Camelia, the Perl 6 bug

IRC log for #cdk, 2011-03-13

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All times shown according to UTC.

Time Nick Message
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07:31 CIA-57 cdk: Egon Willighagen cdk-1.2.x * rf72be81 / AUTHORS : Added two new authors - http://bit.ly/f7Ytih
08:20 CIA-57 cdk: Egon Willighagen cdk-1.4.x * rc0ede3f / (2 files in 2 dirs):
08:20 CIA-57 cdk: Fixed a concurrency error, caused by the use of a static field which was not supposed to be static, as the classes are instantiated just to allow customization
08:20 CIA-57 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> (+6 more commits...) - http://bit.ly/f8t0EI
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12:56 CIA-57 cdk: Egon Willighagen cdk-1.4.x * r595cc9f / AUTHORS : Updated the author list - http://bit.ly/eVJAx7
12:56 CIA-57 cdk: Egon Willighagen cdk-1.4.x * ra3e25e6 / (2 files): Added missing dependencies - http://bit.ly/e6lHbP
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14:57 maclean hi
14:57 zarah ni hao maclean
14:58 egonw hi maclean
14:58 maclean hi egonw
14:58 egonw I think I have a Groovy Cheminformatics section that might interest you
14:58 maclean ?
14:59 maclean 2D graphics? or discrete maths?
15:00 maclean Or, I don't know ... minecraft?
15:00 maclean I guess that's unlikely.
15:02 egonw mom, let me make a PDF of the pages
15:02 maclean ok
15:05 egonw sent
15:06 maclean got, takk.
15:08 maclean Damn. I should have used &lt; and &gt; not < and >.
15:09 egonw yeah, suspected that :)
15:09 egonw but I got the point
15:09 maclean :)
15:12 * maclean is currently trying to fix the PDBReader tests after some alterations.
15:13 egonw sounds interesting...
15:14 maclean PDBReader/Writer should also roundtrip small molecules - so CONECT records are written, for example.
15:14 maclean Also, element symbol and charge at the end of the line.
15:15 egonw sounds promising indeed!
15:15 egonw taking advantage of the STRICT/RELAXED design?
15:15 egonw to complain about non-standard things
15:16 maclean Ah...no. Uses IOSettings for 'backward compatibility', though.
15:17 egonw STRICT/RELAXED is not a IOSetting, actually :)
15:17 egonw RELAXED is to allow non-standard PDB syntaxes
15:17 maclean No, no - I knew what you meant .. kindof.
15:17 egonw not that there is a standard syntax really :)
15:17 maclean Well, I've been using the 2008 version 3.20 guide.
15:18 maclean There's still lots of stuff that it won't recognise or expect.
15:18 egonw want to review a small 1.4.x patch?
15:18 egonw https://sourceforge.net/tracker/​?group_id=20024&amp;atid=320024
15:19 egonw if so, please check and sign-off if you think's it's good
15:19 egonw git commit --amend --signoff
15:19 maclean 3208951?
15:19 egonw yes
15:19 maclean Ok.
15:28 CIA-57 cdk: Egon Willighagen cdk-1.4.x * r74bfbc9 / (2 files): Fixed second half of patch a3e25e69419e53291e093d9365b4187843f03736 :( - http://bit.ly/hAoxU4
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15:50 maclean Well that took like 1/2 hr of messing around for 5 changed documentation lines...
15:53 maclean Note to future self : Use "git am --signoff $patchfile" not "git apply $patchfile; git commit --amend --signoff"
16:04 egonw yeah, impressive
16:05 egonw it git that hard?
16:05 egonw thanx for reviewing still!
16:07 CIA-57 cdk: Egon Willighagen cdk-1.4.x * r49eb772 / (2 files in 2 dirs):
16:07 CIA-57 cdk: Added a missing reference for Floyd's algorithm
16:07 CIA-57 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://bit.ly/e60Hez
16:08 maclean Remembering the exact sequence of steps is hard, yes.
16:08 egonw yeah, something like gerrit would be cool
16:08 egonw or likely something in between github and gerrit
16:09 maclean Well, or the 'cricket' tool I mentioned before, that a) downloads the patch b) applies to a branch c) does signoff with a checkbox d) uploads the signed patch
16:10 maclean Also: keeps a list of patches to review or patches to submit for review...
16:11 egonw yeah, sounds perfect
16:12 maclean In general, I find that I forget what branches were for after a while. I know that branching is cheap, but perhaps too cheap :)
16:12 egonw yeah, some naming convention is useful
16:15 maclean Well, true. Eg 'patch30930598' or somesuch.
16:15 maclean But just some metadata description of _why_ this branch for experimental ones.
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17:55 maclean egonw : the RebondTool doesn't deal with bond order...
17:55 egonw yeah, noted that too
17:55 maclean There's the javadoc comment : "Returns the bond order for the bond. At this moment, it only returns
17:55 maclean * 0 or 1, but not 2 or 3, or aromatic bond order."
17:56 egonw the method assumes angstrom bond length scale
17:59 maclean Hmmm. So a list of bond distances for single and double bonds... like : "C=C" : "1.2", "C-C" : "1.5", etc
18:00 egonw right
18:00 maclean Well, anyway. I have a solution for pdb ligands (that are in the CIF dictionary)
18:00 egonw for cryst PDBs an additional problem is the lack of hydrogens
18:02 maclean cryst PDBs? surely they are all crystals?
18:05 maclean haha! ace slashdot tag : "nobodynormalcares".
18:15 CIA-57 cdk: Egon Willighagen master * r9b48adb / (43 files in 27 dirs): Merge branch 'cdk-1.4.x' (+20 more commits...) - http://bit.ly/eOYOxV
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