counting methyl, methylene, methine and quaternary carbons

KNIME Analytics Platform
1

Does anyone know how to use Knime (or other software) to count methyl, methylene, methine and quaternary carbons of each structure in a structure database?

2

I guess you could use the RDKit substructure counter. if you are familiar with the SMARTS notation you can do pretty interesting things with it

 

3

As Giovanni pointed out, you can do this with the RDKit substructure counter.

I've attached a sample workflow that shows how to do this. It counts four different types of saturated carbon: CH3, CH2, CH, and C. To add a new type, you just need to add the relevant SMARTS query to the table in the Table Creator node.

There's a reference to SMARTS available here: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

Best,

-greg

4

Thanks greg!