Creating a "NOT" structure search using Marvin Ske

User ec47cc00a1

24-09-2010 20:21:00

I am using MarvinSketch to create a structure query for database (Jchem Base in the back-end)


I have a question
about the use of the "NOT list" function. Specifically, I would like to
find compounds of the structure:


C-NH-C

Where the carbon atoms are not bonded to oxygen atoms (ie,
I'm looking for amines, not amides). I can do this in the structure
editor by setting up  a query:

notO-C-NH-C-notO

Unfortunately, it still pulls up compounds that have the structure:


C-NH-C=O

I've even changed the bond between the "C" and the "notO" to "any", and it still doesn't limit the compounds.


Is there a syntax I can use to find these?

ChemAxon a3d59b832c

27-09-2010 13:31:31

Dear Anna,


 


Your not list atoms match the implicit Hydrogens of the C atoms.


However, you can exclude them in the not list: not[H,O]-C-NH-C-not[H,O].


 


Let me know if it helps.


 


Best regards,


Szabolcs