Hi,
What if you simply compute interatomic distances, and deduce bond existence
and type from the distance values (and perhaps angles)?
But such code it's probably already written somewhere, I think :)
Depends if it's a one or two times only task, and molecule size, unusual
atomes presence, coordinates data quality (e.g. expect problems with
interatomic distances if using PDB)... of course, too.
Regards,
Pascal
2013/1/12 Alexander Betz <alexander.b...@gmail.com>
> Hi there,
> for a program i am writing, i need to perceive the atom connectivity from
> the 3D cartesian coordinates alone. I have been looking into the open babel
> source code and found the calculateConnectivityMatrix method. But due to my
> limited c knowledge i don't know what exactly it does. So how does babel
> address this issue?
> Thanks.
> Alex
>
> PS:
> the reference to the Chemical Graph theory book did not help because i
> will only have access to the book in 1week+
>
>
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