Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-24

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All times shown according to UTC.

Time Nick Message
06:17 jbrefort joined #cdk
07:47 egonw joined #cdk
08:01 egonw_ joined #cdk
09:13 jonalv joined #cdk
09:45 Julio joined #cdk
09:47 Julio hi guys
09:47 Julio I have a question about the structure generator in CDK
09:49 egonw just ask.. no need to announce you have a question
09:49 Julio I saw there are some functions named like "structure generator"
09:49 egonw cdk used to have two structure generators
09:49 Julio I was wondering if they are up to date and working or they are just an attempt
09:49 egonw now only one
09:50 egonw they were both working
09:50 egonw but not well tested
09:50 egonw and one had just a bit too many bugs for its purpose and was pulled again
09:50 Julio is anybody working on them now?
09:51 egonw I think Christoph Steinbeck's group is...
09:51 egonw talk to shk3 or gilleain when they show up
09:52 Julio ok thks
09:53 Julio and another question
09:53 Julio is there any tool to visualize structures in CDK
09:53 Julio like a viewer
09:53 Julio ?
09:53 Julio jchempaint?
09:53 egonw right
09:54 Julio I haven't explained why I want to know this...
09:54 Julio I'm working with Miguel Rojas
09:54 egonw yes, please do
09:55 Julio let's say my project is about generating structures from an elemental composition
09:55 Julio we work with metabolites in the Netherlands Metabolomics Center (NMC)
09:55 egonw PhD or postdoc?
09:55 Julio PhD
09:55 Julio just started
09:55 CIA-37 cdk: goglepox * r13235 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/HighlightGenerator.java:
09:55 CIA-37 cdk: Implemented IGenerator and centers the elements on
09:55 CIA-37 cdk: 0
09:55 egonw how is your mathematics background?
09:56 CIA-37 cdk: goglepox * r13236 /cdk/branches/jchempaint-primary/s​rc/main/org/openscience/cdk/contro​ller/Controller2DModuleMove.java:
09:56 CIA-37 cdk: Chaged println to use LoggingTool and only log when
09:56 CIA-37 cdk: chemObjectRealy is null.
09:56 Julio Im not a matematician
09:56 Julio just a bioinformatician
09:56 CIA-37 cdk: goglepox * r13237 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/IRenderer.java: Interface common to renderes
09:57 CIA-37 cdk: goglepox * r13238 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java: Some changes to the transform
09:57 jpansanel moin
09:57 zarah hi jpansanel
09:59 Julio CIA-37: thx
10:00 Julio eventually I won't make silly questions and even I would contribute with something useful
10:01 CIA-37 cdk: goglepox * r13239 /cdk/branches/jchempaint-primary/src/main/org/ope​nscience/cdk/renderer/IntermediateRenderer.java: Updated to use IGenerator interface
10:09 egonw Julio: CIA-37 is a bot that posts changes made to the source code repository
10:09 egonw is a logging bot
10:09 egonw but don't remeber where it actually puts the logs
10:09 egonw zarah is a bot too...
10:10 egonw all others are human
10:11 jonalv zarah: you are the smart one
10:11 zarah jonalv: no, YOU are the smart one!
10:12 jonalv zarah: seen Julio?
10:12 zarah Julio was last seen 12 m 3 s ago in #cdk saying 'eventually I won't make silly questions and even I would contribute with something useful'
10:12 jonalv Julio++
10:12 Julio ahahhahahaa
10:12 jonalv zarah: karma Julio
10:12 zarah Julio has a karma of 1
10:12 Julio ok ok
10:12 jonalv Julio++
10:12 jonalv zarah: karma Julio
10:12 zarah Julio has a karma of 2
10:13 Julio Julio the Rookie
10:13 jonalv zarah: help
10:13 zarah jonalv: avaliable commands are botsnack clear-messages google help hi karma messages pelezilla ping plan replan restart seen slap start stop tell thanks unplan
10:15 shk3 joined #cdk
10:16 CIA-37 cdk: shk3 * r13240 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (7 files in 4 dirs): closing of windows and saving works
10:16 Julio hi shk3
10:25 CIA-37 cdk: egonw * r13241 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (2 files in 2 dirs): Added missing module assignments
10:50 gilleain joined #cdk
10:53 Julio bye and thx guys
10:53 Julio left #cdk
11:08 CIA-37 cdk: gilleain * r13242 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (4 files in 2 dirs): Copyright statements.
11:22 CIA-37 cdk: gilleain * r13243 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (4 files in 2 dirs): Fixing copyright statements.
12:24 CIA-37 cdk: shk3 * r13245 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (7 files in 4 dirs): proper handling of button actions (further renderer modules need to be added in the JCPActionChangeMode and the JChemPaintResources.properties)
13:20 CIA-37 blueobelisk: pansanel * r256 /structures/trunk/tools/ (8 files): Updating the make file tools
13:21 CIA-37 blueobelisk: pansanel * r257 /structures/trunk/src/acid_​anhydrides/CMakeLists.txt: Update CMakeLists.txt to enable out-of-source build
13:25 CIA-37 blueobelisk: pansanel * r258 /structures/trunk/src/CMakeLists.txt: Enable out-of-source builds
13:29 CIA-37 blueobelisk: pansanel * r259 /structures/trunk/ (CMakeLists.txt TODO):
13:29 CIA-37 blueobelisk: Enable out-of-path builds
13:29 CIA-37 blueobelisk: Updating TODO
13:36 CIA-37 cdk: shk3 * r13246 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (JCPToolBar.java action/JCPActionChangeMode.java): cleaned up things a bit
13:37 CIA-37 cdk: gilleain * r13247 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (9 files in 3 dirs): Reverted to the translate-to-origin, scale, translate-to-drawing-centre way of doing things.
13:46 carsten joined #cdk
13:51 CIA-37 blueobelisk: pansanel * r260 /structures/trunk/src/ (32 files in 32 dirs): Enabling out-of-path builds
14:06 CIA-37 cdk: shk3 * r13248 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (3 files in 3 dirs): correct usage of enterelement/element draw mode
14:18 CIA-37 cdk: gilleain * r13249 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (Controller2DHub.java Controller2DModuleAddBond.java): Made an AddBond Module.
14:18 egonw joined #cdk
14:26 CIA-37 cdk: shk3 * r13250 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (2 files in 2 dirs): added all draw mode selections to buttons
14:50 CIA-37 cdk: gilleain * r13251 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (3 files): Changed the AddBondModule to use IChemModelRelay.addAtom(String, IAtom)...
14:59 shk3 how should the copyright notice in jcp read?
14:59 shk3 jchempaint project?
14:59 shk3 cdk project?
14:59 CIA-37 cdk: egonw * r13252 /cdk/branches/jchempaint-primary/sr​c/main/org/openscience/cdk/controll​er/Controller2DModuleAddBond.java: Add missing cdk module info
15:00 egonw shk3: depends...
15:01 shk3 on what?
15:01 egonw who wrote it
15:01 shk3 hm?
15:01 egonw the copyright cannot be CDK or JCP project
15:01 egonw no legal entity
15:01 egonw you remember that discussion?
15:01 shk3 I do
15:01 shk3 but cdk still says cdk project
15:01 egonw so, the copyright should list the people who contributed code to that source file
15:01 shk3 afaik
15:01 egonw yeah...
15:02 egonw only those which 'we' have not fixed yet
15:02 gilleain so, egonw, you added the line "@cdk.module control"..
15:02 egonw right
15:02 egonw because that's where it belongs
15:03 egonw if you do not put a line in like that... then it'll end up in the module 'extra'
15:03 egonw and the 'control' module may not depend on extra
15:04 shk3 it looks like the $X $ annotations do not get updated.
15:04 shk3 can that be true?
15:04 egonw yes
15:04 egonw because the proper svn:bla property has not been set
15:04 egonw check this script:
15:05 egonw cdk/tools/checkSVNKeywords.pl
15:07 shk3 hm, this is per module
15:07 shk3 jcp isn't a module...
15:07 egonw true :)
15:07 egonw well, I'm sure you can work out what it does
15:07 egonw and apply it file by file for the JCP source code
15:08 shk3 should we still have the @author in files
15:09 shk3 if we have an author list in copyright?
15:09 Gpox joined #cdk
15:15 egonw shk3: no need, I guess
15:16 egonw however, the stuff in the copyright/license header does not show up in the JavaDoc
15:16 gilleain I hope this is okay...
15:16 CIA-37 cdk: gilleain * r13253 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (15 files):
15:16 CIA-37 cdk: - Made ControllerModules names better.
15:16 CIA-37 cdk: - Added a DrawRing Module.
15:16 egonw gilleain: as in?
15:16 gilleain I changed Controller2DModuleDoX to DoCModule
15:17 gilleain er, DoXModule, that is.
15:17 egonw sounds fine :)
15:17 gilleain it was impossible to read through a list of them otherwise
15:17 egonw sounds like a perfect reason to rename
15:17 egonw thanx for doing that...
15:17 egonw people seem to forget to make such trivial but rather useful commits
15:18 egonw because the end up as TODOs that never get done
15:18 CIA-37 cdk: shk3 * r13254 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (23 files in 5 dirs): added headers everywhere, removed module etc. Note I added myself as author, everybody contributing should add his/her (any female jcp developers, btw?) name.
15:19 gilleain Ah. What if I am adding a ring to an empty canvas.
15:19 egonw shk3 is looking for a date?
15:19 egonw gilleain: one atom at 0,0?
15:19 shk3 whom would you suggest?
15:19 gilleain no, I mean that (your?) addring method assumes that you pass in an atom.
15:19 egonw hotchick@ebi.ac.uk
15:20 gilleain I hoped that passing in a null atom (I'm not cliking on that link, btw) would work, but it didn't.
15:20 egonw ah... yes, add ring to empty canvas
15:20 egonw add an atom
15:20 egonw then add a ring to that atom
15:20 egonw the dirty work around
15:21 egonw please file a bug report to request addRing(Point2d)
15:21 gilleain hmm. that would work, yes. I'll do that.
15:21 gilleain and that.
15:21 egonw tack
15:21 gilleain tack fernade.
15:21 gilleain (or however it is spelled).
15:25 gilleain hmmmm. ..o0(void addFragment(String smiles, Point2d coord))
15:26 egonw yeah, interesting one...
15:26 egonw and the IAtom variant
15:30 egonw gilleain: http://friendfeed.com/e/801c6135-8​318-764e-f351-1dc666a0af5a/chalky/
15:31 zarah egonw's link is also http://tinyurl.com/6cl8ft
15:32 gilleain :)
15:34 Gpox gilleain: check your ide settings please, you reformated Renderer with tabs
15:35 gilleain oops. dammit eclipse, I told you to set that for all projects!
15:35 gilleain (a bad workman blames his tools, I suppose).
15:48 egonw gilleain: nah... a bad workman just leaves it at that
15:48 gilleain hmm. probably.
15:48 gilleain this hack to addRing isn't working so well.
15:48 egonw no, that does not suprise me:
15:48 egonw @pz 143
15:48 zarah http://tinyurl.com/55t8ok
15:49 egonw huh, not bug title??
15:49 egonw and I even had the wrong number ... hahaha
15:49 egonw @pz 139
15:49 zarah http://tinyurl.com/54rkap
15:50 egonw @pz added first atom
15:50 zarah [Bug 139] Exception upon added a firs... http://tinyurl.com/54rkap
15:50 zarah Entire list at http://tinyurl.com/5q9658
15:50 egonw that's better :)
15:50 egonw so, it seems to apply to Swing too...
15:50 egonw which would mean it is not a SWT problem at all...
16:12 jbrefort joined #cdk
16:28 gilleain umm assertTrue(chemModel.getBuilde​r().newRing(6).getAtomCount() == 6)?
16:29 egonw try:
16:29 egonw assertEquals(6, chemModel.getBuilder().newRing(6).getAtomCount())
16:29 egonw btw, who wrote that test?!?!
16:29 egonw or is it a CDK unit test?
16:30 gilleain No, it was me asking a question in the form of a unit test :)
16:31 gilleain or pseudo-unit test, clearly.
16:31 gilleain it seems not to be true, is what I am saying.
16:33 gilleain hmmm. it's by design, I suppose.
16:33 gilleain AtomContainer(int atomNumber, int bondNumber...) makes an empty container. oh well.
16:34 egonw ah, in that way
16:34 egonw yes, you're right...
16:34 egonw you;r using the builder
16:34 egonw that constructor indeed only presets the array lengths
16:35 gilleain I think I should use the newRing(int, String) method
16:35 gilleain it does make sense that it won't make you atoms of an unspecified type...
16:36 egonw right
16:37 egonw btw, Pierre left an URL to a PDF with sketching lines...
16:37 egonw in reply to chalky
16:37 egonw which adds random noise to straight lines
16:38 gilleain oh yes? interesting.
16:39 gilleain got empty canvas ring-add working.
16:40 gilleain but only by adding a method to RingPlacer
16:40 gilleain is that ok?
16:40 egonw email me the patch, please
16:41 gilleain Owww. the noise for promoting to operator in Colloquy is some sort of record scratch.
16:42 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit CDK 1.2.x: 7760, 80 fails + 17 errors (1.12%) | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores: http://www.cdknews.org/ | CDK News Feed: http://beta.friendfeed.com/ro​oms/chemistry-development-kit
16:43 gilleain hmm. okay.
16:57 CIA-37 cdk: egonw * r13255 /cdk/branches/cdk-1.2.x/build.props: Bumped version
16:58 CIA-37 cdk: egonw * r13256 /cdk/tags/cdk-1.1.2/: Released CDK 1.1.2
17:00 gilleain soo, egonw: is that patch okay? it's a single method, so it could be removed as easily as it was added...
17:01 egonw yes it si
17:01 egonw didn't I mention that in my reply?
17:01 gilleain oh, right sorry.
17:02 gilleain my desktop is responsible for cheking my gmail,  but it's asleep.
17:02 egonw :)
17:02 gilleain it's a bit expensive to have a whole desktop machine just to ping google every 5 mins. hmmm.
17:02 egonw hehehehe
17:03 egonw true... you should have it check every 500 ms
17:03 gilleain oh, and I can't use ArrayList (which I would normally) as the AtomPlacer's method consumes a Vector.
17:03 egonw ok, file a bug report please
17:03 egonw against CDK 1.2.x branch please
17:04 egonw btw, will be offline tomorrow
17:04 gilleain ok.
17:04 egonw just to warn you
17:04 gilleain for a birthday party?
17:04 egonw Gpox: that might affect you too... I won't be at UU tomorrow
17:04 egonw gilleain: right
17:11 CIA-37 cdk: gilleain * r13257 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (4 files in 3 dirs):
17:11 CIA-37 cdk: - Ring adding capability.
17:11 CIA-37 cdk: - Refomated Renderer back to no-tabs.
17:40 CIA-37 cdk: gilleain * r13258 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (5 files):
17:40 CIA-37 cdk: - Cleanup (removed unused import statements).
17:40 CIA-37 cdk: - Removed 'Cleanup' from the list of modes, as it is not a mode.
17:45 jbrefort joined #cdk
17:50 Gpox joined #cdk
17:55 CIA-37 cdk: gilleain * r13259 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (RenderPanel.java application/JChemPaint.java): RenderPanel uses getVisibleRectangle instead of getBounds
17:57 timvdm joined #cdk
18:13 CIA-37 cdk: shk3 * r13260 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (JChemPaintPanel.java action/SaveAsAction.java): added the changed/unchanged status stuff. due to chemobjectlistener, a file is always considered to be changed. we need a solution for this...
18:23 CIA-37 cdk: shk3 * r13261 /jchempaint/trunk/src/main/org/openscience/jchem​paint/resources/JChemPaintResources.properties: typo prevented use of bond down
19:41 CIA-37 cdk: gilleain * r13262 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (4 files in 2 dirs):
19:41 CIA-37 cdk: - Bonds now cycle order (upwards).
19:41 CIA-37 cdk: - Refactored the HighlightModule to make the code clearer, but may have broken it.
19:41 CIA-37 cdk: - IntermediateRenderer draws bonds other than singles.
21:22 edrin joined #cdk
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