Dear Vaibhav, I think the pattern you specified (first one) is trying to match an oxygen connected to aliphatic C (in 6 membered ring). I tried this more general SMARTS pattern and it seems to match phenols:
*~[#6][OH1] babel myfile.sdf -s"*~[#6][OH1]" sim-alcohol.smi This web resource and reference articles (under About link) might also help with creating SMARTS queries: https://smartsview.zbh.uni-hamburg.de/ Vin From: Vaibhav Dixit <vaibhavadi...@gmail.com> Sent: Tuesday, September 10, 2019 8:06 AM To: Noel O'Boyle <baoille...@gmail.com> Cc: babel <openbabel-discuss@lists.sourceforge.net> Subject: Re: [Open Babel] substructure search fails Dear Noel, nabilone is one such example, but there are many phenol containing drugs in the drugbank database, all of which are being missed. I just tried to find alcohols with the following command and it gave me 334 structures. Thus can't understand why it should fail with phenols. babel Drugbank-3D-structures.sdf -s"OC1CCCCC1" sim-alcohol.smi 334 molecules converted 96253 audit log messages babel Drugbank-3D-structures.sdf -s"OC1=CC=CC=C1" sim-alcohol.smi 0 molecules converted 95585 audit log messages Thanks a lot for your quick reply and best regards On Tue, Sep 10, 2019 at 6:22 PM Noel O'Boyle <baoille...@gmail.com<mailto:baoille...@gmail.com>> wrote: Can you provide a single example of a molecule that it misses? We can then try to explain why or work out a solution. Regards, - Noel On Tue, 10 Sep 2019 at 13:33, Vaibhav Dixit <vaibhavadi...@gmail.com<mailto:vaibhavadi...@gmail.com>> wrote: Dear Openbabel community, I'm trying to extract all compounds from an sdf file which contain an OH group (phenolic or aliphatic). For this I have tried the following command in my anaconda prompt installation of babel. But I'm not getting the expected result and no molecule is retrieved. I get results using similarity cutoff but these also include compounds with ether linkages which I don't want. Can you please suggest the usage to get the expected result if this is possible in babel? babel Drugbank-3D-structures.sdf -sOC1=CC=CC=C1 sim-phenol.smi 0 molecules converted 95585 audit log messages babel Drugbank-3D-structures.fs -ifs -sOC1=CC=CC=C1 sim-phenol.smi -at0.5 23 molecules converted 335 audit log messages Thank you. -- Regards, Dr. Vaibhav A. Dixit, Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. AND Assistant Professor, Department of Pharmacy, ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031. India. Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: vaibhav.di...@pilani.bits-pilani.ac.in<mailto:vaibhav.di...@pilani.bits-pilani.ac.in>, vaibhavadi...@gmail.com<mailto:vaibhavadi...@gmail.com> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra • Please consider the environment before printing this e-mail _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net<mailto:OpenBabel-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Regards, Dr. Vaibhav A. Dixit, Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. AND Assistant Professor, Department of Pharmacy, ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031. India. Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: vaibhav.di...@pilani.bits-pilani.ac.in<mailto:vaibhav.di...@pilani.bits-pilani.ac.in>, vaibhavadi...@gmail.com<mailto:vaibhavadi...@gmail.com> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra • Please consider the environment before printing this e-mail
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