A follow-up question, Is it possible to extract coordinates (xyz) from these O, N atoms which are attached to one/two Hs using babel (lets say from a mol2/sdf file)? Or I need to use rdkit or custom python scripts for such tasks? thanks a lot.
On Thu, Sep 12, 2019 at 11:14 AM Vaibhav Dixit <vaibhavadi...@gmail.com> wrote: > 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 > > -- 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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