Dear Thomas,
I'm not aware of any RDKit function that distinguishes macrocycles .
However, based on the definition of 12 or more membered rings, you may use
the following function to get molecules that have rings with 12 or more
atoms from a list of molecules:
def GetMacrocycles(mols):
Macrocycles = [ ]
for mol in mols:
for RingAtoms in mol.GetRingInfo().AtomRings():
if len(RingAtoms) >= 12: Macrocycles.append(mol)
return Macrocycles
I hope this helps.
Best regards,
Omar
On Wed, Oct 9, 2019 at 2:25 PM 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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