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/
>
>
>
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