec_model = json_pMuTT.json_to_pMuTT(json_obj['elec_model'])
nucl_model = json_pMuTT.json_to_pMuTT(json_obj['nucl_model'])
notes = json_obj['notes']
return cls(name=name,
trans_model=trans_model,
vib_model=vib_model,
rot_model=rot_model,
elec_model=elec_model,
nucl_model=nucl_model,
notes=notes)
def from_dict(cls, json_obj):
"""Recreate an object from the JSON representation.
Parameters
----------
json_obj : dict
JSON representation
Returns
-------
Nasa : Nasa object
"""
json_obj = remove_class(json_obj)
# Reconstruct statmech model
json_obj['statmech_model'] = json_to_pMuTT(json_obj['statmech_model'])
json_obj['references'] = json_to_pMuTT(json_obj['references'])
json_obj['cat_site'] = json_to_pMuTT(json_obj['cat_site'])
json_obj['mix_models'] = json_to_pMuTT(json_obj['mix_models'])
return cls(**json_obj)
def from_dict(cls, json_obj):
"""Recreate an object from the JSON representation.
Parameters
----------
json_obj : dict
JSON representation
Returns
-------
EmpiricalBase : EmpiricalBase object
"""
json_obj = remove_class(json_obj)
# Reconstruct statmech model
json_obj['statmech_model'] = \
json_to_pMuTT(json_obj['statmech_model'])
json_obj['references'] = \
json_to_pMuTT(json_obj['references'])
json_obj['mix_models'] = \
[json_to_pMuTT(mix_model) for mix_model in json_obj['mix_models']]
return cls(**json_obj)
def from_dict(cls, json_obj):
"""Recreate an object from the JSON representation.
Parameters
----------
json_obj : dict
JSON representation
Returns
-------
PhaseDiagram : PhaseDiagram object
"""
json_obj = remove_class(json_obj)
json_obj['reactions'] = [json_to_pMuTT(reaction)
for reaction in json_obj['reactions']]
return cls(**json_obj)
def from_dict(cls, json_obj):
"""Recreate an object from the JSON representation.
Parameters
----------
json_obj : dict
JSON representation
Returns
-------
References : References object
"""
json_obj = remove_class(json_obj)
json_obj['offset'] = np.array(json_obj['offset'])
json_obj['references'] = [json_to_pMuTT(ref_dict)
for ref_dict in json_obj['references']]
return cls(**json_obj)
def find(self, **kwargs):
"""Find records in collection using desired criteria
Parameters
----------
max_records : int
Maximum number of records to return
kwargs : keyword arguments
Arguments to use for `self.collection.find` method. See
`pymongo.collection.Collection.find`_ method
Returns
-------
results : list of pMuTT objects
.. _`pymongo.collection.Collection.find`: http://api.mongodb.com/python/current/api/pymongo/collection.html#pymongo.collection.Collection.find
"""
return [
json_to_pMuTT(result) for result in self.collection.find(**kwargs)
]
def get_specie_from_smiles(self, smiles, obj_type=None, max_records=1):
"""Searches database for object matching SMILES string
Parameters
----------
smiles : str
Smiles representation of interested species
obj_type : str, optional
Type of object to return. Default will return the first
encountered specie matching the smiles string regardless of
type. Suggested types are:
- 'nasa'
- 'shomate'
- 'statmech'
max_records : int, optional
Maximum number of records to find. Set this parameter to a
-1 if all records are desired. Default is 1
Returns
-------
specie : pMuTT model object or list of pMuTT model objects
Object(s) representing the interested species
"""
# Set up filter to find records
db_filter = {'smiles': smiles}
if obj_type is not None:
db_filter['type'] = obj_type
# Get species from database
species = []
for i, result in enumerate(self.collection.find(filter=db_filter)):
specie = json_to_pMuTT(result)
# Only return one record if desired
if max_records == 1:
species = specie
break
species.append(specie)
# Determine if record limit reached
if (i + 1) == max_records:
break
return species