Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-25

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All times shown according to UTC.

Time Nick Message
06:05 thomas_ku joined #cdk
06:05 jbrefort joined #cdk
06:33 CIA-37 blueobelisk: pansanel * r261 /structures/trunk/ (42 files in 37 dirs): Fix out-of-source build
06:35 CIA-37 blueobelisk: pansanel * r262 /structures/trunk/INSTALL: Update the installation instruction
06:38 thomas_ku moin
06:38 zarah hi thomas_ku
06:53 Gpox joined #cdk
06:58 Gpox joined #cdk
08:19 CIA-37 cdk: goglepox * r13263 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (2 files in 2 dirs):
08:19 CIA-37 cdk: Added AtomContainer bounds and fixed transforming
08:19 CIA-37 cdk: with AffineTransform
08:20 CIA-37 cdk: goglepox * r13264 /cdk/branches/jchempaint-primary/sr​c/main/org/openscience/cdk/renderer​/elements/IRenderingVisitor.java:
08:20 CIA-37 cdk: Added method for RectanleElement
08:20 CIA-37 cdk: and AtomSymbolElement.
08:20 CIA-37 cdk: goglepox * r13265 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java:
08:20 CIA-37 cdk: Chaged method to take a IRenderer,
08:20 CIA-37 cdk: that can be used to the transform for the rendering
08:20 CIA-37 cdk: visitor
08:21 CIA-37 cdk: goglepox * r13266 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (Renderer.java generators/AtomContainerBoundsGenerator.java): Removed transform to center Point2d parameter
08:21 CIA-37 cdk: goglepox * r13267 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/IRenderer.java: Removed IRenderer interface as it only had one usefull method
08:22 CIA-37 cdk: goglepox * r13268 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (11 files in 3 dirs):
08:22 CIA-37 cdk: Changed IRenderingVisitor interface
08:22 CIA-37 cdk: Added visit(IRenderingVisitor) implementation that
08:22 CIA-37 cdk: calls currently defined methods. Can be made to use
08:22 CIA-37 cdk: either reflection or add visit( ElementType) to the
08:22 CIA-37 cdk: interface again.
09:12 jonalv joined #cdk
09:40 jpansanel moin
09:40 zarah hi jpansanel
09:40 jpansanel moin jonalv
09:40 jonalv hi jpansanel
09:41 jpansanel jonalv : egonw told be that a plugin for Mychem would be fine in Bioclipse
09:41 jonalv okey
09:41 * jonalv isn't that familiar with Mychem...
09:41 jpansanel I think it would be better to have a plugin for chemisql
09:42 jpansanel and loading the right db driver at run time
09:42 jonalv oh hang on is this those databases?
09:42 jonalv those chemical databases?
09:44 jonalv jpansanel?
09:44 jpansanel yes
09:44 jonalv I have been thinking about that...
09:44 jpansanel we should define a standard database structure
09:45 jpansanel and use it for a chemical cartridge
09:45 jonalv It would be nice to wrap those under the api I am using for structuredb in BNioclipse...
09:45 jpansanel do you have an overview of structuredb ?
09:45 jonalv because I am am starting to build gui for it now
09:46 jpansanel (UML shema ?)
09:46 jonalv hang on
09:46 jpansanel jonalv : I've start to write a GUI, but it was only for Mychem
09:46 jpansanel an idea was to develop an independant GUI for chemisql
09:47 jpansanel we should work together on that topic
09:47 jonalv yea
09:49 jonalv http://wiki.bioclipse.net/imag​es/StructuredbClassDiagram.png
09:49 zarah jonalv's link is also http://tinyurl.com/5z5cvk
09:49 jonalv I guess you will have questions... Ö=
09:50 jonalv oh wrong keyborad layout... :)
09:58 jonalv jpansanel: ping
10:06 jpansanel jonalv
10:06 jpansanel pong
10:06 jonalv jpansanel: did you understand my classidagram? :)
10:07 jpansanel yes
10:07 jpansanel jonalv : it may be better to split the structure database
10:08 jpansanel it may accelerate the query
10:08 jonalv jpansanel: split how?
10:08 jpansanel a smile db
10:08 jpansanel a fingerprint db
10:08 jpansanel a molecule db
10:08 jonalv separate databasees?
10:08 jpansanel yes
10:09 jonalv hm feels strange
10:09 jonalv And I am not sure iBatis will like that...
10:09 jpansanel iBatis ?
10:09 jonalv it's and ORM
10:09 jpansanel ok
10:09 jonalv are you familiar with Hibernate?
10:10 jpansanel no
10:10 jpansanel I've used Zend PHP framework that contains an ORM
10:10 jonalv but you know what ORMs are anyway...
10:10 jonalv oki
10:10 jpansanel it works perfectly with seraparate database
10:10 jonalv mhm
10:10 jpansanel we need a central key index
10:11 jonalv which one is based on MySQL?
10:11 jpansanel yes
10:11 jpansanel but should work also on PostgreSQL and Oracle
10:12 jonalv Mychem?
10:15 jpansanel Mychem is only working with MySQL
10:15 jpansanel Pgchem is working with PostgreSQL
10:15 jpansanel and Orchem with Oracl
10:16 jpansanel the three project are coverd by the ChemiSQL project
10:17 jonalv which one is you working on?
10:19 jpansanel Mychem and ChemiSQL
10:20 jonalv okey
10:20 jonalv then it's you that I have been planning to talk to
10:20 jonalv the original plan with structuredb was to use mysql for a shared database later on
10:20 jonalv for the moment hsqldb is used...
10:21 jonalv I am guessing you can never get the same speed with my solution as you can with your...
10:22 jonalv But I want it to be easy to migrate from the local hsqldb database to a mysql database and that the gui in Bioclipse looks more or less the same
10:23 jpansanel ok
10:23 jonalv does it sound reasonable?
10:23 jpansanel yes
10:23 jonalv the big benefit of hsqldb-structuredb is that it works out of the box
10:23 jpansanel of course
10:23 jonalv you don't need to install and setup mysql...
10:23 jpansanel you don't need a sql server
10:24 jpansanel :)
10:24 jonalv but sooner or later you will probably outgrow it and then it should be easy to upgrade...
10:24 jpansanel jonalv : did you try to work with a large amount of molecules ?
10:25 jpansanel ( > 100.000)
10:25 jonalv jpansanel: yea about that...
10:25 jonalv it does not work yet...
10:25 jpansanel With less than 20.000 molecules, you can work with a single database
10:26 jonalv strucuteedb is not very usefull yet...
10:26 jonalv I hope it's not cdk that is leaking memoery but I have has outofmemeryexceptions during import..
10:26 jonalv *had
10:27 jpansanel ok
10:27 jonalv also the editor for browsing is not lazy yet. But we are working on that
10:29 jonalv I need to get myself a profiler and see what's going on during import. It's on my list...
10:29 jonalv right now I need to get some order to Brunn though... :)
10:31 jpansanel many work !
10:32 jpansanel I'm working on the next release of Mychem
10:32 jpansanel (v0.6.0)
10:32 jpansanel I try to compile on Win32
10:32 jonalv sounds good
10:32 jonalv but?
10:32 jonalv :)
10:38 jpansanel Two version of Open Babel are supported :
10:38 jpansanel v2.1.1
10:38 jpansanel v.2.2.0
12:13 gilleain joined #cdk
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12:55 CIA-37 cdk: goglepox * r13269 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/BasicBondGenerator.java:
12:55 CIA-37 cdk: Made black default color
12:55 CIA-37 cdk: if no color is avaiable from the color hash.
12:56 CIA-37 cdk: goglepox * r13270 /cdk/branches/jchempaint-primary/sr​c/main/org/openscience/cdk/renderer​/elements/AtomSymbolElement.java: Enabeld AtomSymbolElements
12:56 CIA-37 cdk: goglepox * r13271 /cdk/branches/jchempaint-primary/src/main/org/o​penscience/cdk/controller/HighlightModule.java: Fixed it so that if Atom is closer than the bond it get highlighted
14:45 carsten_ joined #cdk
14:53 CIA-37 cdk: shk3 * r13272 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (JCPStatusBar.java JChemPaintPanel.java RenderPanel.java): added a status bar
14:57 CIA-37 cdk: gilleain * r13273 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/application/JChemPaint.java: Minor change to set the current working directory to the parent directory of the file argument.
15:01 timvdm joined #cdk
15:19 CIA-37 cdk: gilleain * r13274 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (3 files in 2 dirs):
15:19 CIA-37 cdk: - Fixed cycling of bond order.
15:19 CIA-37 cdk: - Minor change to highlighting.
15:42 CIA-37 cdk: shk3 * r13275 /jchempaint/trunk/src/main/org/openscience/ (7 files in 5 dirs): the periodic table works (removed update of status bar, since this causes problems)
15:45 CIA-37 cdk: shk3 * r13276 /jchempaint/trunk/src/main/org/opensci​ence/jchempaint/dialog/PTDialog.java: the periodic table works (removed update of status bar, since this causes problems)
15:53 CIA-37 cdk: shk3 * r13277 /jchempaint/trunk/src/main/org/openscience/ (3 files in 3 dirs): relocated resource
16:12 Julio joined #cdk
16:13 Julio left #cdk
16:41 CIA-37 cdk: shk3 * r13278 /cdk/branches/jchempaint-primary/src/ (3 files in 2 dirs): added a cycleelement module
16:42 CIA-37 cdk: shk3 * r13279 /cdk/branches/jchempaint-primary/src/main/org/ope​nscience/cdk/controller/IController2DModel.java: added a cycleelement module
16:44 CIA-37 cdk: shk3 * r13280 /jchempaint/trunk/src/main/org/opensci​ence/jchempaint/JChemPaintPanel.java: cycling through elements works
17:00 CIA-37 cdk: shk3 * r13281 / (4 files in 3 dirs): ok, one more rename of field
17:12 CIA-37 cdk: shk3 * r13282 /jchempaint/trunk/ (3 files in 2 dirs): the ant build works again
17:15 CIA-37 cdk: gilleain * r13283 /cdk/branches/jchempaint-primary/src/main/org/op​enscience/cdk/controller/CycleSymbolModule.java: Fixed a null-pointer exception when clicking far from an atom.
17:16 shk3 what's the jcp "Specification-Version"?
17:40 jbrefort joined #cdk
19:01 CIA-16 joined #cdk
21:02 jbrefort joined #cdk
21:23 CIA-16 cdk: gilleain * r13284 /cdk/branches/jchempaint-primary/src/main/org/op​enscience/cdk/controller/CycleSymbolModule.java: Minor fix to cyclesymbolmodule.
21:26 CIA-16 cdk: gilleain * r13285 /jchempaint/trunk/src/main/org/openscience/​jchempaint/action/JCPActionChangeMode.java: Both octagon and heptagon were adding 7-membered rings.
21:43 timvdm joined #cdk
22:20 CIA-16 cdk: gilleain * r13286 /cdk/branches/jchempaint-primary/src/main/org/o​penscience/cdk/controller/Controller2DHub.java: Fix for bug where adding an atom to a blank canvas throws a NPE.
23:13 CIA-16 cdk: gilleain * r13287 /cdk/branches/jchempaint-primary/src/main/org/​openscience/cdk/controller/AddBondModule.java: Minor fix to the AddBondModule.
23:48 CIA-16 cdk: gilleain * r13288 /cdk/branches/jchempaint-primary/src/main/org/ope​nscience/cdk/renderer/IntermediateRenderer.java: Converted the IntermediateRenderer to use AffineTransform. Bit nasty, but it works.

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