Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-27

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All times shown according to UTC.

Time Nick Message
04:10 Conrad joined #cdk
06:13 CIA-16 cdk: miguelrojasch * r13323 /cdk/branches/cdk-1.2.x/src/ (2 files in 2 dirs): Even charge are count as neutral molecule for Nitrogen Rule
06:14 slyrus_ joined #cdk
06:15 slyrus_ wow. didn't really expect there to be a #cdk here :)
06:15 slyrus_ is cdk a successor to jumbo?
06:51 CIA-16 cdk: egonw * r13324 /cdk/branches/jchempaint-primary/src/main/org/​openscience/cdk/controller/ControllerHub.java: Saver to not add what you do not want added, instead of removing it afterwards
06:52 CIA-16 cdk: egonw * r13325 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (AddRingModule.java ControllerHub.java IChemModelRelay.java): Fixed bad API I introduced earlier: removed the isBenzene param completely.
07:43 egonw joined #cdk
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08:49 Gpox joined #cdk
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09:20 CIA-16 cdk: goglepox * r13326 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (Renderer2DModel.java generators/BasicAtomGenerator.java):
09:20 CIA-16 cdk: Added null checks for atoms passed in,
09:20 CIA-16 cdk: for Renderer2DModel.getAtomColor(...) and
09:20 CIA-16 cdk: BasicAtomGenerator generate(IAtomContainer,IAtom)
09:21 CIA-16 cdk: goglepox * r13327 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/BasicBondGenerator.java: Update to line generation
09:21 CIA-16 cdk: goglepox * r13328 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/BasicBondGenerator.java:
09:21 CIA-16 cdk: Updated line generation
09:21 CIA-16 cdk: Added function for generate lines with vecmath and
09:21 CIA-16 cdk: switch coorinates
09:21 CIA-16 cdk: goglepox * r13329 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (Renderer2DModel.java generators/BasicBondGenerator.java): Changed bondDistatns to world coordinates
09:27 CIA-16 cdk: egonw * r13330 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (ControllerHub.java IChemModelRelay.java): Enabled and implemented addRing(IBond, int)
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10:44 CIA-16 cdk: shk3 * r13331 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (6 files in 4 dirs): added the exit action
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11:04 CIA-16 cdk: egonw * r13332 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (ControllerHub.java IChemModelRelay.java): Fixed adding rings to bonds: the sharedAtoms container must include the bond too
11:05 egonw r13332... you want that patch
11:06 gilleain ack. now ControllerHub doesn't implement addPhenyl(IBond)
11:08 Julio joined #cdk
11:09 egonw gilleain: no, not yet
11:09 egonw working on that now
11:09 gilleain ok
11:09 Julio left #cdk
11:11 egonw gilleain: sorry, that IChemModelRelay change sneaked in...
11:11 gilleain oops, sorry. I maligned the addPhenyl(IBond, int) method. It was working.
11:11 egonw that was not supposed to be commited yet...
11:11 egonw huh?
11:11 egonw addRing(IBond, int) you mean?
11:12 gilleain I think that the case of (closestAtom == null && closestBond != null) never happens
11:12 gilleain yes, I mean;t addRing(IBond, int), sorry.
11:12 egonw ah, ok
11:12 egonw well, you needed that fix anyway
11:12 egonw but it seems your problem was different :0
11:13 egonw s/:0/:)/
11:14 gilleain that's a weird smiley.
11:14 gilleain :-}
11:15 jonalv >(
11:15 jonalv :)
11:17 CIA-16 cdk: gilleain * r13333 /cdk/branches/jchempaint-primary/src/main/org/​openscience/cdk/controller/AddRingModule.java: Adding rings to bonds now works.
11:18 gilleain *_|_*
11:18 gilleain (saw this today, meant to be a cat)
11:18 egonw gilleain: please file bug reports for other missing functionality in the IChemModelRelay
11:18 gilleain okay
11:19 gilleain -_-
11:20 CIA-16 cdk: egonw * r13334 /cdk/branches/jchempaint-primary/src/main/org/o​penscience/cdk/controller/IChemModelRelay.java: Removed premature commit: incomplete patch accidentally commited
11:26 CIA-16 cdk: shk3 * r13335 /cdk/branches/jchempaint-pr​imary/META-INF/MANIFEST.MF: exported the inchi package
11:38 CIA-16 cdk: shk3 * r13336 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (4 files in 3 dirs): added input as text
11:50 CIA-16 cdk: egonw * r13337 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (ControllerHub.java IChemModelRelay.java): Implemented addPhenyl(IBond)
12:12 CIA-16 cdk: shk3 * r13338 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (7 files in 3 dirs): added showtoolbar/statusbar/menu
12:59 gilleain joined #cdk
13:33 CIA-16 cdk: gilleain * r13339 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (5 files in 4 dirs): Exporting images now works.
13:38 egonw gilleain: what about SVG?
13:39 gilleain um, well.
13:40 gilleain do we want to use batik, or should I make a simple visiting svg generator.
13:40 gilleain ?
13:40 gilleain hmmm.
13:40 egonw I'd go for batik
13:41 egonw should work well, as it now properly uses Graphics2D
13:41 gilleain I know.
13:45 shk3 question: the save as has a svg option. But that's nonsense, should be in export, right?
13:46 CIA-16 cdk: shk3 * r13340 /jchempaint/trunk/ (8 files in 6 dirs): added the renderer options dialog - can't test right now, since renderer doesn't really use them
13:48 egonw shk3: yes, guess so... as we can't read svg
13:49 gilleain It's a vector export format, as opposed to a raster export format, so you are right, yes :)
13:50 shk3 on the other hand, many formats are not in save as, like rxn
13:51 shk3 any reason for this?
13:52 egonw probably
13:52 egonw lazyness maybe?
13:53 shk3 i add a TODO
13:55 CIA-16 cdk: shk3 * r13341 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (4 files in 3 dirs): removed the svg from save, some cleanups
14:10 CIA-16 cdk: shk3 * r13342 /jchempaint/trunk/src/main/org/openscie​nce/jchempaint/JChemPaintMenuBar.java: activated the key sequences
14:33 CIA-16 cdk: shk3 * r13343 /jchempaint/trunk/src/main/org/openscien​ce/jchempaint/action/ExportAction.java: the export dialog can now be cancelled
14:43 CIA-16 cdk: gilleain * r13344 /cdk/branches/jchempaint-primary/src/main/org/​openscience/cdk/controller/AddRingModule.java: Adding benzene to bonds works.
15:00 CIA-16 cdk: gilleain * r13345 /jchempaint/trunk/src/main/org/openscien​ce/jchempaint/action/ExportAction.java: Minor clean.
15:14 CIA-16 cdk: shk3 * r13346 /jchempaint/trunk/src/main/org/openscience/jchem​paint/resources/JChemPaintResources.properties: artifact in here
15:26 CIA-16 cdk: shk3 * r13347 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (RenderPanel.java dialog/editor/Renderer2DModelEditor.java): added choosing of background color (more a gimmick, ok)
15:31 CIA-16 cdk: gilleain * r13348 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (3 files in 2 dirs): Minor changes to generating multiple bonds.
15:43 CIA-16 cdk: gilleain * r13349 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/BasicBondGenerator.java: Fix to bond distances.
15:48 CIA-16 cdk: goglepox * r13350 /cdk/branches/jchempaint-primary/src/main/org/ope​nscience/cdk/renderer/color/CDK2DAtomColors.java: atomicNumber may not be set, this handles that case
15:51 gilleain goglepox : I've been messing with the bond distance in the Renderer2DModel, but it occurs to me that what looks good in jcp on swing might not be the same for swt.
15:52 gilleain oh, and also, I implemented rendering of charges on awt, and it occured to me that the vist(IRenderingElement) dispatcher method is sensitive to the order.
15:53 gilleain so, that if you have "if (element instanceof TextElement)" before "if (element instanceof AtomMassSymbol", then you don't get things drawn right.
15:54 Gpox ah yes, my implementations of that method in SWTRenderer uses reflection
15:56 Gpox on the bond distance, I did set it to a good value for SWT when setting up my Renderer2DModel but then you hardcoded it in the generator :)
15:58 gilleain yes, I did that temporarily, then forgot when I commited, sorry.
16:00 gilleain The generation now does double at d, triple at 2*d, and quadruple at 4 * d.
16:00 Gpox you would have to set them to good values when not using the standard renderer
16:08 Gpox gilleain: do you draw charge and hydrogen count with the same font as the symbol?
16:09 Gpox i think there should be a second smaller font you can get from the font manager
16:09 gilleain I haven't done hydrogens, and I admit that I hadn't thought about it.
16:09 gilleain yes, that would make sense.
16:09 gilleain getFont() and getSmallFont()
16:09 gilleain or so.
16:09 gilleain I really should fix the fontmanager to work properly...
16:16 shk3 egonw: you copied org.os.cdk.applications.swing and org.os.cdk.applications.undoredo into the jchempaint project.
16:17 shk3 any reason for this?
16:17 shk3 none of the classes is currently used.
16:26 CIA-16 cdk: gilleain * r13351 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/application/JChemPaint.java: Minor cleanup.
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17:08 CIA-16 cdk: shk3 * r13352 /jchempaint/trunk/src/main/org/o​penscience/jchempaint/resources/ (JCPGUI_stable.properties JChemPaintResources.properties): removed insertSMILES action, since this is done via the insertstructure field
17:10 slyrus_ is the cdk trunk the canonical home for the isotopes.xml file?
17:11 CIA-16 cdk: shk3 * r13353 /jchempaint/trunk/src/main/org/openscience/jc​hempaint/resources/JCPGUI_stable.properties: removed insertSMILES action, since this is done via the insertstructure field
17:12 shk3 there should be a isotopes.xml in every branch
17:52 slyrus_ and, on a slightly related note, anyone know if there's an updated version of the elementdata.xml file from jumbo lying around anywhere?
17:52 slyrus_ shk3: right, but my questions was is that the where this thing came from in the first place or is there some upstream source?
17:55 gilleain sorry, not sure :(
17:55 shk3 neither me
17:55 shk3 I thought these files are from cdk and developed alongside cdk
17:55 shk3 but I don't really know
17:56 shk3 it's sort of atomtyping stuff...
17:56 slyrus_ atomtyping?
17:58 shk3 well, not exactly
17:58 shk3 I am just getting angry about atomtyping anyway, so it fits in
17:58 gilleain there's the org.openscience.cdk.config.data package.
17:58 gilleain that has isotopes.xml
18:00 gilleain which has such crazy info as the magnetic moment of K39...
18:03 shk3 isotopes.xml should be used for the isotopefactory
18:03 shk3 and this was written by cdk over time
18:03 shk3 but no idea about elementdata.xml and jumbo
18:05 CIA-16 cdk: shk3 * r13354 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (3 files in 3 dirs): added create smiles
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18:25 slyrus_ shk3: what is atomtyping?
18:29 CIA-16 cdk: gilleain * r13355 /jchempaint/trunk/src/main/org/opens​cience/jchempaint/RenderPanel.java: Platform-independent way to get images.
18:30 shk3 if I only would know...
18:32 gilleain slyrus_ : atoms have to have a type. atomtyping is (or atom typing) is giving a type to an atom
18:32 gilleain that's not the most helpful answer, I know :)
18:33 slyrus_ gilleain: ah, the old class vs. instance question.
18:33 gilleain hmm. not types like programming types, really.
18:34 slyrus_ are you referring to some sort of formal type theory or just a loose concept of "type"?
18:35 gilleain chemical type.
18:35 gilleain I think.
18:35 gilleain I should really know...
18:36 slyrus_ I guess there's the theoretical/chemical issue of type and then the machine representation of the "type" of atom. I'm more interested in the latter ATM.
18:37 gilleain well, there's an atom-types.owl file in the package org.openscience.cdk.dict.data
18:39 slyrus_ oh, thanks gilleain
18:40 gilleain right, so for example, in cdk-atom-types.owl, there's <at:AtomType rdf:ID="C.plus.sp1"> which is for positive carbon sp1 atoms.
18:41 gilleain (where "sp1" has some chemical meaning)
18:41 gilleain but, in general, a carbon atom in a ring can have a different type to one in a chain.
18:41 gilleain because of the attached atoms, the charge, etc
18:43 gilleain although frankly, a lot of this xml stuff seems like overkill. Elements will (hopefully) always be the same everywhere, for all time...
18:54 egonw hi slyrus_
18:54 egonw isotope.xml comes from the BODR project: bodr.sf.net
18:58 slyrus_ hi egonw, thanks!
18:58 egonw the data is also available via Ubuntu and Debian GNU/Linux
18:59 egonw an 'aptitude install bodr' does the job
18:59 slyrus_ egonw: I'm hoping to poach isotope.xml and something like the elementdata.xml from jumbo (or suitable workalikes for both) for my own project.
19:00 egonw why from jumbo?
19:00 slyrus_ the MIT license on isotope.xml seems to suggest that the authors would be ok with that
19:00 slyrus_ egonw: that's where I found it first :) but what do I know :)
19:00 slyrus_ I'm open to suggestions
19:00 egonw have not checked, but jumbo might very well use the bodr data
19:00 egonw bodr := blue obelisk data repository
19:01 egonw jubmo == peter murray-rus == blue obelisk
19:01 egonw bodr is MIT
19:01 egonw (-licensed)
19:01 egonw kalzium, the KDE periodic table tool, uses the bodr data too
19:01 egonw yes, bodr is deliberately very open, so please do use it
19:02 slyrus_ ah, I wasn't sure about the equivalence between peter murray-rust and bo. I knew there was some relationship but not that it was so strong :)
19:02 egonw using the same isotope abundancies and ratios is really important
19:02 egonw google for 'blue obelisk JCIM'
19:02 zarah egonw: http://chem-bla-ics.blogspot.com/2007/05/j​cim-is-linking-to-planet-blue-obelisk.html
19:02 egonw umm... no, not that link
19:02 slyrus_ the blue obelisk SVN repo doesn't seem to be live :(
19:03 egonw well... isotope abundances don't often change :)
19:06 egonw http://pubs.acs.org/doi/abs/10.1021/ci050400b
19:06 zarah egonw's link is also http://tinyurl.com/6qg7pn
19:06 egonw that's the right link
19:07 egonw slyrus_: going offline now...
19:07 egonw I am online here quite regularly...
19:07 egonw just let me know if you have further questions...
19:07 egonw bye
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21:36 CIA-16 cdk: gilleain * r13356 /cdk/branches/jchempaint-primary/src/main/org/ope​nscience/cdk/renderer/IntermediateRenderer.java: Draws the whole ChemModel, not just AtomContainers.
21:36 CIA-16 cdk: gilleain * r13357 /jchempaint/trunk/src/main/org/opens​cience/jchempaint/RenderPanel.java: Draws the whole ChemModel, not just AtomContainers.
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22:59 CIA-16 cdk: gilleain * r13358 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (3 files in 3 dirs): Filled wedge bonds now render.
22:59 CIA-16 cdk: gilleain * r13359 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (RenderPanel.java action/ChangeModeAction.java): Filled wedge bonds now render.

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