Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-08

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All times shown according to UTC.

Time Nick Message
01:06 CIA-31 jmol: hansonr * r8220 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs):
01:06 CIA-31 jmol: version=11.3.17_dev
01:06 CIA-31 jmol: # new feature: setting Jmol,Rasmol,Shapely,Amino,Roygb,Rwb
01:06 CIA-31 jmol: # color schemes makes those colors the default colors for
01:06 CIA-31 jmol: # these schemes.
01:06 CIA-31 jmol: # colorManager clean-up
02:08 LaserJock joined #cdk
06:40 jbrefort joined #cdk
07:11 jpansanel matin
07:16 jbrefort salut Jérôme
07:33 jpansanel how works bkchem ?
07:53 jbrefort did not test, still have to install cairo
07:53 jbrefort btw, seems I'll have to compile it
07:57 neksa joined #cdk
08:13 rojasm joined #cdk
09:07 carsten joined #cdk
09:22 Nout joined #cdk
09:31 Nout morning
09:32 rojasm moin
10:36 egonw joined #cdk
10:37 egonw moin
10:41 rojasm moin
10:44 rojasm egonw; I found a easy solution to validate the molecular forumla but it fails for the compound in question has charge.
10:45 rojasm Do you about a class of MolecularFormula
10:45 rojasm think
10:46 egonw yes, I think it is a good idea
10:46 egonw let's take this to the list...
10:46 egonw this is important to do right...
10:46 rojasm The idea is to make like for smiles
10:46 egonw as it will have important application in metabolomics...
10:47 egonw we need to be able to add things to the MF, not just cahrges
10:47 egonw I think it would be nice to be able to say [M+H]+
10:47 egonw and [M+Na]+
10:47 egonw etc
10:47 rojasm ok
10:48 rojasm but the problem is that there is not protocol about MF how it should be writen, right
10:48 rojasm Or I am wrong
10:48 egonw yes, it should be done right...
10:48 egonw but there are more metabolomics people on the cdk-devel list...
10:49 egonw so 'we' (the CDK community) should be able to figure this out
10:49 rojasm that sounds great
11:01 egonw Nout: around?
11:02 nielsout joined #cdk
11:03 CIA-31 cdk: nielsout * r8894 /trunk/cdk/src/org/openscience/cdk/ren​derer/progz/SwingMouseEventRelay.java:
11:08 egonw hi nielsout
11:08 nielsout hey
11:09 egonw might you blog an item with your plans for the last week or so?
11:09 egonw I will have lunch first now...
11:09 nielsout that update was nothing much, was just synchronising :)
11:09 egonw but let's discuss shortly after that how to wrap things up...
11:09 nielsout yup that's cool
11:09 egonw would be nice if you could hack up a simple next-generation JCP editor...
11:09 nielsout I got this whole weekend plan to work
11:09 nielsout *planned
11:09 egonw that would be an excellent demo
11:10 egonw OK, please write up what you plan to do this weekend then...
11:10 egonw will be back in a short hour or so
11:10 nielsout oki
11:56 * egonw is back
11:56 nielsout welcome back :)
13:50 egonw nielsout: so, what are your plans regarding finishing things up?
14:25 egonw doing some shoppinh
14:41 egonw nielsout: around?
14:58 nielsout hey, i'm here now, dont'got the full plan yet.. had to do stupid stuff in the garden :/
15:00 nielsout if i'm ever getting a house with a garden i'll just put only grass on it :x
15:06 egonw no grass... too much work
15:06 egonw you have to mow(?) that once a week
15:09 egonw nielsout: please tell what your plans are for next week...
15:09 egonw so that I can decide how I can help when I have a bit of time...
15:09 egonw don't want to interfere with what you are doing...
15:20 nielsout ok
15:24 nielsout well I think the next nice thing to do is to show tooltips
15:24 nielsout or to make it possible to move objects
15:27 egonw yes, moving atoms is an important feature
15:27 egonw tooltips is more difficult..
15:28 egonw as that works differently for SWT and Swing again...
15:28 egonw but then again...
15:28 egonw making an API for that would fit perfectly in your project
15:28 nielsout aye
15:32 nielsout hm settings such as highlightRadius are in screensize now, what would be the 'cleanest' way to make them based on chem-model size?
15:32 egonw rojasm: btw, if you want to do some more CDK work... you still have a number of bugs open
15:33 nielsout just changing it is bad as old cold will kinda fail then.. but creating a new variable name seems such an overhead
15:33 egonw that radius should be in model based indeed
15:33 egonw true
15:33 egonw ummm
15:33 egonw ok, refactor the old method name into:
15:34 egonw highlightScreenRadius
15:34 egonw and make that method deprecated
15:34 egonw ummm...
15:34 egonw no
15:34 egonw make highlightRadius() deprecated
15:35 egonw and make a new method highlightRadiusModel()
15:35 egonw that replaces the first
15:35 nielsout ack
15:35 egonw ah... no, that's not ideal either...
15:36 egonw ok, do the latter...
15:36 egonw and add a remark that the meaning of that method will change
15:36 nielsout so just add a variable and methods for the model-based? and make all old deprecated?
15:36 egonw with respect to the radius system
15:36 egonw yes
15:45 nielsout Unable to reverse affine transformation
15:45 nielsout hmz.. wonder what went wrong there
15:46 nielsout works fine at next try, odd
15:48 CIA-31 cdk: egonw * r8895 /trunk/cdk/src/org/openscience/cd​k/config/data/cdk_atomtypes.xml: Fixed element type for O.sp2.
15:59 egonw dinner time...
15:59 egonw will be back later
15:59 nielsout oki
16:19 carsten joined #cdk
16:23 * nielsout goes to dinner aswell
17:16 * nielsout is back
17:24 rojasm /time
17:30 nielsout egonw stop eating.. you'll grow too fat ;)
17:33 nielsout I got some code to move an atom around now.. but how to I get it to update the screen? (moving works now if you move something, and then make the window larger so it'll repaint it :P)
17:33 nielsout I guess firechange() does that job normally?
17:54 * egonw is back
17:55 egonw nielsout: repaint() I think
18:02 nielsout hm that's quite possible yeh.,. but euhhm I don't see atm at what place to call it
18:03 egonw the controller has access to the renderer, not?
18:03 nielsout hm think it has yeh
18:03 egonw ummm...
18:03 nielsout gawn stupid eclipse not responding atm :|
18:03 egonw but the Frame needs to make the repaint call...
18:04 nielsout yeah, it's not the renderer who knows 'where' to repaint
18:04 egonw the old JCP used a listener approach for that...
18:05 egonw what about making the Frame that calls the paintMol() a ModelUpdatedListener...
18:05 egonw or something like that...
18:06 nielsout seems like a fix
18:06 egonw mom
18:09 egonw use the interface ChangeListener
18:10 egonw and have the Controller2D use that interface to have the 'view' do a repaint...
18:10 egonw but note that this would have to go via the new interface again... that is, via:
18:11 egonw SwingMouseEventRelay
18:11 egonw but actually not that one...
18:11 egonw but a new Relay
18:11 egonw or not...
18:11 egonw ummm...
18:11 egonw mom
18:12 nielsout heh
18:12 nielsout seems like it's messed up already ;)
18:19 egonw mmm...
18:19 nielsout I gtg asap btw, birthday party from a friend
18:19 egonw so, the Controller2DHub constructor needs an additional parameter
18:20 nielsout i'll do a commit from what I got now
18:20 egonw a CDKChangeListener
18:20 egonw ack
18:20 CIA-31 cdk: nielsout * r8896 /trunk/cdk/src/org/openscience/cdk/ (4 files in 3 dirs):
18:20 CIA-31 cdk: attempt to move atoms around
18:20 CIA-31 cdk: to be added: repainting after moving
18:22 egonw nielsout: OK, I will do something for that interface...
18:22 nielsout ok that would be cool, else I can have a look tommorrow
18:25 rojasm egonw I am trying to make a look into cdk.bugs but the pages is not working for me
18:25 rojasm could you confirm that also
18:25 egonw URL?
18:28 rojasm_ joined #cdk
18:28 rojasm_ http://sourceforge.net/mailarchi​ve/forum.php?forum_name=cdk-bugs
18:28 nielsout Your mailing list, cdk-bugs, appears to be either not archived yet, or has had no e-mails sent to it. If it is a new list, please wait 2-4 hours after the first message is sent for the archive to show up.
18:29 rojasm_ ach so
18:29 rojasm_ I do it
18:29 rojasm_ left #cdk
18:29 egonw do what??
18:29 egonw that list is supposed to be *not* archived...
18:29 egonw because that's the BTS...
18:32 rojasm But you remenber some bug werewith you think I could try
18:33 nielsout <- gone
18:33 egonw nielsout: ack, cu tomorrow
18:33 egonw rojasm: why not use the BTS?
18:33 egonw http://sourceforge.net/tracker/​?group_id=20024&amp;atid=120024
18:35 rojasm my firefox explot explodes wenn I try to open this page :(
18:35 egonw mmm... sounds like time for a different browser :)
18:36 rojasm what then
18:36 rojasm you don't use firefox
18:36 egonw I do
18:36 CIA-31 cdk: egonw * r8897 /trunk/cdk/src/org/openscience/cdk/ (4 files in 3 dirs): Added atom types for charged oxygens
18:37 rojasm now I can see it
18:37 rojasm oh a lot of ....
18:37 rojasm to do
18:38 egonw 4 bug reports...
18:38 egonw not that many :)
18:38 rojasm :)
18:39 rojasm I now
18:39 rojasm oder question! what about the molecularformula class
18:40 egonw what about it?
18:42 rojasm If it makes sense to create one class
18:42 rojasm with all functionalities like smiles!!
18:42 egonw like SMILES?
18:42 egonw why like SMILES?
18:42 egonw that implies connectivity
18:43 rojasm ah ok
18:43 rojasm but a molecularformula must have a validation with conectivity as well
18:44 rojasm if you put C2H11
18:44 rojasm you can not create a connectivity
18:44 egonw no, let's not mix data container with algorithms
18:44 rojasm ok
18:48 rojasm so what you suggest a class into cdk.MolecularFormula and other class in cdk.tools.MolecularFormulachecker
18:49 egonw ask on list
18:49 egonw not sure
18:50 rojasm ok
18:56 CIA-31 jmol: hansonr * r8221 /trunk/Jmol/ (9 files in 5 dirs): (log message trimmed)
18:56 CIA-31 jmol: version=11.3.17
18:56 CIA-31 jmol: # bug fix: problem with unescaping comma-separated point strings "{1,2,3}" as a point.
18:56 CIA-31 jmol: # bug fix: drawn arrows scale improperly when zooming; arrow heads off-kilter
18:56 CIA-31 jmol: # new feature: set defaultDrawArrowScale # 0.5 initially
18:56 CIA-31 jmol: # Drawn arrows now have a head size that can be set and a dimension that
18:56 CIA-31 jmol: # scales with the model, so arrow head:atom size ratio remains constant
19:09 CIA-31 cdk: egonw * r8898 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added atom types for charged nitrogens
19:21 CIA-31 cdk: egonw * r8899 /trunk/cdk/src/org/openscience/cdk/test/atomt​ype/CDKAtomTypeMatcherTestFileReposTest.java: Removed some invalid chemistry files, which exist for other kinds of tests
19:44 CIA-31 jmol: hansonr * r8222 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): 11.3.17 if still available -- minor math addition aPlane.distance("some atoms")
19:57 neksa joined #cdk
22:26 LaserJock joined #cdk
23:50 CIA-31 jmol: hansonr * r8223 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java Jmol.properties Token.java):
23:50 CIA-31 jmol: 11.3.17 extends Jmol math capabilities by allowing nested functions
23:50 CIA-31 jmol:  x = distance(point(3,4,5),point(0,2,1))

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