Try using [O;H0;D2;r6] lower-case r.  Sorry I'm not at a computer to check
this.
R6 means in 6 rings.
r6 means in ring of size 6.

http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

TJ O'Donnell

On Wed, Sep 6, 2017 at 4:34 PM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Hello,
>
>     Given the following SMILES for a macrocyclic hexaose
>
>    OCC1OC2OC3C(CO)OC(OC4C(CO)OC(OC5C(CO)OC(OC6C(CO)OC(OC7C(CO)
> OC(OC1C(O)C2O)C(O)C7O)C(O)C6O)C(O)C5O)C(O)C4O)C(O)C3O
>
>     can anyone suggest a SMARTS pattern that will distinguish ether oxygens
> in the smaller 6-membered rings versus the ethers in the larger macrocyclic
> structure?
>
>     For example, using RDkit, I have tried (e.g., pattern =
> Chem.MolFromSmarts('[O;H0;D2]') )
>
>     [O;H0;D2]  ===>  gives 12 matches (all ether oxygens)
>
>     [O;H0;D2;R]  ===>  gives 12 matches (all ether oxygens)
>
>     [O;H0;D2;!R]  ===>  gives 0 matches
>
>     [O;H0;D2;R6]  ===>  gives 0 matches
>
>
>     I am stumped.  Any ideas?
>
>     If it is necessary to write more complicated PYTHON/RDkit/SMARTS code,
> I am certainly willing to try that.
>
>     Thanks!
>
>     Regards,
>     Jim Metz
>     Northwestern University
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to