TJ,
Your suggestion solved my problem. Thanks! I need to pay closer attention
to the SMARTS documentation!
Regards,
Jim Metz
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Today's Topics:
1. Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether
oxygens (James T. Metz)
2. Re: Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic
ether oxygens (TJ O'Donnell)
3. Re: Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic
ether oxygens (TJ O'Donnell)
----------------------------------------------------------------------
Message: 1
Date: Wed, 6 Sep 2017 19:34:02 -0400
From: "James T. Metz" <jamestm...@aol.com>
To: RDkit-discuss@lists.sourceforge.net, jamestm...@aol.com
Subject: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs
macrocyclic ether oxygens
Message-ID: <15e598b1b33-c09-48...@webjas-vab043.srv.aolmail.net>
Content-Type: text/plain; charset="utf-8"
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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Message: 2
Date: Wed, 6 Sep 2017 18:04:01 -0700
From: "TJ O'Donnell" <t...@acm.org>
To: "James T. Metz" <jamestm...@aol.com>
Cc: RDKit Discuss <RDkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs
macrocyclic ether oxygens
Message-ID:
<CADqA_h-+KDW=wbtEdGPMvM8vz=1rzskxkkpqzo5iqh1cb33...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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
>
>
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Message: 3
Date: Wed, 6 Sep 2017 19:16:45 -0700
From: "TJ O'Donnell" <t...@acm.org>
To: "James T. Metz" <jamestm...@aol.com>
Cc: RDKit Discuss <RDkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs
macrocyclic ether oxygens
Message-ID:
<cadqa_h-kkwokfvysxj44rwo+mq0atokyb5nru+mpj9og7uu...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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 <t...@acm.org> 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 <
> 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
>>
>>
>
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