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> 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> > 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, 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 >> >> P Please consider the environment before printing this e-mail >> >> _______________________________________________ >> OpenBabel-discuss mailing list >> 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, 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 P Please consider the environment before printing this e-mail
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