Hi Ivan, There is an RDKit extension to SMARTS that allows something like [r12-20]. I can’t check the exact syntax at the moment. You might want to check that atoms are not in smaller rings as well, so as not to pull up things like anthracene which might not be something you’d want to class as a macrocycle. Cheers, Dave
On Wed, 9 Oct 2019 at 14:39, Ivan Tubert-Brohman < ivan.tubert-broh...@schrodinger.com> wrote: > Hi Thomas, > > I don't know of an RDKit function that directly recognizes macrocycles, > but you could find the size of the largest ring this way: > > ri = mol.GetRingInfo() > largest_ring_size = max((len(r) for r in ri.AtomRings()), default=0) > if largest_ring_size > 12: > ... > > You can also find if a molecule has a ring of a certain size using SMARTS, > but only for rings up to size 20 at the moment (this is an RDKit-specific > limit). For example, if you are happy with finding rings of size 12-20, you > could use SMARTS [r12,r13,r14,r15,r16,r17,r18,r19,r20]. It's ugly but can > be handy if you already have SMARTS-based tools to reuse. > > Ivan > > On Wed, Oct 9, 2019 at 7:25 AM Thomas Evangelidis <teva...@gmail.com> > wrote: > >> Greetings, >> >> Is there an automatic way to distinguish the macrocyclic molecules within >> a large chemical library using RDKit? For example, according to this >> definition: Macrocycles are ring structures composed of at least twelve >> atoms in the central cyclic framework [1,2,3]. Maybe someone here has a >> better definition. Could anyone give me some hints on how to program this? >> >> I thank you in advance. >> Thomas >> >> 1. Yudin AK (2015) Macrocycles: lessons from the distant past, recent >> developments, and future directions. Chem Sci 6:30–49. >> 2. Marsault E, Peterson ML (2011) Macrocycles are great cycles: >> applications, opportunities, and challenges of synthetic macrocycles in >> drug discovery. J Med Chem 54:1961–2004. >> 3. Heinis C (2014) Drug discovery: tools and rules for macrocycles. Nat >> Chem Biol 10:696–698. >> >> >> -- >> >> ====================================================================== >> >> Dr. Thomas Evangelidis >> >> Research Scientist >> >> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech >> Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> >> , Prague, Czech Republic >> & >> CEITEC - Central European Institute of Technology >> <https://www.ceitec.eu/>, Brno, Czech Republic >> >> email: teva...@gmail.com, Twitter: tevangelidis >> <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis >> <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk
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