I would like to count the number of aromatic systems in a series of molecules, i.e. not the number of aromatic rings but the number of separate aromatic ring systems.
For example, if two aromatic rings are fused together, this would count as one aromatic system.
Is there are way to calculate this?
Thanks and regards,
in the Topology Analysis plugin you can choose different ring-related descriptors to be calculated. Among them there is Ring System Count, which counts the ring systems in the molecule, and handles aromatic rings as one.
With cxcalc command line tool you can use the ringsystemcount function for the same purpose.
cxcalc "C1=CC=C2C(C=CC3=CC=CC=C23)=C1" ringsystemcount
id Ring system count
while for the same molecule
cxcalc "C1=CC=C2C(C=CC3=CC=CC=C23)=C1" ringcount
id Ring count
is the result.
As an example, how would you calculate the number of aromatic ring systems in this molecule? The answer should be 2.
Aromatic ring count = 3
Ring count = 4
Ring system count = 3
This special descriptor could not be calculated directly, so we had to come up with a workaround. The attached script calculates the number of aromatic ring systems for each molecule in the input file, and has to be used like
You can find the details of the calculation in the comments of the script. Please note that process might be slow as many pipeline steps are concatenated in it.
I hope you find it useful.