def get_molecule_from_identifier(identifier):
"""
Get species according to the string identifier input
Args:
identifier (str): Identifiers used to generate species, currently
support SMILES, InChI, adjacency list and common names
Return:
spc (RMG Species): An RMG species object corresponding to the identifier
"""
known_names = {
'o2': '[O][O]',
'oxygen': '[O][O]',
'benzyl': '[CH2]c1ccccc1',
'phenyl': '[c]1ccccc1',
}
identifier = identifier.strip()
molecule = Molecule()
if not identifier:
logging.error('Invalid empty identifier.')
return
elif identifier.startswith('InChI=1'):
try:
molecule.from_inchi(identifier)
except:
logging.error('Invalid InChI identifier.')
return
elif identifier.lower() in known_names:
molecule.from_smiles(known_names[identifier.lower()])
else:
for char in ['u', 'p', 'c', '{']:
if char not in identifier.lower():
try:
molecule.from_smiles(identifier)
except (KeyError, AtomTypeError):
logging.error('Invalid SMILES identifier.')
return
except (IOError, ValueError):
url = "https://cactus.nci.nih.gov/chemical/structure/{0}/smiles".format(
urllib.parse.quote(identifier))
try:
f = urllib.request.urlopen(url, timeout=10)
except:
logging.error('Invalid identifier for NCI resolver.')
return
smiles = f.read().decode('utf-8')
try:
molecule.from_smiles(smiles)
except (KeyError, AtomTypeError):
logging.error('Invalid identifier.')
break
else:
try:
molecule.from_adjacency_list(identifier)
except:
logging.error('Invalid adjacency list identifier.')
return
return molecule
def clean_deposit(self):
"""
Return molecular representation of input deposit structure
"""
try:
deposit = Molecule()
deposit.from_adjacency_list(self.cleaned_data['deposit'])
except Exception:
import traceback
traceback.print_exc()
raise forms.ValidationError('Invalid SMILES entry.')
return self.cleaned_data['deposit']
def clean_species(self):
"""
Custom validation for the species field to ensure that a valid adjacency
list has been provided.
"""
try:
molecule = Molecule()
molecule.from_adjacency_list(self.cleaned_data['species'])
except Exception:
import traceback
traceback.print_exc()
raise forms.ValidationError('Invalid adjacency list.')
return self.cleaned_data['species']
def clean_adjlist(self):
"""
Custom validation for the adjlist field to ensure that a valid adjacency
list has been provided.
"""
try:
adjlist = self.cleaned_data['adjlist']
if adjlist == '':
return ''
molecule = Molecule()
molecule.from_adjacency_list(adjlist)
except Exception:
import traceback
traceback.print_exc()
raise forms.ValidationError('Invalid adjacency list.')
return adjlist
