Hello,
The atom numbers start with 0. From the middle atom, there are no
environments with radius 2. You will get a result if you use the first (=0)
or the last (=2) atom. Try this:
m = Chem.MolFromSmiles("NCO")
i = Chem.FindAtomEnvironmentOfRadiusN(m, 1, 0)
Chem.MolToSmiles(Chem.PathToSubmol(m, i))
i = Chem.FindAtomEnvironmentOfRadiusN(m, 2, 0)
Chem.MolToSmiles(Chem.PathToSubmol(m, i))
i = Chem.FindAtomEnvironmentOfRadiusN(m, 3, 0)
Chem.MolToSmiles(Chem.PathToSubmol(m, i))
and you will get:
'CN'
'NCO'
''
Is this more intuitive to you?
Best,
Peter
On Mon, Mar 27, 2017 at 9:35 AM Pavel Polishchuk <pavel_polishc...@ukr.net>
wrote:
> Dear RDKitters,
>
> I found the issue with FindAtomEnvironmentOfRadiusN but this can be a
> feature. However, I did not findthis information in help and did not
> expect such behavior.
> If I apply FindAtomEnvironmentOfRadiusN function to a small molecule
> and specify the radius greater than the size of the molecule the
> function returns empty list of bond indices (and empty mol).
>
> m = Chem.MolFromSmiles("NCO")
>
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 1, 1)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
>
> returns "NCO"
>
> i = Chem.FindAtomEnvironmentOfRadiusN(m, 2, 1)
> Chem.MolToSmiles(Chem.PathToSubmol(m, i))
>
> returns ""
>
> In the latter case I expected the same output "NCO". Were my
> expectations mistaken?
>
> Kind regards,
> Pavel.
>
>
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