Hi, What is the file format of the input structure? Converting from SMILES to SMARTS isn’t really necessary since all SMILES are valid SMARTS and can be put into the query directly. For other, more advanced queries you could always try to convert to SMILES with the options -xn (to suppress name) and -xh 1 (to suppress the addition of implicit hydrogens on aromatic nitrogens, needs a value i.e. the ”1”, but it can be anything).
Regardless of how you prepare the SMARTS, I can really recommend http://smartsview.zbh.uni-hamburg.de to visualize the result to make sure you got the correct structure. Kind regards, Fredrik > 18 jan. 2016 kl. 16:43 skrev Stefano Forli <fo...@scripps.edu>: > > Hi Mohammad, > when I had to do it myself, I used the CACTVS web service at NIH: > > > http://cactus.nci.nih.gov/chemical/structure/[YOUR-SMILES-HERE]/file?format=smarts > > Not very straightforward, but you can automate the process using some > scripting (bash, python?). > Hope this helps, > > S > > -- > > Stefano Forli, PhD > > Assistant Professor of Integrative > Structural and Computational Biology, > Molecular Graphics Laboratory > > Dept. of Integrative Structural > and Computational Biology, MB-112F > The Scripps Research Institute > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > fax: +1 (858)784-2860 > email: fo...@scripps.edu > http://www.scripps.edu/~forli/ > ________________________________________ > From: Mohammad Mehdi Ghahremanpour [ghahramanpou...@gmail.com] > Sent: Monday, January 18, 2016 6:55 AM > To: openbabel-devel@lists.sourceforge.net > Subject: [OpenBabel-Devel] Generating SMARTS format > > Hi, > > I am updating gaff.prm file by defining new SMARTS format to support all GAFF > atom types for different molecules. > Is there any routine or function in the code which generates SMARTS from a > given molecular structure as the output or even as the stderr? > > > Cheers, > Mohammad > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > -- > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
