Aromatic ring system count.

User fca09bdbff

16-05-2014 04:30:49


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,

Tim Ritchie.

ChemAxon d51151248d

19-05-2014 09:51:41

Dear Tim, 

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.

An example:

cxcalc "C1=CC=C2C(C=CC3=CC=CC=C23)=C1" ringsystemcount 
id Ring system count
1 1

while for the same molecule


cxcalc "C1=CC=C2C(C=CC3=CC=CC=C23)=C1" ringcount
id Ring count
1 3

is the result.

Best regards, 



User fca09bdbff

20-05-2014 04:07:17

Thanks Daniel.

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

Regards, Tim.

ChemAxon d51151248d

22-05-2014 14:55:33

Dear Tim, 

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

./ mols.sdf

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.

Best regards,