Dear Vincent, and Babel community, I have tried these and slight modifications to get the desired results. Just wondering what modification will give molecules with only -NH2 and exclude molecules that have in-addition -NH or amides. These have worked as expected and are given below in case they are useful to others on the list (the name of the second sdf file in the command shows the type of compounds extracted from the main.sdf). Thanks a lot for your valuable suggestions. Best regards
babel main.sdf -s"[OH]CC" ethanols.sdf babel main.sdf -s"[OH]c1ccccc1" phenols.sdf babel main.sdf -s"[OH]C1CCCCC1" cyclohexanols.sdf babel main.sdf -s"*~[#6][NH0]" amines.sdf babel main.sdf -s"*~[#6][NH1]" secondary-&-primary-amines.sdf babel main.sdf -s"*~[#6][NH2]" amines.sdf On Tue, Sep 10, 2019 at 7:00 PM Scalfani, Vincent <vfscalf...@ua.edu> wrote: > 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> 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 > -- 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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