Chemical term to count the no. of sp3 carbons in a molecule?

I would like to count the number of sp3 hybridized carbons in a molcule. Is there an easy way to do this, e.g. as a Chemical Term?

CT expression for counting carbon atoms with 4 connected ligands:

$ evaluate -e "count(filter('atno()==6 && connections()==4'))" "C\C=C\C(C)C"
4

We have no functions for filtering spn hybridization states yet.

I hope this helps.

Zsolt

 

 

Hello,

Thanks for the prompt reply.

count(filter('atno()==6 && connections()==4')) worked fine in IJC.

Hello,

I would like to count the number of aromatic carbon atoms in a set of molecules.

"count(filter('atno()==6 && connections()==3'))" will give me all the sp2-hybridised carbons but this includes carbonyls etc.

Is there a way to exclude these?

Yes, there is.

Example:

$ evaluate -e "count(filter('atno()==6 && connections()==3')) - matchCount(carbonyl)" "CCC(=O)C\C=C\C"
2

The number of carbonyl groups is subtracted from the number of sp2 carbons.

Same for aromatic carbons:

$ evaluate -e "count(filter('atno()==6 && connections()==3 && aromaticAtom()')) - matchCount('[c;X3:1]=[O;X1:2]')" "CC(=O)C\C=C\C1=CC=CC=C1"
6

For more functional groups and predefined molecule sets see: http://www.chemaxon.com/jchem/marvin/help/chemicalterms/ChemicalTerms.html#molsets

Zsolt

Hello,

Is it possible to evaluate two CT expressions in one line, e.g. combine

-e "count(filter('atno()==6 && connections()==4'))" with

-e "count(filter('atno()==6'))"

so the output would be the number of sp3 carbons and the number of all carbons.

Regards,

Tim Ritchie.

Yes, it is possible. Separate the expressions with semicolon.

Example:

evaluate -e "count(filter('atno()==6 && connections()==4')); count(filter('atno()==6'))" "CCCC=C"
3;5 

Zsolt

Great. Many thanks.

Tim Ritchie.

Hello,

Is there a way to count the number of sp3 carbon atoms in a SMILES string using cxcalc rather than IJC/evaluate?

Thanks, Tim Ritchie.

No, cxcalc cannot be used for that.

Zsolt

OK. Thanks.

Is it possible to do something as a function in JChem Excel?

Regards, Tim Ritchie.

Yes, Chemical Terms is available in Excel.

Zsolt

Thanks. Could you give me the syntax to generate a function in Excel to calculate the number of sp3 carbons please? Thanks, Tim Ritchie.

Try this:

matchCount("[CX4]")

Hello,

When I insert a JChemExcel.Function, I have to select from a predefined list, e.g. JCAliphaticAtomCount, JCCarboAromaticRingCount etc.

Is it possible to add additional custom functions such as counting sp3 carbons etc?

Thanks and regards,

Tim Ritchie.

Hello,

I found that the following worked as a Chemical Term in JChem/Excel.

Regards,

Tim Ritchie.

=JCChemicalTerms(A1,"count(filter('atno()==6 && connections()==4'))")