Re: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether oxygens

2017-09-06 Thread TJ O'Donnell 
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  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
>>
>>
>> 
>> --
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>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>
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Re: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether oxygens

2017-09-06 Thread TJ O'Donnell 
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
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[Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether oxygens

2017-09-06 Thread James T. Metz via Rdkit-discuss 


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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Re: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)

2017-09-06 Thread Greg Landrum 
The plan here is that this code will eventually be merged onto master so
that it becomes part of the main RDKit distribution.

I will try to do some more testing so that this can be done before the
2017_09 release, but I'm not sure that I will be able to do that. Feedback
from the rest of the community is very welcome and would help with this
process.

Best,
-greg


On Fri, Sep 1, 2017 at 5:43 AM, Paul Czodrowski <
paul.czodrow...@merckgroup.com> wrote:

> Malitha, this is a great piece of work and I highly recommend all
> RDKitters to have a look at it..
>
>
>
> Paul
>
>
>
> *Von:* Malitha Kabir [mailto:malitha12...@gmail.com]
> *Gesendet:* Donnerstag, 31. August 2017 01:54
> *An:* rdkit 
> *Betreff:* [Rdkit-discuss] News on 3D molecule visualization in RDKit
> (project: RDKit - 3Dmol.js integration)
>
>
>
> Dear all,
>
>
>
> I am about to share news on 3D molecule visualization in RDKit.
>
>
>
> This summer I have worked as Google Summer Of Codes (GSoC) participant
> under supervision of  Paul Czodrowski and Greg Landrum. The codes were
> reviewed several times by Peter Gedeck and finally merged by Brian Kelley
> at rdkit:GSoC2017 branch.
>
>
>
> I would like to request you to check whether those can come in use and
> drop your feedback for the improvement. I will keep working on it's
> improvement throughout the coming month also. Kindly feel free to visit the
> following link for work details: https://github.com/
> malithakabir/RDKitGSoC2017
>
>
>
> In future, I will request information in mailing list whenever I face in
> trouble in codes rdkit code related issues. I wish, you will gladly helping
> me providing information and directions. Many thanks in advance for that.
>
>
>
> I am extremely sorry of being unresponsive in mailing list due to the lack
> of my knowledge/ability to answer those. I am trying my best to be
> responsive in mailing list to provide community support.
>
>
>
> On a personal note I would like to express my sincere gratitude to my
> mentors (paul and greg) and reviewer (peter) for their time and guidance
> throughout the summer 2017. And warm thanks to Brian for merging the codes.
>
>
>
> Thank you very much for your time. Have a great day!
>
>
>
> Sincerely,
>
> - malitha
>
>
>
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Re: [Rdkit-discuss] recent packages for Ubuntu

2017-09-06 Thread Greg Landrum 
Michael Banck, who did the work to make the RDKit part of debichem, would
be the person I'd think is best qualified to comment on this.

Aside from this github issue (https://github.com/rdkit/rdkit/issues/911) I
haven't seen much here.

-greg


On Wed, Sep 6, 2017 at 2:59 AM, Francois BERENGER <
beren...@bioreg.kyushu-u.ac.jp> wrote:

> Hello,
>
> If the update of the binary packages for Ubuntu/Debian
> is documented somewhere, it would help people who
> want to make available binary packages of rdkit as soon as there
> is a new rdkit release.
>
> I think we should have a ppa for people who want to use
> the bleeding edge version of rdkit.
>
> Regards,
> F.
>
> 
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