Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-21

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All times shown according to UTC.

Time Nick Message
04:03 CIA-31 cdk: egonw * r11081 /cdk/trunk/build.xml: Removed some jar/libio refs here too
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05:00 thomas_ku moin
06:50 rojasm joined #cdk
06:52 rojasm moin
07:13 egonw joined #cdk
07:47 * egonw is applying Aleksey's patch for CML
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07:52 CIA-31 cdk: egonw * r11082 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/ (libio/cml/Convertor.java test/io/cml/CMLRoundTripTest.java): Added unit test + patch for saving aromatic bonds in CML (patch by Aleksey Tarkhov)
07:54 CIA-31 bioclipse: ospjuth * r5647 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (8 files in 5 dirs): Refactored out MDLFileEditor to its own package.
07:59 CIA-31 bioclipse: ospjuth * r5648 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.sdfeditor/src/net/bioclipse/cdk10/sd​feditor/editor/StructureTablePage.java: Modified to support refactored MDLFileEditor.
08:00 jpansanel moin
08:07 CIA-31 cdk: egonw * r11083 /cdk/branches/cdk-1.0.x/src/org/opens​cience/cdk/libio/cml/Convertor.java: Fixed customizing of IBond's (patch by Aleksey Tarkhov)
08:08 CIA-31 bioclipse: ospjuth * r5649 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (6 files in 5 dirs): Added CMLFileEditor, updated ID for MDLFileEditor, and made Outline use interface IJCPBasedEditor instead of MDLFileEditor.
08:10 egonw hi jpansanel
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08:41 CIA-31 bioclipse: jonalv * r5650 /bioclipse2/trunk/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/business/StructuredbManagerTest.java: Substructuresearch returning a list seems to work. Now going for the one returning an iterator (probably much more useful)
09:24 CIA-31 cdk: egonw * r11084 /cdk/trunk/src/ (2 files in 2 dirs): Ported commit 11082 from cdk-1.0.x/: Added unit test + patch for saving aromatic bonds in CML (patch by Aleksey Tarkhov)
09:33 CIA-31 cdk: egonw * r11085 /cdk/trunk/src/main/org/openscien​ce/cdk/libio/cml/Convertor.java: Ported commit 11083 from cdk-1.0.x/: Fixed customizing of IBond's (patch by Aleksey Tarkhov)
10:08 CIA-31 cdk: egonw * r11086 /cdk/branches/miguelrojasch-IP/s​rc/META-INF/reaction.cdkdepends: Removed non-existing dep
10:24 CIA-31 bioclipse: jonalv * r5651 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): Tests and code for substructure iterator in structuredb
10:46 JimDowning joined #cdk
10:47 JimDowning egonw: Thanks for cleaning up those libs! Will make things waaay easier for me!
10:47 JimDowning I've been sidetracked on the mvn stuff, btw - need to write a project plan :-(
10:50 egonw ah, right....
10:50 egonw the bureaucracy
11:18 CIA-31 cdk: miguelrojasch * r11087 /cdk/branches/miguelrojasch-IP/src/ (2 files in 2 dirs): Only take into account bonds when determining the connectivity matrix, and not lone pairs! WTF ?!?! Why did no one run into this problem before??
11:20 JimDowning left #cdk
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11:59 CIA-31 cdk: miguelrojasch * r11088 /cdk/branches/miguelrojasch-IP/src​/main/org/openscience/cdk/charges/​GasteigerPEPEPartialCharges.java: Removed dependencies charges with smiles module
12:01 CIA-31 cdk: miguelrojasch * r11089 /cdk/branches/miguelrojasch-IP/s​rc/META-INF/charges.cdkdepends: Removed dependencies charges with smiles module 2
12:09 CIA-31 bioclipse: carl_masak * r5652 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java: [JsThread] removed finite wait for actions to be initialized
12:37 CIA-31 jmol: hansonr * r9399 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs): (log message trimmed)
12:37 CIA-31 jmol: version=11.5.38 adds RANDOM; upgrades quaternion
12:37 CIA-31 jmol: # bug fix: select n-m:c chain selection inappropriately case sensitive
12:37 CIA-31 jmol: # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way
12:37 CIA-31 jmol: # bug fix: draw CIRCLE for multiple models
12:37 CIA-31 jmol: # bug fix: application -- "make crystal..." menu item does nothing -- removed
12:37 CIA-31 jmol: # bug fix: zap of quaternion also zaps model inappropriately
12:44 CIA-31 cdk: miguelrojasch * r11090 /cdk/trunk/src/ (8 files in 3 dirs): removed the class set/getproperties, clone for formula object. It will be extend from IObject
12:47 thomas_ku joined #cdk
12:49 jpansanel moin thomas_ku
12:50 thomas_ku hi
12:53 CIA-31 cdk: miguelrojasch * r11091 /cdk/trunk/src/ (8 files in 3 dirs): reversed to previous commit: 11098. It was erronously removed the properties staff
12:57 egonw (that was my mistake :)
13:00 CIA-31 bioclipse: jonalv * r5653 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: added empty test as a reminder
13:10 CIA-31 bioclipse: ospjuth * r5654 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (5 files in 4 dirs): CMLFileEditor is able to read and show molecules. JCPPage further refactored to support other IJCPBasedEditors.
13:10 CIA-31 cdk: egonw * r11092 /cdk/trunk/src/main/org/openscience/cdk/ (13 files in 5 dirs): Made IMolecularFormula(Set) and IAdductFormula part of the main interfaces
13:10 CIA-31 bioclipse: ospjuth * r5655 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: Adapted for API changes in JCPPage. Single Molecule Page not working (yet).
13:25 CIA-31 jmol: hansonr * r9400 /trunk/Jmol/src/org/jmol/shapespecial/Draw.java:
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13:57 CIA-31 bioclipse: jonalv * r5656 /bioclipse2/trunk/plugins/net.biocli​pse.biojava.business/src/net/bioclip​se/biojava/business/Activator.java: cleaned up a bit
14:12 CIA-31 cdk: egonw * r11093 /cdk/trunk/src/main/org/openscience/cdk/ (12 files in 4 dirs): Added the IMolecularFormula(Set), IAdductFormula .getBuilder() methods
14:19 CIA-31 bioclipse: ospjuth * r5657 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java:
14:19 CIA-31 bioclipse: Tried to refactor out initialization so that JCPPage can be initialized as a
14:19 CIA-31 bioclipse: second tab in the SDFileEditor. Still no luck, but I don't think I have broken
14:19 CIA-31 bioclipse: anything in the CMLEditor and MDLEditor. Functionality moved from
14:19 CIA-31 bioclipse: createPartControl() to updateJCPModel(). Egonw: Please verify I have not broken
14:19 CIA-31 bioclipse: anything.
14:48 CIA-31 bioclipse: jonalv * r5658 /bioclipse2/trunk/plugins/net.bioclipse.core/ (9 files in 5 dirs): Wrote a molecule manager but I can't get it to show up in the console. /me feels a bit silly. Perhaps someone can see what I made wrong? :)
14:50 CIA-31 bioclipse: jonalv * r5659 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: Removed has3dCoords from Structure
14:51 CIA-31 cdk: miguelrojasch * r11094 /cdk/branches/miguelrojasch-IP/src/ (2 files in 2 dirs): added test to check if mdlReader is parsing correctly radicals
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15:17 CIA-31 bioclipse: jonalv * r5660 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added createFromMolecule to cdk manager
15:43 jonalv is there a way to copy a atomContainer
15:43 jonalv ?'
15:45 jonalv is clone implemented in cdk?
15:47 rojasm yes it is. all IChemObject has the function clone
15:48 jonalv oki good :=
15:48 jonalv I should be safe then :)
16:06 CIA-31 bioclipse: jonalv * r5661 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Wrote toCDKMolecule( Structure s) in structuredb and switched to using it on a few places
16:08 CIA-31 bioclipse: jonalv * r5662 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Addded all-params constructor to cdkMolecule
16:37 CIA-31 cdk: egonw * r11095 /cdk/trunk/src/ (11 files in 5 dirs): The formula module is now independent from the data module
16:47 CIA-31 cdk: egonw * r11096 /cdk/trunk/src/main/org/openscience/cdk​/formula/IsotopePatternGenerator.java: Fixed creating the isotope factory
16:49 CIA-31 cdk: egonw * r11097 /cdk/trunk/src/test/org/openscience/cdk/for​mula/MolecularFormulaManipulatorTest.java: My JUnit installation complained about it: use assertEquals(double,double, margin) instead
16:51 CIA-31 cdk: miguelrojasch * r11098 /cdk/branches/miguelrojasch-IP/sr​c/data/mdl/332727182.radical.mol: added test to check if mdlReader is parsing correctly radicals. Missed the file
17:06 CIA-31 cdk: miguelrojasch * r11099 /cdk/branches/miguelrojasch-IP/ (33 files in 12 dirs): Synchronized with trunk the branches.miguelrojasch-IP, Rev=11076:11098
17:41 CIA-31 cdk: egonw * r11100 /cdk/trunk/ (15 files in 3 dirs): Removed hyphens from the module names pdb_cml and qsar_pdb
17:52 CIA-31 cdk: egonw * r11101 /cdk/trunk/src/META-INF/ (6 files): Removed deps on no-longer-existing modules
19:23 CIA-31 jmol: hansonr * r9401 /trunk/Jmol/src/org/jmol/ (8 files in 5 dirs): (log message trimmed)
19:23 CIA-31 jmol: version=11.5.38
19:23 CIA-31 jmol: # bug fix: select n-m:c chain selection inappropriately case sensitive
19:23 CIA-31 jmol: # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way
19:23 CIA-31 jmol: # bug fix: draw CIRCLE for multiple models
19:23 CIA-31 jmol: # bug fix: application -- "make crystal..." menu item does nothing -- removed
19:23 CIA-31 jmol: # bug fix: zap of quaternion also zaps model inappropriately
19:27 CIA-31 jmol: hansonr * r9402 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:
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21:03 CIA-31 cdk: rajarshi * r11102 /cdk/trunk/src/data/mdl/lobtest2.sdf: Added a test case for LOB, to make sure that atomtyping is working
21:18 CIA-31 cdk: rajarshi * r11103 /cdk/trunk/src/test/org/openscience​/cdk/qsar/descriptors/molecular/Len​gthOverBreadthDescriptorTest.java:
21:18 CIA-31 cdk: Added a test case for bug 1965254. The original report obtained the 3D structre
21:18 CIA-31 cdk: for the SMILES using the CDK. But if the 3D structure is obtained using smi23d
21:18 CIA-31 cdk: it works fine. The actal bug seems to be in the 3D structre code of the CDK
22:30 CIA-31 cdk: rajarshi * r11104 /cdk/trunk/src/main/org/openscience/cdk/​pharmacophore/PharmacophoreMatcher.java:
22:30 CIA-31 cdk: Updated code so that if the user gets the unique matches just after matching,
22:30 CIA-31 cdk: the code will first get the full set of non-unique matches. Since we get the non
22:30 CIA-31 cdk: USA matches lazily, the USA method was working with a NULL object rather than
22:30 CIA-31 cdk: the expected matching pharmacophore atoms
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