Dear Openbabel Users
I am seeking some assistance in understanding and using SMARTS based
substructure searching with Openbabel.
The overall goal would be to search large molecular data sets using
sophisticated substructure patterns.
What I need to help do that are pointers to documentation or examples of
such searches.
The documentation page on Fingerprints was quite useful.
http://openbabel.org/docs/dev/Features/Fingerprints.html
With this I was able to take a set of (say) 10 thousand molecules and
generate a fast search index with the command
obabel -ican 10k.can -ofs
which creates the fast index search file 10k.fs.
Then search for a specific substructure as SMARTS and seeking output as
SMILEs seems to work well.
obabel -ifs 10k.fs -osmi -s"C1CCNCC1C#N"
=> One result
However if I try a simple SMARTS patter [CX4] for an alkyl carbon, I get an
error.
obabel -ifs 10k.fs -osmi -s"[CX4]"
=> ==============================
*** Open Babel Error in ObtainTarget
Cannot read the SMILES string
0 molecules converted
Ideally I want to use the syntax [C;R] for an aliphatic carbon in a ring
or perhaps
[C;r5,r6] to specify an aliphatic carbon in a five or six membered ring.
Any examples or advice appreciated.
Mark
------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
