Hi Yingfeng,
Let me remind you some chemistry basics:
Chlorine atom has 17 electrons. In last orbit it has 7 electrons hence it
requires 1 electron to complete octet. Hence it's valency is 1.
Thus it's not a surprise that your smiles is generating an error.
In order to check for get the charge state of a compound, you should loop
through every atom of the molecule and check its charge; you will find all
useful function here:
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Atom-class.html
(For instance GetFormalCharge).
Some readings for you:
http://www.rdkit.org/docs/GettingStartedInPython.html
Best,
Gregori
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