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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