The SMARTS patterns (not the text descriptions) are all valid for the OpenBabel GUI. It's pretty easy to search the Open Babel forum: Google, Bing, and most search engines work well, and of course you can post your own messages to the list.
There are several introductions to SMARTS online: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html http://en.wikipedia.org/wiki/Smiles_arbitrary_target_specification http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html#INTRO http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html Hope that helps, -Geoff On Apr 20, 2013, at 2:50 PM, Alex Gorbounov <river_b...@yahoo.com> wrote: > > Doctor Hutchison, > > I am a little stuck and need some further direction if you could kindly give > me a few more moments of your precious time. > > You suggested that I organize the functional groups into SMARTS and I found > this 2005 file (attached), which you may or may not be familiar with. It has > some 300 functional groups but the problem is that, for example OpenBabelGUI > - a popular resource from what it seems like - does not recognize this > notation as input. I noticed that you are also a member of that community. > Their forum is not searchable and instructions are not very detailed, but is > there a good place that you know of where I can start the learning process of > understanding the SMARTS so that eventually I can achieve the objective of > converting functional groups to SMARTS and make my database of about 400 > polymers searchable by these functional groups when the molecules are > converted to SMILES? My database needs, at this point, are pretty basic. Is > there documentation that I missed, or, perhaps, there is a simpler tool that > can fit this purpose? Any help would be greatly appreciated. > > Have a great day, > > Alex Gorbounov > > > From: Alex Gorbounov <river_b...@yahoo.com> > To: Geoffrey Hutchison <geo...@pitt.edu> > Sent: Tuesday, April 9, 2013 12:48 PM > Subject: Re: [BlueObelisk-discuss] Database question > > Geoff, thanks a lot. > > I will go in that direction exactly. > > Alex > > From: Geoffrey Hutchison <geo...@pitt.edu> > To: Alex Gorbounov <river_b...@yahoo.com> > Cc: "blueobelisk-disc...@lists.sourceforge.net" > <blueobelisk-disc...@lists.sourceforge.net> > Sent: Tuesday, April 9, 2013 12:38 PM > Subject: Re: [BlueObelisk-discuss] Database question > > > I would like to design a database to support group contribution methods. > > Since the model is the primary focus of this project at the moment, I only > > need a primitive DB, with main requirement of being able to represent the > > groups correctly. If anyone can offer any tips, thoughts, references, > > links; those would be highly appreciated. > > It depends on how big you intend to grow this database, but you can stick to > flat-file organization for many things (e.g., hundreds or thousands of > groups). I’d organize the functional groups into SMARTS, which can be used > with many toolkits. > > Hope that helps, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geo...@pitt.edu > web: http://hutchison.chem.pitt.edu/ > > > > > > <smarts-pattern.txt> ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
