Hi Nick,
On Wed, Nov 14, 2012 at 4:43 PM, Nicholas Firth <[email protected]>wrote:
>
> I have encountered an issue with constructing a molecule from a graph
> representation, it's a particularly nasty molecule but all the charges and
> valencies are correct.
>
> Then when trying to sanitise the molecule I get the error 'could not find
> a ring for the bond between atoms ** and **' (where stars are numbers),
> that would be fine if I could work round the error, however it seems to get
> caught in an infinite loop of these error messages, which I can't seem to
> get around.
>
>
Which version of the RDKit are you using? There were some bug fixes in the
ring-finding code (which is where these error messages are coming from) in
the 2012_09 release.
If you're using an up-to-date version, the problem is likely going to be
difficult to track down via mailing list. Can you send me the molecule in
question so I can have a look in the debugger? If there's a problem sending
the full structure, you could try converting the whole molecule to Cs and
all bonds to single, check that the error messages still occur, and then
send that instead.
-greg
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