Camelia, the Perl 6 bug

IRC log for #cdk, 2008-02-04

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All times shown according to UTC.

Time Nick Message
04:15 egonw joined #cdk
05:24 CIA-18 jmol: nicove * r8949 /trunk/Jmol-FAH/projects/p2589.xyz.gz: Folding@Home
06:23 jbrefort joined #cdk
06:38 egonw joined #cdk
07:42 rojasm joined #cdk
07:43 rojasm moin
07:43 egonw hi rojasm
07:43 rojasm hi egonw
07:43 egonw was just about to do some hacking on branches/reaction/...
07:43 rojasm I saw your email
07:43 egonw to better explain what I meant...
07:43 rojasm Now I understood what you mean
07:44 rojasm But For each new reaction we should put a test in atomtype. Or it is only for hacking now
07:44 egonw no, for each reaction...
07:44 egonw a lot of work...
07:44 egonw have not to be done overnight...
07:44 rojasm I mean for the futur
07:45 egonw but it is our best shot at debugging all this...
07:45 rojasm ok
07:45 rojasm I do it
07:46 egonw please only make stubs as much as possible...
07:46 egonw stub... empty test, stating this compound X should be tested
07:46 egonw without actually writing the full test...
07:46 egonw that would allow me (and others) to help implement the actual tests...
07:47 egonw e.g. put the expected pseudo-SMILES in a comment in the emtpy unit test or so
07:47 egonw after that... we need unit tests for expected reaction products for those reactions which currently fail...
07:47 egonw brb...
07:48 rojasm ok einverstanden :)
07:55 carsten joined #cdk
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09:01 CIA-18 cdk: miguelrojasch * r10013 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ResonanceStructuresTest.java: New class to test the fragments of structures resonance
09:01 rojasm egonw: could you please take a look teh new class if it is how it should be
09:02 egonw was just doing that :)
09:03 egonw please fix the copyrigh line
09:03 jonalv joined #cdk
09:03 rojasm ups
09:04 egonw use a global static matcher
09:04 egonw mom... I will do that...
09:04 egonw won't do the copyright line though
09:04 rojasm ok, thanks
09:05 egonw oh, and please add it to the MatomtypeTests in cdk.test.modulesuites
09:07 CIA-18 cdk: egonw * r10014 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ResonanceStructuresTest.java: Use a global final static matcher
09:08 CIA-18 cdk: miguelrojasch * r10015 /branches/miguelrojasch/reaction/src/org/opensci​ence/cdk/test/modulesuites/MreactionTests.java: added ResonanceStructuresTest to module modulesuites Mreaction
09:09 rojasm Egonw the copyright 2008, right?
09:09 egonw right
09:11 CIA-18 cdk: miguelrojasch * r10016 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ResonanceStructuresTest.java: Corrected the copyright line to 2008
09:11 egonw ok, getting some more coffee
09:11 rojasm :)
09:13 jpansanel moin
09:13 rojasm moin
09:16 egonw back
09:32 egonw rojasm: there is actually an improvement you can make to the class
09:32 egonw instead of just testing that an atom type is defined, we should test that the correct atom type is detected...
09:32 egonw will upload an example...
09:33 rojasm perfect
09:42 CIA-18 cdk: egonw * r10017 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ResonanceStructuresTest.java: Also test the perceived atom types, not just that anything is perceived
09:42 egonw rojasm: you can use that as template
09:42 egonw I have not applied it to both structures yet...
11:38 Annzi left #cdk
12:15 CIA-18 cdk: miguelrojasch * r10018 /branches/miguelrojasch/reaction/src/org​/openscience/cdk/qsar/descriptors/atomic​/AtomHybridizationVSEPRDescriptor.java: modified the table to html script.
12:36 CIA-18 cdk: miguelrojasch * r10019 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ResonanceStructuresTest.java: added one test for the atomtype O.plus.radical with double bond
12:39 rojasm egonw I put the test with the carbonyl wich was ionized. It has double bond neighboor and charge +1 and sinble electron
12:40 egonw yes, saw the commit
12:40 egonw keep them coming...
12:40 egonw I will run them tonight, and work on missing atom types...
12:40 egonw btw, feel free to file bug reports for missing atom types...
12:40 egonw while pointing the methods in this new class...
12:40 egonw but then again...
12:41 egonw I'll see the unit tests fail anyway...
12:43 rojasm should I create some identical class withe structureReactionTest in cdk.test.atomtype ?
12:44 rojasm for reactions
12:44 egonw ok
14:27 carsten joined #cdk
14:52 * egonw is heading home
14:52 egonw been a long day already
14:52 egonw will be online tonight
15:24 CIA-18 cdk: miguelrojasch * r10020 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ReactionStructuresTest.java: New class to test the fragments of structures coming from reactions
15:40 carsten joined #cdk
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16:01 CIA-18 cdk: miguelrojasch * r10021 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (2 files in 2 dirs): added Inchi definition, cleaning staff.
16:08 de_maas left #cdk
16:13 CIA-18 cdk: miguelrojasch * r10022 /branches/miguelrojasch/reaction/src/o​rg/openscience/cdk/test/reaction/type/​CarbonylEliminationReactionTest.java: added test method for testing mapping and manually search of reaction center.
16:29 CIA-18 cdk: miguelrojasch * r10023 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/CleavageBondReactionTest.java: Added test mapping
16:34 CIA-18 cdk: miguelrojasch * r10024 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ReactionStructuresTest.java: added some explanation.
17:35 CIA-18 cdk: miguelrojasch * r10025 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (3 files in 3 dirs): added atMatcher.findMatchingAtomType after was cloned the reaction.
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18:36 egonw joined #cdk
19:11 rojasm egonw: around?
19:11 egonw yes
19:12 rojasm I want to create in reaction-types all examples for a good documentation
19:12 rojasm but
19:12 rojasm for example it is possible to make example for BreakingBondReaction as
19:13 rojasm X(H)(H)=Y(H)(H)
19:13 rojasm sorry
19:13 rojasm X(R)(R)=Y(R)(R)
19:13 rojasm meaning that X and Y are atoms necessaries
19:13 rojasm but R can be there or not and can be anything
19:13 rojasm or it is not good
19:14 rojasm other thing! could you see the mail I sent you
19:14 egonw about C#O?
19:14 egonw yes, replied to it
19:14 rojasm yes
19:14 rojasm ups ok
19:15 egonw sorry, can't focus...
19:15 egonw please ask me tomorrow...
19:15 egonw too tired now...
19:17 rojasm no problem
19:17 egonw OK, going offline...
19:17 rojasm cu
19:17 rojasm ruh dich aus
19:17 rojasm :)
19:17 egonw please check the outcommented code...
19:17 egonw why is it commented out?
19:17 egonw if obsolete, then remove...
19:17 egonw at least add some comment on why it is commented out...
19:17 egonw ok, talk to you later...
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22:16 CIA-18 cdk: miguelrojasch * r10026 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/reaction/type/ (BreakingBondReaction.java CarbonylEliminationReaction.java): corrections with the spelling
23:32 CIA-18 cdk: miguelrojasch * r10027 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ReactionStructuresTest.java: added new test

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