def test_openbabel(self):
from cinfony import obabel
mol = obabel.readstring("smi", "CCC")
desc = mol.calcdesc(obabel.descs[0:3])
for d in desc:
if desc[d] != desc[d]:
desc[d] = '?'
expectedDesc = {'HBA1': 0.0, 'HBD': 0.0, 'HBA2': 0.0}
self.assertEqual(desc,expectedDesc)
def hide_test_openbabel(self):
from cinfony import obabel
mol = obabel.readstring("smi", "CCC")
desc = mol.calcdesc(obabel.descs[0:3])
for d in desc:
if desc[d] != desc[d]:
desc[d] = '?'
#expectedDesc = {'HBA1': 0.0, 'HBD': 0.0, 'HBA2': 0.0}
expectedDesc = {'abonds': 0.0, 'atoms': 3.0, 'bonds': 2.0}
self.assertEqual(desc,expectedDesc)
def getObabelDescResult(data,descList):
""" Calculates the descriptors for the descList using obabel
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 "obabel" not in toolkitsEnabled:
return None
smilesName = getSMILESAttr(data)
if not smilesName: return None
myDescList = [desc.replace(obabelTag,"") for desc in descList if obabelTag in desc]
if not myDescList: return None
resData = orange.ExampleTable(orange.Domain([data.domain[smilesName]] + [orange.FloatVariable(obabelTag+name) for name in myDescList],0))
for ex in data:
newEx = orange.Example(resData.domain)
newEx[smilesName] = ex[smilesName]
mol = obabel.readstring("smi", str(newEx[smilesName].value))
moldesc = mol.calcdesc(myDescList)
for desc in myDescList:
newEx[obabelTag+desc] = moldesc[desc]
resData.append(newEx)
return resData
def getObabelDescResult(data,descList):
""" Calculates the descriptors for the descList using obabel
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 "obabel" not in toolkitsEnabled:
return None
smilesName = getSMILESAttr(data)
if not smilesName: return None
myDescList = [desc.replace(toolkitsDef["obabel"]["tag"],"") for desc in descList if toolkitsDef["obabel"]["tag"] in desc]
if not myDescList: return None
resData = orange.ExampleTable(orange.Domain([data.domain[smilesName]] + [orange.FloatVariable(toolkitsDef["obabel"]["tag"]+name) for name in myDescList],0))
for ex in data:
newEx = orange.Example(resData.domain)
newEx[smilesName] = ex[smilesName]
mol = obabel.readstring("smi", str(newEx[smilesName].value))
moldesc = mol.calcdesc(myDescList)
for desc in myDescList:
newEx[toolkitsDef["obabel"]["tag"]+desc] = moldesc[desc]
resData.append(newEx)
return resData