Re: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether oxygens
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'Donnellwrote: > 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
Re: [Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether oxygens
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
[Rdkit-discuss] Fwd: Need SMARTS to distinguish 6-ring vs macrocyclic ether oxygens
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
Re: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)
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 > > > > This message and any attachment are confidential and may be privileged or > otherwise protected from disclosure. If you are not the intended recipient, > you must not copy this message or attachment or disclose the contents to > any other person. If you have received this transmission in error, please > notify the sender immediately and delete the message and any attachment > from your system. Merck KGaA, Darmstadt, Germany and any of its > subsidiaries do not accept liability for any omissions or errors in this > message which may arise as a result of E-Mail-transmission or for damages > resulting from any unauthorized changes of the content of this message and > any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its > subsidiaries do not guarantee that this message is free of viruses and does > not accept liability for any damages caused by any virus transmitted > therewith. > > > > Click http://www.merckgroup.com/disclaimer to access the German, French, > Spanish and Portuguese versions of this disclaimer. > > > -- > 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
Re: [Rdkit-discuss] recent packages for Ubuntu
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. > > > -- > 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