On Dec 11, 2011, at 6:36 AM, Greg Landrum wrote:
> Assuming I implemented your FPs correctly (code attached), this is what I get:
...
> pubchem pieces:
> [05:30:38] INFO: FINISHED 50001 (41150823 total, 2948920 searched,
> 964883 found) in 80.68
> [05:30:38] INFO: screenout: 0.07, accuracy: 0.33
> #--------------------
I got your code working against my copy of Zinc (110907 compounds), with the
fragments you pointed me to. On my computer I get:
[18:14:37] INFO: FINISHED 50001 (41150823 total, 2647252 searched, 880194
found) in 100.49
[18:14:37] INFO: screenout: 0.06, accuracy: 0.33
(I'm testing with a slightly older version of RDKit, which might explain the
differences in the searched/found numbers.)
I'm confused about how to compare this to the other numbers you reported. You
wrote about the new work you've been doing:
> New fingerprint:
> - Zinc fragments: 50 million pairs, 4413 hits, 0.9 seconds seconds
> - Zinc leads: 50 million pairs, 1875 hits, 0.7 seconds
> - pubchem pieces; 82.3 million pairs, 2.5 million hits, 166 seconds
Does this mean the screenout for your new fingerprints is 2.5/82.3 = 0.03 for
the pubchem pieces? That means it's twice as good as a screenout of 0.06,
right? But then how did your new fingerprints give 166 seconds while the
fragments I sent yesterday run in 81 seconds on what I presume is the same
machine?
Andrew
da...@dalkescientific.com
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