1. Andrew Dalke
  2. cyclops_mysql

Commits

Author Commit Message Date Builds
da...@viepcldx-e2c.eu.boehringer.com
split the new substructure fingerprint code away from the OEChem code since the latter requires a license even to instantiate an OEFingerprint, which is what I did in my State class. Added license checks in the MACCS and hash fingerprints so I get a error message and not a hard exit if I call them on unlicensed machines.
dalke
Updated to use the correct nibble order
dalke
added tests for the query fingerprints.
dalke
fixed test which had depended on a bug in the fingerprinter
dalke
migrated the test code to use MySQL instead of the shared library
dalke
Added the query fingerprint code. Added aromaticity selection
dalke
Cleaned up some of the SMILES (my validation wasn't as strict as I thought it was)
dalke
addd the substructure fingerprints
dalke
fixed a couple of SMARTS typos I had inadvertantly introduced. Made the #define for the C helper be conditionally defined
dalke
fix because I got the nibble order wrong
dalke
cyclops substructure definitions
dalke
fixes because I got the SMARTS closer to what CACTVS does
dalke
added the cyclops_fp function
dalke
had the wrong nibble order for the hex representation
dalke
It's a header file. What else do you expect here?
dalke
expanded the API put things inside a C++ namespace
dalke
support for the Cyclops substructure fingerprinter
dalke
New tests for the cyclops substructure fingerprinter
dalke
Modified the definitions based on what I learned from Evan and by looking at the CDK and the PubChem implementation from NIH Chemical Genomics Center
dalke
added documentation so Raja could understand it
dalke
Changed the patterns to use c:c instead of [#6]:[#6]. (Got the inspiration after looking at http://www.ncgc.nih.gov/pub/openhts/code/NCGC_PubChemFP.java.txt ) Disabled debugging code
dalke
Don't use OEChem now (preprocess to get the right aromaticity) Also ignore false bits
dalke
even more test patterns. This time with CACTVS goodness!
dalke
>= 2, not just >2
dalke
Yes, (=O) can be aromatic. And there's a few cases I decided to allow as aromatic even if I don't think they can ever occur
dalke
And I need to allow aromatics for that case
dalke
SMARTS translation put the ) in the wrong place
dalke
Grr, another place where I mistranslated the environment test
dalke
Okay, this time around I'm much closer to what PubChem gives me
dalke
fixed a problem in bit 379; I was only checkin for C(:N) not C(-N)(:N)
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