I verified that r6 does the trick. Using my rdchord cartridge, I get
tjo=> select
rd.list_matches(rd.rdmol('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'),
'[O;H0;D2;r6]',0,1);
list_matches
--------------------------------
{{4},{11},{18},{25},{32},{39}}
(1 row)
tjo=> select
rd.list_matches(rd.rdmol('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'),
'[O;H0;D2;!r6]',0,1);
list_matches
--------------------------------
{{6},{13},{20},{27},{34},{41}}
(1 row)
Here's an image showing the atom numbers corresponding to the list_matches
output.
TJ
[image: Inline image 2]
On Wed, Sep 6, 2017 at 6:04 PM, TJ O'Donnell <[email protected]> wrote:
> 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 <
> [email protected]> 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
>>
>>
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