do you just have to check if an atom is in a 6-membered ring? If so then
In [8]: m =
Chem.MolFromSmiles('COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1')
In [9]: [a.IsInRingSize(6) for a in m.GetAtoms()]
Out[9]:
[False,
False,
True,
True,
True,
True,
True,
True,
False,
False,
False,
False,
False,
False,
False,
False,
True,
True,
True,
True,
False,
True,
True]
Should help.
Sorry - maybe I do not fully understand your question
Ciao
Nik
On 1/21/13 4:13 PM, "Paul Emsley" <[email protected]> wrote:
>
>I am making heavy weather of the following problem - and am wondering if
>I am missing something (such as a useful RDKit function).
>
>I am working on this beasty (as an example):
>
>http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=0CP
>
>COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1
>
>which has a norbornane substituent. I am trying to prepare input for a
>downstream program that needs to know if the norbornane atoms are in a
>6-membered ring [1]. RingInfo gives me the 2 5-membered rings. I am
>strugging to make use of that information to find 6-membered rings. I
>have been using makeRingNeighborMap() and pickFusedRings(). Am I
>missing an RDKit function that finds all rings?
>
>Cheers,
>
>Paul.
>
>
>[1] actually, all atoms but it is the norbornane atoms with which I
>struggle.
>
>
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