Calculating no. of atoms in molecular framework &side chains

Hello,

I would like to count the number of heavy atoms in the molecular framework of a structure (i.e. the ring systems that remain after side chains are removed), and also count the number of atoms in the side chains.

Is this possible as a Chemical Term?

Regards,

Tim Ritchie (GSK Stevenage UK).

 Hi,

You can get the heavy atom count of the molecule by subtracting the Hydrogen atom count from the atom count:

$ evaluate -e "atomCount() - atomCount('1')" "C1CCCCC1CCCCCCCC"
14

The number of heavy atoms in the molecular framework of a structure is returned if you use the following command:

$ evaluate -e "atomCount(bmf(mol())) - atomCount(bmf(mol()),'1')" "C1CCCCC1CCCCCCCC"


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Find more information on structural framework options: https://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html#structuralframeworks_functions

Calculating the number of heavy atoms of the sidechain, you need to substract the above two functions, i.e., the number of heavy atoms of the whole molecule - the number of heavy atoms of the molecular framework

$ evaluate -e "(atomCount() - atomCount('1')) - (atomCount(bmf(mol())) - atomCount(bmf(mol()),'1'))" "C1CCCCC1CCCCCCCC"


8

 

Best Regards,

Viktoria

Thanks for that.

Is it possible to do something similar using Chemical Terms within JChem/Excel?

Yes, you can use the "JCChemicalTerms" function to apply Chemical Terms functions in JChem for Excel.

Find more help and examples at: http://www.chemaxon.com/jchem4excel/userguide/chemical_terms.html

Regards,

Viktoria

Could you please give me an example of a CT that would work in Excel, equivalent to

evaluate -e "atomCount(bmf(mol())) - atomCount(bmf(mol()),'1')"

Thanks, Tim Ritchie.

Hi,

 

The following function returns the heavy atom count of the molecule in the A1 cell:

=JCChemicalTerms(A1;"(atomCount() - atomCount('1')")

while this example returns the heavy atom count of the molecular farmework of the molecule in the A1 cell:

=JCChemicalTerms(A1;"(atomCount(bmf())) - atomCount(bmf(),'1')")

BR,

Viktoria

Many thanks.

In Excel, I needed to change the semicolon for a comma for it to work, but this was exactly what I wanted.

Regards, Tim Ritchie.