Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-24

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All times shown according to UTC.

Time Nick Message
07:17 egonw_ joined #cdk
07:23 jbrefort joined #cdk
07:28 egonw_ LaserRock: saw the #ubuntu-classroom announcement...
07:28 egonw_ will try to join in...
08:15 CIA-16 cdk: egonw * r9489 /trunk/cdk/src/org/openscience/cdk/test/ (AtomtypeCoverageTest.java modulesuites/MatomtypeTests.java): Added coverage testing for the atomtype module
08:24 CIA-16 cdk: egonw * r9490 /trunk/cdk/build.xml: Reorder to match functional dependencies.
08:29 CIA-16 cdk: egonw * r9491 /branches/egonw/ibondorder/ (42 files in 11 dirs): Synched with trunk 9480:9490
08:48 CIA-16 cdk: egonw * r9492 /branches/egonw/ibondorder/src/org/openscienc​e/cdk/tools/manipulator/BondManipulator.java: Moved to atomtype module.
09:16 edrin joined #cdk
10:05 jpansanel moin
10:14 CIA-16 cdk: egonw * r9493 /branches/egonw/ibondorder/src/org/openscience/cdk​/applications/undoredo/AdjustBondOrdersEdit.java: Fixed bond order type.
10:24 CIA-16 cdk: egonw * r9494 /branches/egonw/ibondorder/src/org/​openscience/cdk/qsar/descriptors/mo​lecular/BondCountDescriptor.java: Fixed error message: corrected param type.
10:24 CIA-16 cdk: egonw * r9495 /branches/egonw/ibondorder/src/org/ope​nscience/cdk/test/qsar/descriptors/mol​ecular/BondCountDescriptorTest.java: Fixed test: parameter to be passed has changed.
10:27 CIA-16 blueobelisk: pansanel * r186 /structures/trunk/src/carboxylic_acids/ (18 files):
10:27 CIA-16 blueobelisk: Renaming the file according the trivial name
10:27 CIA-16 blueobelisk: Adding missing french translations
10:27 jpansanel egonw : I think some french translation is missing on JChemPaint
10:28 egonw_ very likely...
10:28 egonw_ you know where to find the translation files?
10:28 jpansanel jchempaint-2.3.2.jar
10:28 jpansanel no
10:28 jpansanel but I'll find it on the svn
10:28 egonw_ OK, it's not .po like, but java like...
10:29 egonw_ so look for cdk.applications.jchempaint.data or something...
10:29 egonw_ it's a .properties file
10:29 jpansanel ok
10:29 jpansanel I'll do it using eclipse
10:29 egonw_ sounds interesting...
10:30 egonw_ never done that in Eclipse
10:30 egonw_ is there a special plugin for translating Java property files?
10:31 jpansanel maybe
10:32 jpansanel I'll tell you
10:33 egonw_ jpansanel: I will look at the NL translation for chemical-files today
10:34 jpansanel ok
10:34 jpansanel thx
10:36 jpansanel I need to find a way to export 2D picture of each compound and upload them on Wikipedia
10:36 jpansanel many pictures are missing
10:36 jpansanel 3D pictures can also be interesting
10:42 egonw_ jpansanel: use the CDK
10:42 egonw_ you could make a Taverna workflow for that
10:43 egonw_ CDK-Taverna that is
10:46 jpansanel ok
10:48 carsten joined #cdk
10:50 CIA-16 blueobelisk: pansanel * r187 /structures/trunk/src/drugs/ (2S-1-phenylpropan-2-amine.cml D-amphetamine.cml index.xml):
10:50 CIA-16 blueobelisk: Adding missing translations
10:50 CIA-16 blueobelisk: Renaming according trivial name
11:02 jpansanel egonw : JCPBundle_fr.properties
11:02 egonw_ yesh, something like that :)
11:08 carsten jpansanel: I have one q: Is it possible to release a new chem-file release in the next days?
11:08 carsten jpansanel: so that my school takes a really new one?
11:08 carsten jpansanel: Our PCs are updated perhaps once a year
11:10 carsten egonw_: a collegue ask me why he should not use Chime
11:10 carsten egonw_: I showed him Avogadro and JMol
11:10 carsten JMol inside chem-file
11:10 egonw_ not supported, buggy, not compatible, unmaintained
11:10 carsten not supported by?
11:10 * egonw_ mumbles "lower case 'm'" ...
11:10 carsten Jmol, ok :)
11:10 egonw_ not supported by anyone
11:10 jpansanel carsten : I'll try to release this week
11:11 jpansanel egonw : http://www.eclipseplugincentral.com/Web​_Links-index-req-viewlink-cid-331.html
11:11 egonw_ ask him why he wants to use Chime at all?
11:11 egonw_ Chime has nothing Jmol does not have too
11:11 egonw_ and Jmol has lots more
11:11 carsten ok, that is important to know
11:11 jpansanel Chime is "has been"
11:11 egonw_ Chime does not run in any recent web browser
11:11 carsten egonw_: we a re a windows-only environment
11:11 egonw_ Chime is past tense
11:11 carsten http://www.mdl.com/products/f​ramework/isis_excel/index.jsp looks cool
11:12 jpansanel Chime is from last century
11:12 egonw_ no, from before that
11:12 carsten jpansanel: the #1 request for chem-file (well, for any database, of course) is 2d AND 3d
11:13 carsten jpansanel: where do I add the german names for molecules?
11:14 carsten ah, inside the index!
11:15 carsten no... the index.xml is autogenerated I guess?
11:21 jpansanel no
11:21 jpansanel it is not
11:21 jpansanel all translations of molecule are inside
11:23 carsten oh, you crteate that xml bgy hand?
11:23 carsten oh, you created that xml by hand?
11:37 CIA-16 blueobelisk: pansanel * r188 /structures/trunk/src/esters/index.xml: Adding missing french translations
12:12 jpansanel carsten : yes
12:12 egonw_ lovely discussion over at the OpenSMILES mailing list
12:15 jbrefort joined #cdk
12:37 CIA-16 cdk: egonw * r9496 /branches/egonw/ibondorder/src/org/​openscience/cdk/test/RingTest.java: Extra testing, uncovered a bug in the branch.
12:38 CIA-16 cdk: egonw * r9497 /branches/egonw/ibondorder/src/​org/openscience/cdk/Ring.java: Fixed returning sum equivalents of IBond.Orders.
12:39 egonw_ yeah, only 503 commits away from 10.000
13:22 CIA-16 jmol: hansonr * r8656 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs):
13:22 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
13:22 CIA-16 jmol: # new feature: Spartan06 file format reader
13:22 CIA-16 jmol: # new feature: ZIP file reading for multiple models
13:44 CIA-16 cdk: egonw * r9498 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added two more nice test examples
13:53 CIA-16 cdk: egonw * r9499 /trunk/cdk/src/org/openscience/cdk/Atom.java: Removed atom type field from IAtom.toString.
13:55 CIA-16 cdk: egonw * r9500 /trunk/cdk/src/org/openscience/cdk/test/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Removed duplicate atom typing
13:56 CIA-16 cdk: egonw * r9501 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java: Fixed perception of N.plus.sp2
13:57 CIA-16 cdk: egonw * r9502 /branches/egonw/ibondorder/src/META-INF/ (5 files): Added missing deps
14:05 CIA-16 cdk: egonw * r9503 /trunk/cdk/src/org/openscience​/cdk/smiles/SmilesParser.java: Be more informative when failing on a SMILES
14:07 CIA-16 cdk: egonw * r9504 /branches/egonw/ibondorder/src/org/openscie​nce/cdk/test/smiles/SmilesParserTest.java: Fixed a test for the new IBond.Order syntax
14:09 CIA-16 cdk: egonw * r9505 /branches/egonw/ibondorder​/src/org/openscience/cdk/ (6 files in 6 dirs): Synched with trunk 9490:9504
14:15 egonw__ joined #cdk
14:20 CIA-16 blueobelisk: pansanel * r189 /structures/trunk/src/ethers/ (17 files):
14:20 CIA-16 blueobelisk: Renaming chemical files according usual names
14:20 CIA-16 blueobelisk: Adding missing french translations
14:59 dleidert joined #cdk
16:58 CIA-16 jmol: hansonr * r8657 /trunk/Jmol/src/org/jmol/ (6 files in 4 dirs):
16:58 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
16:58 CIA-16 jmol: # new feature: Spartan06 file format reader
16:58 CIA-16 jmol: # new feature: ZIP file reading for multiple models
16:59 CIA-16 jmol: hansonr * r8658 /trunk/Jmol/src/org/jmol/viewer/FileManager.java:
16:59 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
16:59 CIA-16 jmol: # new feature: Spartan06 file format reader
16:59 CIA-16 jmol: # new feature: ZIP file reading for multiple models
17:21 CIA-16 jmol: hansonr * r8659 /trunk/Jmol/src/org/jmol/util/ZipUtil.java:
17:21 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
17:21 CIA-16 jmol: # new feature: Spartan06 file format reader
17:21 CIA-16 jmol: # new feature: ZIP file reading for multiple models
17:27 CIA-16 cdk: egonw * r9506 /branches/egonw/ibondorder/src/org/openscie​nce/cdk/test/smiles/SmilesParserTest.java: The smiles parser does not resolve bond orders.
17:30 CIA-16 jmol: hansonr * r8660 /trunk/Jmol/src/org/jmol/ (adapter/smarter/SmarterJmolAdapter.java util/ZipUtil.java):
17:30 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
17:30 CIA-16 jmol: # new feature: Spartan06 file format reader
17:30 CIA-16 jmol: # new feature: ZIP file reading for multiple models
17:31 CIA-16 jmol: hansonr * r8661 /trunk/Jmol/src/org/jmol/util/ZipUtil.java:
17:31 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
17:31 CIA-16 jmol: # new feature: Spartan06 file format reader
17:31 CIA-16 jmol: # new feature: ZIP file reading for multiple models
17:33 CIA-16 cdk: egonw * r9507 /branches/egonw/ibondorder/src/org/opensc​ience/cdk/templates/MoleculeFactory.java: New syntax: IBond.Order
17:35 CIA-16 jmol: hansonr * r8662 /trunk/Jmol-datafiles/ (4 files in 3 dirs):
17:35 CIA-16 jmol: version=11.3.48_dev spartan06 and generic ZIP file-set reading
17:35 CIA-16 jmol: # new feature: Spartan06 file format reader
17:35 CIA-16 jmol: # new feature: ZIP file reading for multiple models
17:35 egonw_ miguelrojasc1: around?
17:51 egonw_ LaserJock: did you get my message the other day?
17:51 egonw_ yuor ORTEP friend needs to email a CIF file with ORTEP info...
17:51 LaserJock egonw_: yes I did
17:51 LaserJock I'm waiting on it
17:51 LaserJock I told him to send it
17:52 LaserJock I think he's just busy, but he said he was going to send one of a sulfur crystal I think
17:52 LaserJock said it was something trivial but real data so it'd make a good test file
17:55 egonw_ great
17:55 egonw_ ok, thanx
17:55 LaserJock as soon as I get it I'll send it on
18:27 CIA-16 cdk: egonw * r9508 /branches/egonw/lpchecker/: Made a branch to rewrite the lone pair checker to use the new code.
18:52 CIA-16 jmol: hansonr * r8663 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs): version=11.3.48_dev # new feature: load xxx.zip n # where n is the desired file, starting with 1
18:54 CIA-16 jmol: hansonr * r8664 /trunk/Jmol/src/org/openscience/jmol/​Properties/Jmol-resources.properties: version=11.3.48_dev # bug fix: application animation frame button reset always goes to frame 1
18:54 CIA-16 jmol: hansonr * r8665 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: version=11.3.48_dev # bug fix: application animation frame button reset always goes to frame 1
19:14 CIA-16 jmol: hansonr * r8666 /trunk/Jmol/src/org/jmol/ (2 files in 2 dirs): version=11.3.48_dev # bug fix: multimodel files could have connected atoms between different models.
19:19 CIA-16 jmol: hansonr * r8667 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.48 VERSION -- reading of ZIP files, Spartan06 spardir reader
19:54 jbrefort joined #cdk
22:48 edrin joined #cdk

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