def getAdjacencyList(request, identifier):
"""
Returns an adjacency list of the species corresponding to `identifier`.
`identifier` should be something recognized by NCI resolver, eg.
SMILES, InChI, CACTVS, chemical name, etc.
The NCI resolver has some bugs regarding reading SMILES of radicals.
E.g. it thinks CC[CH] is CCC, so we first try to use the identifier
directly as a SMILES string, and only pass it through the resolver
if that does not work.
For specific problematic cases, the NCI resolver is bypassed and the SMILES
is returned from a dictionary of values. For O2, the resolver returns the singlet
form which is inert in RMG. For oxygen, the resolver returns 'O' as the SMILES, which
is the SMILES for water.
"""
from rmgpy.molecule import Molecule
from rmgpy.exceptions import AtomTypeError
from ssl import SSLError
known_names = {
'o2': '[O][O]',
'oxygen': '[O][O]',
'benzyl': '[CH2]c1ccccc1',
'phenyl': '[c]1ccccc1',
}
# Ensure that input is a string
identifier = str(identifier).strip()
# Return empty string for empty input
if identifier == '':
return HttpResponse('', content_type="text/plain")
molecule = Molecule()
# Check if identifier is an InChI string
if identifier.startswith('InChI=1'):
try:
molecule.fromInChI(identifier)
except AtomTypeError:
return HttpResponse('Invalid Molecule', status=501)
except KeyError, e:
return HttpResponse('Invalid Element: {0!s}'.format(e), status=501)
def getAdjacencyList(request, identifier):
"""
Returns an adjacency list of the species corresponding to `identifier`.
`identifier` should be something recognized by NCI resolver, eg.
SMILES, InChI, CACTVS, chemical name, etc.
The NCI resolver has some bugs regarding reading SMILES of radicals.
E.g. it thinks CC[CH] is CCC, so we first try to use the identifier
directly as a SMILES string, and only pass it through the resolver
if that does not work.
For specific problematic cases, the NCI resolver is bypassed and the SMILES
is returned from a dictionary of values. For O2, the resolver returns the singlet
form which is inert in RMG. For oxygen, the resolver returns 'O' as the SMILES, which
is the SMILES for water.
"""
from rmgpy.molecule import Molecule
from rmgpy.exceptions import AtomTypeError
from ssl import SSLError
known_names = {
'o2': '[O][O]',
'oxygen': '[O][O]',
'benzyl': '[CH2]c1ccccc1',
'phenyl': '[c]1ccccc1',
}
# Ensure that input is a string
identifier = str(identifier).strip()
# Return empty string for empty input
if identifier == '':
return HttpResponse('', content_type="text/plain")
molecule = Molecule()
# Check if identifier is an InChI string
if identifier.startswith('InChI=1'):
try:
molecule.fromInChI(identifier)
except AtomTypeError:
return HttpResponse('Invalid Molecule', status=501)
except KeyError, e:
return HttpResponse('Invalid Element: {0!s}'.format(e), status=501)
for f in os.listdir(folder):
f = os.path.join(folder,f)
stem, ext = os.path.splitext(f)
if ext != '.thermo':
continue
with open(f) as thermofile:
line = thermofile.readline()
match = re.match('InChI = "(.*?)(\/mult\d)*"',line)
if not match: continue
inchi = match.group(1)
mult = match.group(2)
if mult: continue
mol = Molecule()
mol.fromInChI(inchi)
mmol = rmgpy.qm.mopac.MopacMolPM3(mol, settings)
print mmol.uniqueID, f
thermo = mmol.loadThermoData()
if not thermo: continue
assert inchi.startswith('InChI=1S/')
inchimain = inchi[9:]
keystart = keydict[inchimain]
jthermo = thermodict[keystart]
print mol.toSMILES()
print inchi
print keystart
print thermo
print jthermo
