def parseMolecule(self):
'''
turn the input into a toolkit molecule according to user settings
indigo is supposed to read transparently, so we can do away with
the format setting, basically. If it's numeric, we ask pubchem,
if it isn't, we consider it a molecule.
'''
rawinput = self.data_string
try:
pubchemId = int(rawinput)
except ValueError:
pubchemId = None
if pubchemId is not None:
try:
url = common.pubchem_url % pubchemId
pubchemContent = urllib.urlopen(url).read()
except IOError:
raise common.MCFError, 'No connection to PubChem'
self.data_string = pubchemContent
#common.debug('rpc: %s' % self.rpc)
#common.debug('data ---\n%s\n---' % self.data_string)
try:
tkmol = Indigo().loadMolecule(self.data_string)
except IndigoException:
raise common.MCFError, "Invalid input data"
hydrogens = self.options['hydrogens']
if hydrogens == 'add':
tkmol.unfoldHydrogens()
tkmol.layout() # needed to give coordinates to added Hs
elif hydrogens == 'delete':
tkmol.foldHydrogens()
if not tkmol.hasCoord() or self.options['recalculate_coordinates']:
tkmol.layout()
return tkmol
def parseMolecule(self):
"""
turn the input into a toolkit molecule according to user settings
indigo is supposed to read transparently, so we can do away with
the format setting, basically. If it's numeric, we ask pubchem,
if it isn't, we consider it a molecule.
"""
rawinput = self.data_string
try:
pubchemId = int(rawinput)
except ValueError:
pubchemId = None
if pubchemId is not None:
try:
url = common.pubchem_url % pubchemId
pubchemContent = urllib.urlopen(url).read()
except IOError:
raise common.MCFError, "No connection to PubChem"
self.data_string = pubchemContent
# common.debug('rpc: %s' % self.rpc)
# common.debug('data ---\n%s\n---' % self.data_string)
try:
tkmol = Indigo().loadMolecule(self.data_string)
except IndigoException:
raise common.MCFError, "Invalid input data"
hydrogens = self.options["hydrogens"]
if hydrogens == "add":
tkmol.unfoldHydrogens()
tkmol.layout() # needed to give coordinates to added Hs
elif hydrogens == "delete":
tkmol.foldHydrogens()
if not tkmol.hasCoord() or self.options["recalculate_coordinates"]:
tkmol.layout()
return tkmol
