Hi there, is it normal to get, for the same set of smiles, more generic Murcko frameworks that normal frameworks? When running this:
### Generate framework for a SMILES, handling for errors
def framecheck(s):
try:
return Chem.MolToSmiles(ms.GetScaffoldForMol(Chem.MolFromSmiles(s)))
except:
pass
### Generate generic framework for a SMILES, handling for errors
def gframecheck(s):
try:
return
Chem.MolToSmiles(ms.MakeScaffoldGeneric(Chem.MolFromSmiles(s)))
except:
pass
# Count unique frameworks
fraq = [framecheck(s) for s in smis]
fraq = list(set(fraq))
len(fraq)
# Count unique generic frameworks
gfraq = [gframecheck(s) for s in smis]
gfraq = list(set(gfraq))
len(gfraq)
I get for the attached set of smiles 1431 frameworks and 2207 generic
frameworks. The generic frameworks are supposed to have all atom types set
to C and all bonds to single, so I would expect less generic frameworks. Is
it necessary some sort of canonicalization?
Thanks in advance
Gonzalo
examp.smi
Description: Binary data
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