Camelia, the Perl 6 bug

IRC log for #cdk, 2011-11-09

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All times shown according to UTC.

Time Nick Message
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08:36 CIA-50 cdk: Egon Willighagen cdk-1.4.x * rfdd3d22 / src/main/org/openscience/cdk/to​ols/diff/AtomContainerDiff.java : Added missing @cdk.githash. - http://git.io/4jcjdg
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09:54 egonw I'm stunned... already half an hour past my blog spot, and no pull requests yet...
09:54 egonw post, not spot
10:05 jonalv egonw: canät we just automate that dot adding problem?
10:05 jonalv egonw: or did I just miss the point? :)
10:06 egonw hahahaha
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10:12 egonw hi schymane_
10:12 schymane_ hi!
10:12 zarah hi schymane_
10:12 schymane_ AlogP: I get 3 values, e.g. 0.5120000000000002,0.26214400000000027,55.4033
10:12 schymane_ and I had a link somewhere that I thought explained it and now can't find it...
10:12 schymane_ what are those numbers?
10:13 schymane_ 55 is obviously not a logP
10:14 egonw https://github.com/cdk/cdk/blob/master/​src/main/org/openscience/cdk/qsar/descr​iptors/molecular/ALOGPDescriptor.java
10:14 egonw see the JavaDoc on lines 80-82
10:17 schymane_ * <li>ALogP - Ghose-Crippen LogKow * <li>ALogP2 * <li>AMR - molar refractivity
10:17 egonw right
10:18 schymane_ my line Nos are different...but anyway, what is the AlogP2? old (pre 1998) or "new" or ??
10:18 schymane_ e.g. 2.4548,6.02604304,100.0315
10:18 schymane_ now that is a huge difference
10:20 egonw that I don't know
10:21 egonw that may be explained in teh Ghose-Crippen papers cited in the JavaDoc
10:21 egonw try the HTML version to get the full citation
10:21 egonw http://pele.farmbio.uu.se/nightly-1.4.x/cdk​-javadoc-1.4.5.git/org/openscience/cdk/qsar​/descriptors/molecular/ALOGPDescriptor.html
10:21 zarah egonw's link is also http://tinyurl.com/cyh3rhj
10:21 egonw huh?!?
10:22 egonw WTF???
10:22 egonw where *is* the JavaDoc???
10:23 * egonw puzzled why the class JavaDoc is not present in the HTML...
10:23 schymane_ ALOGP2 = ALOGP * ALOGP; (my) line 421
10:23 schymane_ from the first link you sent
10:23 egonw good thinking :)
10:23 egonw (open source)++
10:23 schymane_ :)
10:24 egonw filing a bug report about the missing class JavaDoc in the HTMl
10:25 schymane_ well...that seems to be the answer, AlogP2 is actually (AlogP)^2
10:25 schymane_ why?
10:25 schymane_ so basically, i take the first value, that's the answer...
10:25 schymane_ thanks
10:28 schymane_ it's not actually written anywhere in http://pele.farmbio.uu.se/nightly-1.4.x/cdk​-javadoc-1.4.5.git/org/openscience/cdk/qsar​/descriptors/molecular/ALOGPDescriptor.html is it?
10:29 zarah schymane_'s link is also http://tinyurl.com/cyh3rhj
10:29 schymane_ i had an older version that basti sent...
10:29 schymane_ that's where i started looking...
10:37 egonw schymane_: yeah, there is something wrong with the HTML...
10:38 egonw it should show the JavaDoc as you looked at in the source
10:38 egonw this is the bug that I'm filing...
10:38 schymane_ yeah, i thought last time it was written in there...i have a citation i don't have from anywhere else...and it's not there anymore
10:38 egonw dunno what's going wrong here...
10:38 schymane_ me neither ;)
10:39 schymane_ but it looks like it uses the 1998 values, whereas the original citation was older
10:39 schymane_ Ghose, A.K. and G.M. Crippen, Atomic Physicochemical Parameters for 3- 760 Dimensional Structure-Directed Quantitative Structure-Activity-Relationships 761 .1. Partition-Coefficients as a Measure of Hydrophobicity. Journal of 762 Computational Chemistry, 1986. 7(4): p. 565-577.
10:39 schymane_ sorry bout the line numbers mixed in
10:40 schymane_ http://pubs.acs.org/doi/pdf/10.1021/jp980230o is the newer one
10:40 schymane_ or at least the one i found first
10:41 schymane_ where they present the new parameters
10:47 egonw schymane_: https://sourceforge.net/tracker/?func=detail&amp​;aid=3435367&amp;group_id=20024&amp;atid=120024
10:48 schymane_ :)
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