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:
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
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
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):
4 matches
Mail list logo
