Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-27

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All times shown according to UTC.

Time Nick Message
02:07 CIA-33 jmol: hansonr * r9526 /trunk/Jmol/src/org/jmol/ (9 files in 6 dirs):
02:07 CIA-33 jmol: version=11.5.43_dev quaternion tweaks
02:07 CIA-33 jmol: # bug fix: quaternion definition with dot-product check not effective -- removed
02:07 CIA-33 jmol: # bug fix: quaternion construction from matrix error
02:07 CIA-33 jmol: #
03:58 CIA-33 jmol: hansonr * r9527 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs):
03:58 CIA-33 jmol: version=11.5.43_dev quaternion tweaks
03:58 CIA-33 jmol: # bug fix: quaternion definition with dot-product check not effective -- removed
03:58 CIA-33 jmol: # bug fix: quaternion construction from matrix error
03:58 CIA-33 jmol: #
06:42 egonw joined #cdk
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07:41 jpansanel moin
07:42 olas moin jpansanel
07:42 jpansanel moin olas
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08:14 shk3 joined #cdk
08:15 shk3 wanted to fix a jcp bug yesterday and come across six other problems...
08:16 shk3 question:
08:16 shk3 by using the properties dialog, any symbol can be entered for an atom.
08:16 shk3 Is this intended?
08:18 olas left #cdk
08:19 shk3 egonw, what do you think?
08:19 egonw yes
08:19 egonw pseudo atoms, like R
08:20 egonw it should possibly integrate with your COOH functionality...
08:20 egonw shk3: please mention those six on cdk-jchempaint@
08:20 egonw need to do some other stuff right now
08:21 shk3 R is ok, but right now you can enter anything...
08:21 shk3 I will ask
08:21 shk3 and fix the other stuff
08:32 thomas_ku moin
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10:46 CIA-33 cdk: shk3 * r11447 /cdk/branches/cdk-1.0.x/src/org​/openscience/cdk/applications/ (2 files in 2 dirs): the properties dialog now differenciates atom from pseudo atom, solves bug #1524466
10:54 CIA-33 cdk: shk3 * r11448 /cdk/branches/cdk-1.0.x/src/org/opensc​ience/cdk/test/io/MDLWriterTest.java: added a test for bug #1524466
11:03 CIA-33 cdk: shk3 * r11449 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/ (2 files in 2 dirs): The cdk source code writer did not care about pseudo atoms and therefore produced broken code
11:08 CIA-33 cdk: shk3 * r11450 /cdk/branches/cdk-1.0.x/src/org/opensc​ience/cdk/io/CDKSourceCodeWriter.java: is a pseudoatom always having a label instead of a symbol? not sure, ask egonw about this
12:30 sneumann joined #cdk
12:31 sneumann hi there
12:31 shk3 hi
12:31 sneumann you've got mail
12:31 sneumann ;-)
12:32 shk3 you too
12:33 shk3 ah, your's newer
12:33 shk3 scrollbars should depend on size
12:33 shk3 but it looks a bit like the vertical one is always there
12:34 shk3 I will try to look at this (I now we spent some time on scrollbars)
12:45 sneumann Never mind, I have to convince MassBank people
12:46 sneumann to _not_ use their homegrown viewer in first place.
12:46 sneumann But I guess that theirs is not scriptable,
12:46 sneumann so convincing should be easy
12:47 sneumann http://www.massbank.jp/jsp/Dispatcher.j​sp?type=disp&id=KO000153&site=0
12:55 CIA-33 cdk: shk3 * r11451 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/a​pplications/jchempaint/action/SaveAsAction.java: Check if file exists was only done if complete file name with extension was entered and not if the automatic extension would be used.
13:02 sneumann bye
13:02 sneumann left #cdk
13:09 shk3 just talked to user here
13:09 shk3 he wants to compare two molecules visually
13:09 shk3 we could easily do this in jcp, like superimpose one molecule on the other
13:09 shk3 using mcss
13:10 shk3 Do you think this is a usefull application?
13:10 shk3 Shouldn't be too hard to implement.
13:29 CIA-33 cdk: shk3 * r11452 /cdk/branches/cdk-1.0.x/src/org/openscience​/cdk/controller/AbstractController2D.java: after delete, we look if there is an empty atomcontainer and remove this, because it will show up in saves otherwise.
14:10 egonw joined #cdk
14:23 CIA-33 cdk: shk3 * r11453 /cdk/branches/cdk-1.0.x/src/org​/openscience/cdk/applications/ (2 files in 2 dirs): It is now possible to revert a pseudo atom to a normal atom
14:33 shk3 hi egonw
14:33 shk3 short question
14:33 shk3 [14:09] <shk3> just talked to user here
14:33 shk3 [14:09] <shk3> he wants to compare two molecules visually
14:33 shk3 [14:09] <shk3> we could easily do this in jcp, like superimpose one molecule on the other
14:33 shk3 [14:09] <shk3> using mcss
14:33 shk3 [14:10] <shk3> Do you think this is a usefull application?
14:33 shk3 [14:10] <shk3> Shouldn't be too hard to implement.
14:35 egonw not 3D?
14:35 shk3 no, just 2d
14:48 egonw should not be too difficult
14:48 egonw sounds like a BIoclipse thingy
14:48 egonw sorry, got more stuff to do, bbl
15:03 shk3 time for one more question?
15:07 egonw later
15:08 egonw well, pop the question anyway...
15:08 egonw I'll respond later
15:15 shk3 ok, there is a hydrogens submenu in Edit and in the atom popup.
15:16 shk3 There is the "switch on/off..." menu item
15:16 shk3 it works in edit, but not in the context menu.
15:16 shk3 since I have no idea how the menus are built: Could you have a look?
15:33 egonw yes, please file a bug report
16:21 shk3 will do so

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