Dear Greg, I was wondering whether you could let me know your insights regarding the following error below? Please find the input molecule.mol attached.
Many thanks
Sergio
---------------------------------------------
from rdkit.Chem import AllChem
from rdkit import Chem
m = Chem.MolFromMolFile('molecule.mol')
info={}
fp = AllChem.GetMorganFingerprint(m,2,useChirality=True,bitInfo=info)
for element in fp.GetNonzeroElements():
for i in info[element]:
print i
if i[1]==0:
smarts=m.GetAtomWithIdx(i[0]).GetSmarts()
else:
env = Chem.FindAtomEnvironmentOfRadiusN(m,i[1],i[0])
amap={}
submol=Chem.PathToSubmol(m,env,atomMap=amap)
smarts=Chem.MolToSmarts(submol,isomericSmiles=True)
(12, 2)
(8, 1)
(13, 1)
(2, 2)
[13:15:25]
****
Range Error
idx
Violation occurred on line 153 in file
/home/RDKit_2013_03_2/Code/GraphMol/ROMol.cpp
Failed Expression: 0 <= 12 <= 6
****
Traceback (most recent call last):
File "<stdin>", line 10, in <module>
RuntimeError: Range Error
# When I try the MolToSmarts line that throws the error alone, for some
reason that I don't know it works!
smarts=Chem.MolToSmarts(submol,isomericSmiles=True)
smarts
'[#6](-[#6]=[#6]-[#6H])(-[#6])(-[#6])-[#6]'
molecule.mol
Description: Binary data
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