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