Ivan's solution, using the SMARTS extension [r{12-}], is what I would use
for this.
I would suggest using the permanent documentation link though:
http://rdkit.org/docs/RDKit_Book.html#smarts-support-and-extensions
That's the one that I keep up to date.
A note to Dave's point about anthracene: because the "r" query is
defined in terms of smallest rings, things like anthracene aren't a problem
when using [r{9-}].
>>>
Chem.MolFromSmiles('C1=CC2=CC3=CC=CC=C3C=C2C=C1').HasSubstructMatch(Chem.MolFromSmarts('[r{9-}]'))
False
The next version of the documentation includes a SMARTS reference, so it'll
be easier to look stuff like this up:
https://github.com/rdkit/rdkit/blob/master/Docs/Book/RDKit_Book.rst#smarts-reference
On Wed, Oct 9, 2019 at 6:46 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> Hi David,
>
> Thanks for the tip! I just found it in the documentation; the syntax is
> [r{12-20}]. See
> http://rdkit.org/docs_temp/RDKit_Book.html#smarts-support-and-extensions
>
> Note that this doesn't suffer from the hard-coded limitation I mentioned,
> and you can even specify open ranges such as [r{12-}].
>
> Ivan
>
>
> On Wed, Oct 9, 2019 at 12:35 PM David Cosgrove <davidacosgrov...@gmail.com>
> wrote:
>
>> 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/
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>> _______________________________________________
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>> --
>> David Cosgrove
>> Freelance computational chemistry and chemoinformatics developer
>> http://cozchemix.co.uk
>>
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