Re: [Rdkit-discuss] non-smallest rings

2013-01-22 Thread Paul Emsley
On 22/01/13 05:40, Greg Landrum wrote: Hi Paul, On Mon, Jan 21, 2013 at 4:13 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk 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

Re: [Rdkit-discuss] non-smallest rings

2013-01-22 Thread Patrick Walters
If you're just looking for 6 membered rings, you can define a SMARTS that matches 6 membered rings like this *1~*~*~*~*~*1. You can also use this approach to identify all rings (at least those within reason). You can use an expression like this [*1+string.join([*~]*x,)+*1 for x in range(1,19)]

Re: [Rdkit-discuss] non-smallest rings

2013-01-22 Thread Greg Landrum
On Wed, Jan 23, 2013 at 2:47 AM, Patrick Walters wpwalt...@gmail.com wrote: If you're just looking for 6 membered rings, you can define a SMARTS that matches 6 membered rings like this *1~*~*~*~*~*1. You can also use this approach to identify all rings (at least those within reason). You can

Re: [Rdkit-discuss] non-smallest rings

2013-01-21 Thread Stiefl, Nikolaus
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,