def hide_test_webel(self):
from cinfony import webel
mol = webel.readstring("smi", "CCC")
desc = mol.calcdesc(webel.getdescs()[5:7])
for d in desc:
if desc[d] != desc[d]:
desc[d] = '?'
expectedDesc = {'AtomCountDescriptor_nAtom': 11.0, 'AutocorrelationDescriptorCharge_ATSc5': 0.0, 'AutocorrelationDescriptorCharge_ATSc4': 0.0, 'AutocorrelationDescriptorCharge_ATSc3': 0.0, 'AutocorrelationDescriptorCharge_ATSc2': 0.0, 'AutocorrelationDescriptorCharge_ATSc1': 0.0}
self.assertEqual(desc,expectedDesc)
def test_webel(self):
from cinfony import webel
mol = webel.readstring("smi", "CCC")
desc = mol.calcdesc(webel.getdescs()[5:7])
for d in desc:
if desc[d] != desc[d]:
desc[d] = '?'
expectedDesc = {'AtomCountDescriptor_nAtom': 11.0, 'AutocorrelationDescriptorCharge_ATSc5': 0.0, 'AutocorrelationDescriptorCharge_ATSc4': 0.0, 'AutocorrelationDescriptorCharge_ATSc3': 0.0, 'AutocorrelationDescriptorCharge_ATSc2': 0.0, 'AutocorrelationDescriptorCharge_ATSc1': 0.0}
self.assertEqual(desc,expectedDesc)
def get_IUPAC_name_from_web(inchi):
"""Will try getting name from web service."""
webmol = webel.readstring('inchi', inchi)
try:
name = webmol.write('iupac').capitalize()
if not name:
names = webmol.write('names')
if len(names) == 1:
name = webmol.write('names')[0].capitalize()
else:
name = get_best_name(names)
except IndexError:
name = ''
except AttributeError:
name = ''
return name
def getWebelDescResult(data,descList):
""" Calculates the descriptors for the descList using Webel
It expects an attribute containing smiles with a name defined in AZOrangeConfig.SMILESNAMES
It returns a dataset with the same smiles input variable, and as many variables as the descriptors
returned by the toolkit
"""
if "webel" not in toolkitsEnabled:
return None
smilesName = getSMILESAttr(data)
if not smilesName: return None
myDescList = [desc.replace(webelTag,"") for desc in descList if webelTag in desc]
if not myDescList: return None
#Compute the results
results = {}
for ex in data:
smile = str(ex[smilesName].value)
mol = webel.readstring("smi", smile)
results[smile] = mol.calcdesc(myDescList)
# Get all the different descriptor names returned by webel
varNames = []
for res in results:
for desc in results[res]:
if desc not in varNames:
varNames.append(desc)
# Generate the dataset assuring the same order of examples
resData = orange.ExampleTable(orange.Domain([data.domain[smilesName]] + [orange.FloatVariable(webelTag+name) for name in varNames],0))
for ex in data:
newEx = orange.Example(resData.domain)
smile = str(ex[smilesName].value)
newEx[smilesName] =smile
for desc in results[smile]:
newEx[webelTag+desc] = results[smile][desc]
resData.append(newEx)
return resData
def getWebelDescResult(data,descList):
""" Calculates the descriptors for the descList using Webel
It expects an attribute containing smiles with a name defined in AZOrangeConfig.SMILESNAMES
It returns a dataset with the same smiles input variable, and as many variables as the descriptors
returned by the toolkit
"""
if "webel" not in toolkitsEnabled:
return None
smilesName = getSMILESAttr(data)
if not smilesName: return None
myDescList = [desc.replace(toolkitsDef["webel"]["tag"],"") for desc in descList if toolkitsDef["webel"]["tag"] in desc]
if not myDescList: return None
#Compute the results
results = {}
for ex in data:
smile = str(ex[smilesName].value)
mol = webel.readstring("smi", smile)
results[smile] = mol.calcdesc(myDescList)
# Get all the different descriptor names returned by webel
varNames = []
for res in results:
for desc in results[res]:
if desc not in varNames:
varNames.append(desc)
# Generate the dataset assuring the same order of examples
resData = orange.ExampleTable(orange.Domain([data.domain[smilesName]] + [orange.FloatVariable(toolkitsDef["webel"]["tag"]+name) for name in varNames],0))
for ex in data:
newEx = orange.Example(resData.domain)
smile = str(ex[smilesName].value)
newEx[smilesName] =smile
for desc in results[smile]:
newEx[toolkitsDef["webel"]["tag"]+desc] = results[smile][desc]
resData.append(newEx)
return resData
