Yes, the radius is a number of bonds.
I'm not going to argue that this is particularly intuitive (since I can
fall either way on the question), but I would say that it's consistent: the
environment is provided as a list of bond ids and the function is
documented to "find bond subgraphs of a particular radius around an atom"
on the C++ side or "Finds the bonds within a certain radius of an atom in a
molecule" on the Python side.


On Mon, Mar 27, 2017 at 4:43 PM, Peter Gedeck <>

> Good point. It seems the algorithm uses bonds and not atoms, so radius 3
> means include the next three bonds. Maybe Greg can comment here.
> Best,
> Peter
> On Mon, Mar 27, 2017 at 10:39 AM Pavel Polishchuk <
>> wrote:
>> Thank you!
>> That was a bug in my expectations. :)
>> BTW, as I see from test examples for the 0 atom in CC1CC1 an environment
>> with radius 3 exists. Thus, radius should be interpreted as a number of
>> bonds from the rooted atom, not a number of atoms. I did not expect this as
>> well.
>> Pavel.
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