Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-18

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All times shown according to UTC.

Time Nick Message
07:30 Gpox joined #bioclipse
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08:38 olass hi
08:38 * olass is in sthlm today
08:45 masak hi olass
08:45 olass hi
08:45 olass read about git yesterday on the plane
08:45 olass seems convenient
08:46 masak aye.
08:46 olass you like?
08:46 masak do I like git?
08:46 masak yes.
08:46 olass bettr than svn?
08:46 masak yes, better than svn.
08:46 olass all in all I mena
08:46 masak aye.
08:46 olass mena mean
08:46 masak it's easier to work with git.
08:47 olass ok
08:47 masak IMHO.
08:47 olass well, I don't think I need to ask egonw, or? :-)
08:47 olass I read the 2 articles you gave me. Good reading
08:48 olass I liked "git from the bottom up" most
08:48 masak me too.
08:48 masak did you follow along in the shell while reading it?
08:48 olass no
08:48 masak I did that on the second reading.
08:49 olass read when plane took off
08:49 olass I thought I was gonna be in Uppsla today, but my car has died :-(
08:49 olass really died
08:49 olass it's a wreck
08:49 olass canot be brought back to life
08:49 olass so I need to tow it and wreck it :-(
08:50 masak I heard, meklund told me.
08:51 masak I thought he took care of that.
08:51 olass well, he made it so that the car could be parked until friday
08:51 olass before that I need to get it to the bilskrot
08:52 olass really sad
08:52 olass we just repaired it 2 weeks ago for 5000:-
08:52 * olass wonders if this is the and of his golf career
08:54 masak you had a golf career?
08:54 olass :-)
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09:23 edrin hi
09:25 masak hi edrin
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10:13 jonalv oh hai
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11:23 CIA-55 bioclipse: shk3 * r8900 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/wizards/ (NewSDFileWizardPage.java NewSdfWizard.java):
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11:51 CIA-55 bioclipse: shk3 * r8901 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/handlers/Create3dHandler.java: fixes bug #468
11:52 zarah bug #468 |
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12:23 olass edrin: around?
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12:39 maclean huh. busy today.
12:41 olass maclean: tell me about it
12:41 maclean :)
12:41 olass these weeks have been exhausting
12:41 maclean :(
12:41 olass and a few more until we get BC2 out will probably be the same
12:42 maclean probably.
12:42 olass but really good progress!
12:42 olass maclean++ //doing a good job with JCP
12:42 maclean I am working on the rendering problem - I am nearly there.
12:42 maclean tack
12:42 olass :-)
12:46 olass need to drop my car off at its final port
12:46 olass from where he is going, no car returns
12:46 olass well, maybe as a 1x1 m cube
12:47 maclean coffee table?
12:47 olass good idea
12:47 olass right, se you later
12:47 maclean bye
12:47 olass hmm, do you say "wreck the car"?
12:47 olass salvage?
12:47 maclean As a command, yes
12:48 maclean "You there - wreck the car!"
12:48 olass I am going to .... my car
12:48 maclean salvage, yes
12:48 olass right
12:48 maclean retrieve, recover, fetch...
12:48 olass right, ttl
12:55 maclean oh ffs. that was trivially easy.
12:55 * maclean facepalms
13:00 masak ...and Urban Dictionary delivers, once again!
13:00 maclean :)
13:01 maclean there is, as yet, no textual-graphical depiction
13:01 maclean (comparable to \o/)
13:02 masak no, it's not easy to draw.
13:03 masak *smack* o>
13:03 maclean hmmm
13:03 masak \o>
13:03 maclean that's quite good, actually.
13:03 masak let's try it on for a while before deciding.
13:04 masak it's a big decision.
13:04 maclean :)
13:06 maclean Gpox : I am intending to make a commit that (partially) solves the problem of bug 494
13:06 maclean @pele 494
13:06 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=494
13:07 maclean the thing is : it requires the editor to be set as fitToScreen = false
13:07 maclean (for now)
13:07 maclean I do intend to make this better, however .. what do you think?
13:08 Gpox mhn, it dont use that command any longer, it uses 'Add Bond' the same as the JCP application, but there needs to be a way to bridge two unconnected atoms
13:08 maclean ah - yes, I agree with that, but we are talking about different bugs
13:10 Gpox i dont think the scale should change beyond a initial fit to screen
13:10 maclean the add bond needs to be a hybrid of your approach and mine - so that clicking sprouts a bond, and click-dragging creates and holds so that you can extend
13:11 maclean no, you can't do that in general.
13:11 maclean if you scale ethane to fit, then you have no room to add
13:11 maclean you can't edit with fit-to-screen
13:11 Gpox and it should probably snap to multiples of bondlengths / bond angles
13:12 maclean yes, snapping to angle/length are definitely needed
13:12 Gpox what i mean is, when it knows the initial screen size it set the scale to fit
13:12 maclean well, that's kind of the fix I am applying.
13:13 Gpox or rather the zoom maybe
13:13 maclean the first time you draw, it calculates the scale needed to fit to the desired bond length
13:13 maclean then, subsequently, the scale is not re-calculated (unless you do a cleanup)
13:14 maclean as with cleanup, the scale can change
13:14 Gpox why fit to bond length? isn't it the view size you want
13:15 maclean well, this is what the original jcp did. the user sets the bond length, and then the scale is calculated so that the bonds on screen are that length
13:16 maclean the difficulty here is that the editor widget does not yet have scrollbars, so editing can go off-screen
13:17 maclean http://gilleain.tumblr.com/post/75919533
13:17 zarah maclean's link is also http://tinyurl.com/arrquk
13:17 maclean also :
13:17 maclean http://gilleain.tumblr.com/post/75919771
13:17 zarah maclean's link is also http://tinyurl.com/brb3ow
13:17 Gpox so a method that calculate what bond length from view width/height
13:18 maclean no - that's fit to screen. bond length is user-settable. it's a bit like resetting what '100% zoom' means
13:18 CIA-55 bioclipse: shk3 * r8902 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui/src/net/bioclipse/cdk/ui/handlers/ (Create2dHandler.java Create3dHandler.java): fixes bug #469
13:18 zarah bug #469 | http://tinyurl.com/bwgkja
13:19 maclean so, if you set bond length to 50, then at zoom = 1 (100%), the 'standard' bond length will be 50 on screen
13:19 maclean no matter what length the bonds in your model are
13:20 Gpox so fit to screen only chages the zoom?
13:20 maclean yes
13:21 Gpox ah, i was thinking the fit to screen changed the scale so it was at 100%
13:21 maclean if your diagram on screen would be 300 (pixels?), but your screen is 600 pixels wide/high, then fitToScreen would make the zoom 200% (*= 2.0)
13:22 Gpox fit to view
13:22 maclean yes! that's a much better name.
13:22 maclean hmm
13:23 maclean well, anyway. I'm getting there.
13:25 maclean right, well, I need to commit this for people to test it. the only change to the widget will be one line in the constructor, so it can be trivially reverted.
13:26 CIA-55 bioclipse: gilleain * r8903 /bioclipse2/trunk/ (2 files in 2 dirs): Combined change to renderer and editor widget. Scaling is done the first time that the model is painted. fitToScreen is false for the editor.
13:26 Gpox it is not good to requier the user to know how long a bond should be on the screen to get a decent zoom. Stil the zoom only make sens in the view so haveing crazy like 1000% to fit in view...
13:29 maclean I see your point.
13:30 maclean Christoph said "most chemical editors have the option to set the bond length"
13:30 maclean perhaps I implemented it wrong, though
13:30 Gpox it would be easy to implement now once i know how it works, only need to set fit to false and calculate a good bond lenght to get it to work
13:32 maclean but I don't think that you calculate the bond length on screen to fit the view
13:32 maclean to be honest, I don't see why anyone would want to set the bond length
13:33 Gpox I dont think many users care about how many pixels something is. But setting bond units to 1.4... angstrom or something but that might be the underlying io code
13:33 maclean ah that's the model bond length, and quite a different story, I think.
13:34 maclean and, yes, that has been discussed for the io code
13:35 Gpox but the user should still be able to decide it
13:36 maclean what, decide the model bond length - well, sure that seems reasonable.
13:37 maclean but I have to remind myself that chemical diagrams are not the same as 3D models, where the bond length has a meaning (C-C bonds are a different length to C=O bonds)
13:38 maclean they are more symbolic than representational
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16:20 maclean ola: bug 525 (oval shape in compact mode) - already fixed?
16:20 maclean sorry, I meant olass
16:20 olass yes
16:20 olass closed it too
16:20 olass looks good
16:20 olass just didnät understand the API
16:20 maclean ahh
16:21 olass there was no setAtomShape(...)
16:21 maclean I thought you meant exposing it in the preferences
16:21 olass nope
16:22 maclean what would be great of course, would be some kind of idea of a 'profile' or set of preferences that could be saved
16:22 maclean like a stylesheet
16:22 maclean (apparently ACD has chemical stylesheets)
16:22 maclean and rajarshi mentioned this
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16:49 olass maclean: if you want to take bug #523, please assign it to yourself
16:49 olass or maybe I misunderstood your comment?
16:49 maclean oh, no, whoops I thought I had
16:49 maclean will do
17:22 CIA-55 bioclipse: gilleain * r8904 /bioclipse2/trunk/cdk-externals/trunk/org.opensci​ence.cdk.render/src/org/openscience/cdk/renderer/ (RendererModel.java RenderingParameters.java):
17:22 CIA-55 bioclipse: - Highlight filled parameter added.
17:22 CIA-55 bioclipse: - Highlight distance model removed.
17:26 CIA-55 bioclipse: gilleain * r8905 /bioclipse2/trunk/ (5 files in 3 dirs):
17:26 CIA-55 bioclipse: - Split up highlight element generation into bond and atom classes.
17:26 CIA-55 bioclipse: - No longer highlights invisible hydrogens.
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19:59 CIA-55 bioclipse: gilleain * r8906 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Fill the highlight circle.
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