Outputting chemical descriptors in batches?

User b85e2e3247

01-06-2011 22:19:12

I have the chemical names, their 2D structure, and their smiles columnized, now i am trying to select these molecules and get information from jchem like H bond donors/acceptors, number of rings, and other chemical descriptors. I have attached a screenshot of how my sheet is set up.

Does anyone know how to get an output column of descriptors instead of going one-by-one down the list?

I know many descriptors I am looking for cannot be calculated by JChem, I was wondering if someone could point out which ones are possible from this list:


molecular weight 

number of nitrogens 

number of oxygens 

XlogP (calc n-octanol/water partition coefficient) 

number of hydrogen bond donors 

number of hydrogen bond acceptors 

number of rotatable bonds 

tPSA (topological polar surface area) 

ALOGPs (calc n-octanol/water partition coeff) 

ALOGpS (calculated aqueous solubility) 

number of stereocenters 

number of R stereocenters 

number of S stereocenters

number of rings 

number of aromatic rings 

number of ring systems

number of atoms in largest ring outline


Thank you for any help or suggestions,


ChemAxon bd13b5bd77

02-06-2011 06:24:28

Hi Graham,


have you tried out our automation functions exported to all other Excel function categories?

Please check the screenshot.

If you have chosen the relelvant function you need you can use Excel to extend the calculated field for all molecules pulling down it by the selection (right corner of the cell => ).

When a function requires a molecule by the selector you need to select the cell where the molecule is in.

See the pictures attached.



ChemAxon bd13b5bd77

02-06-2011 06:30:05

Online documentation is also available:





User b85e2e3247

02-06-2011 17:09:36



Thank you for the response. I used the functions in the way shown on your screenshots, this worked well.

I am wondering about the accuracy of the H bond acceptor count however, if you take a look at my screenshot you might see what I mean (JCAcceptor vs. JCAcceptorCount vs. JCAcceptorSiteCount?)

I count 7, 4, and 6 for H bond acceptors for these 3 molecules, and JCAcceptorSiteCount seemed to work for the 1st and 3rd molecules, and neither for the second molecule.

Thank you for your help,



ChemAxon bd13b5bd77

02-06-2011 21:44:58

Dear Graham,

let me forward your question to someone else with different skillset.


ChemAxon bd13b5bd77

02-06-2011 21:46:20

Akos, could you please check Graham's result using these functions.

As if we also had misunderstanding in the past you made clear for us.


Thank you,


ChemAxon 990acf0dec

03-06-2011 03:35:54

Dear Graham,

AcceptorSiteCount is the sum of the lone pairs of the acceptor atoms. In addition, the halogen atoms are excluded from the acceptor count by default, so the elone pairs of Fluor is not counted. Please also note that amide nitrogens are not considered as acceptors in the calculation method.

One more thing: your third example is drawn incorrectly, because neither of the nitrogens of the benzodiazole ring has hydrogens, and therefore both of them are counted as acceptor. The currect structure is:


Best regards,


User b85e2e3247

03-06-2011 17:21:06

Thank you, this cleared things up. Also, thanks for catching the missing Hydrogen.

This is very helpful, the JChem for excel is a GREAT piece of software.

Thanks again,