User c29d691f4a
08-06-2011 15:58:31
Howdy,
My name is Chris and I am having some difficulty defining a search graphically. I've attached the Marvin file for your review. R1 can be anything except fluorine or a carbon bonded to fluorine and R2 can be carbon bonded to anything but fluorine. Seems simple, but based on my search results, I need some expert help. I know my R groups are somewhat contradictory, just messing about, trying to get a hang of it. Thanks in advance for your time.
chris
ChemAxon a3d59b832c
10-06-2011 10:23:32
Hi Chris,
First of all, I have moved this question to the JChem forum, because it is not specific to Markush databases, it is rather a general query question.
There are multiple solutions. One possibility is to use SMARTS atoms:
http://www.chemaxon.com/jchem/doc/user/query_features.html#smarts_atoms
[#6;!$(*F)]C(F)(F)C(F)(F)C(F)(F)[*,#1;!$(F);!$([#6]F)]
(I am not explaining this, please check SMARTS rules on the links above. :) )
The other possibility would be to use R-logic. R1=0 means that R1 cannot be present as defined on that position.
See the attached file using this technique.
You can display R-logic in Marvin Sketch using View / Misc / R-logic.
To set it, you have to use the menu Structure / Attribute / R-logic.
Finally, please note that Fischer projections are not supported by JChem, you have to specifically use wedges to represent stereochemistry. (You may know this already, just the layout was suspicious for me. :) )
Best regards,
Szabolcs