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 >
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