On Mar 29, 2016, at 12:41 PM, Gravestock David GBJH wrote: > I am trying to search for compounds that have a five-membered ring attached > to the para- position of an unsubstituted pyridine ring. > > I have tried the following SMARTS expression: > > [c1ccncc1]-!:aaaa-!:[r5]
There is an excellent SMARTS visualization tool at http://smartsview.zbh.uni-hamburg.de/ which can help understand SMARTS queries. Unfortunately it would not help here because it doesn't like the "c1", saying: SMARTS syntax is not correct: Error: syntax error, unexpected INTEGER, expecting BRACKET_CLOSE at position 4 of input. [c1<- The SMARTS is correct, but unusual. The SMARTS term '[c1ccncc1]' looks for an atom which is: an aromatic carbon, and has atomic mass of 1, an an aromatic carbon, and an aromatic carbon, and an aromatic nitrogen, and an aromatic carbon, and an aromatic carbon, and has atomic mass of 1, an In other words, is both a carbon and a nitrogen, and has a mass of 1, and is aromatic. If I take out the two "1"s from the term, then SMARTSView reports: SMARTS semantic is not correct: ERROR: Elements combined by AND! Removed because it's not possible for an element to be both a carbon and a nitrogen. I believe what you want is: c1cnccc1-[R]~1~[R]~[R]~[R]~[R]~1 Oddly, a PubChem substructure search for that SMARTS returns "InternalError@Get error message from search server" for that error. If I search for c1cnccc1-[R]1[R][R][R][R]1 then it finds such hits as: 4-cyclopentylpyridine 5,8-Methanoisoquinoline, 5,6,7,8-tetrahydro-, 2-oxide 4-(5-bicyclo[2.2.1]hept-2-enyl)-3-butylpyridine and many more. If you want the only substitution to be on the para position, then something like [cX3H1]1[cX3H1][nX2][cX3H1][cX3H1][cX3]1-[R]~1~[R]~[R]~[R]~[R]~1 (or the PubChem usable [cX3H1]1[cX3H1][nX2][cX3H1][cX3H1][cX3]1-[R]1[R][R][R][R]1 ) should work. The "X3H1", etc. require that the atoms not be connected to anything, or anything other than a single atom. The visualization in SMARTView should help make it more understandable. > I was also not sure how to specify explicit hydrogen atoms on the pyridine > ring in the SMARTS expression. Does the above help? Cheers, Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
