I guessed why it occurred. I'm interested is it expected behavior?
So, if a radius is greater than the number of available bonds in all directions from the rooted atom the function will return empty list as it considers that such environment does not exist. Is this a correct expectation?


Pavel.

On 03/27/2017 03:53 PM, Peter Gedeck wrote:
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 <mailto: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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