On Sun, Sep 26, 2010 at 7:22 PM, Steffen Neumann <sneum...@ipb-halle.de> wrote: > Hi, > > I tried to investigate this, but my C++ is quite rusty, > so unless somebody else is on this SMARTS problem, > could anyone point me what to look for ?
The problem seems to be the explicit closure bond at the end of the SMARTS. The source is in src/parsmarts.cpp but I'm not familiar with the code. The error originates from line 1522. If this is removed, a unit test fail to identify these invalid SMARTS: C=1CCCCC#1 C-1CCCCC:1 However, your SMARTS should be valid I think. For example, C1CCC=1 means we should use the bond expression next to the second closure digit. The fix is in svn now. Tim > Yours, > Steffen > > > On Mon, 2010-09-13 at 09:14 +0200, Steffen Neumann wrote: >> Hi, >> >> I've hit a problem using SMILES as SMARTS, >> which in my case requires using *canonical* SMILES as input, >> see the example below. The problem occurs both with ob-2.2.3 >> and todays SVN trunk. >> >> Did I miss anything, or should I open a bug ? >> >> Yours, >> Steffen >> >> #-------- Cut & Paste from here ------------ >> >> echo >> 'InChI=1S/C9H7N5O/c10-8-7-9(12-4-11-8)14(5-13-7)6-2-1-3-15-6/h2-6H,(H2,10,11,12)' >> | babel -i inchi - -o smi >> #C1=CC(n2cnc3c(N)ncnc23)OC=1 >> #1 molecule converted >> #1 info messages 25 audit log messages >> >> echo 'O' | babel -i smi - -s 'C1=CC(n2cnc3c(N)ncnc23)OC=1' -o smi - >> #============================== >> #*** Open Babel Error in SMARTSError >> # SMARTS Error: >> #C1=CC(n2cnc3c(N)ncnc23)OC=1 >> # ^ >> >> echo >> 'InChI=1S/C9H7N5O/c10-8-7-9(12-4-11-8)14(5-13-7)6-2-1-3-15-6/h2-6H,(H2,10,11,12)' >> | babel -i inchi - -o can >> #Nc1ncnc2c1ncn2C1C=C=CO1 >> #1 molecule converted >> #1 info messages 25 audit log messages >> >> # Correct: >> echo 'O' | babel -i smi - -s 'Nc1ncnc2c1ncn2C1C=C=CO1' -o smi - >> #0 molecules converted >> > > -- > IPB Halle AG Massenspektrometrie & Bioinformatik > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 http://msbi.bic-gh.de > 06120 Halle Tel. +49 (0) 345 5582 - 1470 > +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
