Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-13

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
05:03 bag joined #cdk
05:15 bag joined #cdk
05:37 Conrad joined #cdk
05:43 egonw joined #cdk
06:12 egonw joined #cdk
06:16 jbrefort joined #cdk
06:53 carsten joined #cdk
07:02 jonalv joined #cdk
07:03 thomas_ku joined #cdk
07:24 rojasm joined #cdk
07:26 thomas_ku moin
07:26 malick joined #cdk
07:36 jonalv left #cdk
08:01 jonalv joined #cdk
08:03 jonalv joined #cdk
08:05 rojasm hi all
08:05 rojasm one question; is there in cdk one method to extract the valence-state of a element?
08:07 rojasm nitrogen III
08:07 rojasm for example
08:13 thomas_ku joined #cdk
08:14 egonw joined #cdk
08:14 rojasm 10:05:32 AM) rojasm: hi all
08:14 rojasm (10:05:58 AM) rojasm: one question; is there in cdk one method to extract the valence-state of a element?
08:14 rojasm (10:07:06 AM) rojasm: nitrogen III
08:14 rojasm (10:07:11 AM) rojasm: for example
08:14 CIA-23 cdk: miguelrojasch * r11346 /cdk/trunk/src/main/org/openscie​nce/cdk/dict/data/elements.owl: added name of elements in spanish for dictionary.
08:14 egonw the oxidation state?
08:15 egonw basically, that would happen via atom typing
08:15 rojasm yes but what happens if you don't have the structure
08:15 rojasm and you would like to receive all possible
08:15 rojasm N = I, III, V and so on
08:16 CIA-23 cdk: miguelrojasch * r11347 /cdk/trunk/src/main/org/openscie​nce/cdk/dict/data/elements.owl: missed one
08:16 egonw ah, ic
08:16 egonw the common oxidation states
08:16 egonw umm... iterate over all atom types?
08:16 rojasm yes! that
08:16 rojasm ok
08:18 rojasm but we could include in the elements.owl dictionary, maybe?
08:28 egonw no, not in that one...
08:29 egonw more OWL stuff pending...
08:29 egonw will blog about it asap
08:30 rojasm ok! but I see that is a bit complicate to specify the correct. There are to many possibilities
08:30 rojasm http://en.wikipedia.org/wiki/List​_of_oxidation_numbers_by_element
09:02 CIA-23 cdk: miguelrojasch * r11348 /cdk/trunk/src/ (2 files in 2 dirs): Added the Ring Double Bond Equivalents rule to validate elemental composition
09:20 shk3 joined #cdk
09:20 CIA-23 cdk: shk3 * r11349 /cdk/branches/cdk-1.0.x/src/org/openscience/c​dk/modeling/builder3d/TemplateHandler3D.java: Fixes bug #1315823 and probably #1458647
09:21 CIA-23 cdk: shk3 * r11350 /cdk/trunk/src/main/org/openscience/cdk/m​odeling/builder3d/TemplateHandler3D.java: Fixes bug #1315823 and probably #1458647
09:23 thomas_ku_ joined #cdk
09:42 thomas_ku joined #cdk
10:27 jpansanel moin
10:28 jpansanel Mychem works now on Win32 :)
10:55 CIA-23 cdk: shk3 * r11351 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/​test/modeling/builder3d/ModelBuilder3dTest.java: added a test for bug #1241421 (which seems to be fixed)
11:06 CIA-23 cdk: egonw * r11352 /cdk/trunk/src/test/org/openscience​/cdk/tools/PeriodicTableTest.java: Use the proper assert() method. Not sure why this does show up as an error for everyone...
11:09 shk3 hi egonw
11:09 egonw hi shk3
11:09 egonw thanx for the builder3d fixes!
11:09 shk3 you are welcome
11:10 egonw have not tried it yet, but the unit tests not failing again sounds really promosing!
11:10 shk3 there is still one unit test failing: test_LocalWorkerModel3DBuildersWithMM2ForceField
11:10 shk3 do you know what this is about?
11:10 shk3 what is a local worker?
11:10 egonw the patch suggests that it was not really the template look up by fingerprint
11:10 egonw but some final check, is that correct?
11:10 shk3 no
11:10 egonw no correct?
11:10 shk3 that was probably fixed by christoph
11:10 shk3 correct
11:10 egonw ok
11:10 shk3 the problem was the following:
11:11 shk3 it went throuhg all templates looking if the template was a _sub_graph of the rings to lay out
11:11 shk3 so it found the "surrounding ring" as well.
11:11 shk3 there was a test which should obviously avoid this,
11:11 shk3 but it was just to compare the atom counts
11:12 shk3 which is not enough if rings are just merged "via one bond"
11:12 * egonw will go into a meeting right now
11:12 shk3 ok
11:12 shk3 see you later
11:12 egonw will see if we can get the 3D stuff online in BC2 today
11:38 CIA-23 jmol: hansonr * r9478 /trunk/Jmol/src/org/jmol/ (11 files in 3 dirs): (log message trimmed)
11:38 CIA-23 jmol: version=11.5.40_dev new select() function; H1/H3 fix; quaternion second derivative
11:38 CIA-23 jmol: # new feature: full math on individual atom properties using
11:38 CIA-23 jmol: # a new function:
11:38 CIA-23 jmol: #
11:38 CIA-23 jmol: # select(x;{atomexpression};booleanEvaluation)
11:38 CIA-23 jmol: #
11:48 CIA-23 jmol: hansonr * r9479 /trunk/Jmol/src/org/jmol/viewer/Eval.java: (log message trimmed)
11:48 CIA-23 jmol: version=11.5.40_dev new select() function; H1/H3 fix; quaternion second derivative
11:48 CIA-23 jmol: # new feature: full math on individual atom properties using
11:48 CIA-23 jmol: # a new function:
11:48 CIA-23 jmol: #
11:48 CIA-23 jmol: # select(x;{atomexpression};booleanEvaluation)
11:48 CIA-23 jmol: #
12:08 CIA-23 jmol: hansonr * r9480 /trunk/Jmol/src/org/jmol/viewer/Token.java: (log message trimmed)
12:08 CIA-23 jmol: version=11.5.40_dev new select() function; H1/H3 fix; quaternion second derivative
12:08 CIA-23 jmol: # new feature: full math on individual atom properties using
12:08 CIA-23 jmol: # a new function:
12:08 CIA-23 jmol: #
12:08 CIA-23 jmol: # select(x;{atomexpression};booleanEvaluation)
12:08 CIA-23 jmol: #
12:24 thomas_ku shk3: the  test_LocalWorkerModel3DBuildersWithMM2ForceField sounds like a test of cdk-taverna
12:25 thomas_ku there a local worker is used as worker for taverna
12:25 thomas_ku where did you saw this failing?
12:33 shk3 in my eclipse
12:43 thomas_ku ok thats really strange
12:43 thomas_ku did you checked out the cdk-taverna part?
12:43 shk3 no
12:43 shk3 just the cdk-1.0.x trunk
12:48 thomas_ku no idea why this test is called local worker...
12:48 thomas_ku it is possible that he just call it like this because he mainly worked on cdk-taverna
12:49 shk3 so it's basically testing 3d generation, right?
12:49 shk3 and the error seems to be a modelbuilder one?
12:49 shk3 (it's an npe in ModelBuilder3D actually)
12:49 thomas_ku I have not run the test I just looked on the web for it
12:50 shk3 yes
12:51 shk3 but no taverna code in there, is it?
12:52 thomas_ku yes the is no taverna code in there
12:52 thomas_ku did you looked at the bug description http://sourceforge.net/tracker/inde​x.php?func=detail&aid=1610997&a​mp;group_id=20024&atid=120024
12:53 shk3 sorry, no
12:53 shk3 didn't realize there is one
12:53 shk3 ah, it's the flag problem
12:53 shk3 this is on my agenda mittelfristig
12:54 thomas_ku ok perhaps we should rename the method?
12:56 shk3 yes
12:56 CIA-23 cdk: shk3 * r11353 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/​test/layout/StructureDiagramGeneratorTest.java: added a test for bug #1930186
12:56 thomas_ku thanks
13:00 CIA-23 cdk: shk3 * r11354 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/​test/modeling/builder3d/ModelBuilder3dTest.java: renamed a test
13:02 CIA-23 cdk: shk3 * r11355 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/​test/layout/StructureDiagramGeneratorTest.java: too fast with last commit
13:16 egonw_ joined #cdk
14:35 CIA-23 jmol: hansonr * r9481 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java Jmol.properties Token.java): (log message trimmed)
14:35 CIA-23 jmol: version=11.5.40_dev selectX
14:35 CIA-23 jmol: # new feature: new command:
14:35 CIA-23 jmol: #
14:35 CIA-23 jmol: # selectx {atomExpression} booleanEvaluation
14:35 CIA-23 jmol: #
14:35 CIA-23 jmol: # same as select() function, but simpler to implement
14:37 CIA-23 jmol: hansonr * r9482 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: (log message trimmed)
14:37 CIA-23 jmol: 11.5.40 VERSION
14:37 CIA-23 jmol: # new feature: new command:
14:37 CIA-23 jmol: #
14:37 CIA-23 jmol: # selectx {atomExpression} booleanEvaluation
14:37 CIA-23 jmol: #
14:37 CIA-23 jmol: # same as select() function, but simpler to implement
14:59 rguha joined #cdk
15:05 egonw_ hi rguha
15:05 * egonw_ is about to go offline
15:05 rguha hi egon
15:06 rguha what do you think about removing getVanderwaalsRadius() from AtomType?
15:08 CIA-23 jmol: hansonr * r9483 /trunk/Jmol/src/org/jmol/viewer/Eval.java: (log message trimmed)
15:08 CIA-23 jmol: 11.5.40 VERSION (b)
15:08 CIA-23 jmol: # new feature: new command:
15:08 CIA-23 jmol: #
15:08 CIA-23 jmol: # selectx {atomExpression} booleanEvaluation
15:08 CIA-23 jmol: #
15:08 CIA-23 jmol: # same as select() function, but simpler to implement
15:08 egonw_ I second that
15:08 rguha ok, I'll go ahead start cleaning that up
15:08 egonw_ but I even rather see a redesign of the core classes
15:08 egonw_ let's wait for Christoph's confirmation
15:09 rguha oh ok
15:09 rguha what do you mean redeign?
15:09 rguha I was hoping for minimal changes in the core classes
15:10 egonw_ make IAtom have a field IAtomType instead of extending it
15:10 egonw_ so, that if not AT info is present the field would be NULL
15:10 CIA-23 jmol: hansonr * r9484 /trunk/Jmol/src/org/jmol/viewer/Eval.java: (log message trimmed)
15:10 CIA-23 jmol: 11.5.40 VERSION (c)
15:10 CIA-23 jmol: # new feature: new command:
15:10 CIA-23 jmol: #
15:10 CIA-23 jmol: # selectx {atomExpression} booleanEvaluation
15:10 CIA-23 jmol: #
15:10 CIA-23 jmol: # same as select() function, but simpler to implement
15:11 rguha aah, good point
15:11 rguha I think that would implify a lot of things
15:11 rguha i'll send a mail to the list regarding the VdW issue so that it's up for discussion
15:12 egonw_ ok
15:12 shk3 egonw: just fixing minor stuff in nmrshiftdb
15:12 shk3 what do you think about hydrogen count in cml?
15:12 shk3 if there are explicit Hs,
15:12 egonw_ shk3: later
15:13 shk3 should hydrogenCount contain them or not?
15:13 egonw_ about to be on a phone call now
15:13 egonw_ rguha: mom, on the phone
15:13 shk3 I will do one as well
15:24 egonw_ CML counts *all* hydrogens, IIRC
15:24 egonw_ rguha: just asked Christoph about vdw radius
15:24 egonw_ he'll read the email and reply
15:24 egonw_ rguha: regarding IAtom.getAtomType()...
15:25 egonw_ that would be a new trunk branch...
15:25 egonw_ with the current branch leading to 1.2 or so...
15:25 egonw_ but we could start discussing the (dis)advantages...
15:25 egonw_ maybe a simple reference impl for performance testing...
15:26 egonw_ IAtom.getElement() and IAtom.getIsotope() would need to get introduced too...
15:26 egonw_ anyway... got to run now...
16:05 jbrefort joined #cdk
16:08 CIA-23 cdk: rajarshi * r11356 /cdk/trunk/src/main/org/openscience/cdk/qsar/​descriptors/atomic/VdWRadiusDescriptor.java: Updated code to use VdW radii from the periodic table rather than atom typing
16:10 CIA-23 cdk: rajarshi * r11357 /cdk/trunk/src/main/org/openscience/c​dk/protein/ProteinPocketFinder.java: Updated code to use VdW radii from the periodic table rather than atom typing
16:19 CIA-23 cdk: rajarshi * r11358 /cdk/trunk/src/main/org/openscience/cdk/ (AtomType.java interfaces/IAtomType.java): Marked the vwd radius getter/setter as deprecated in anticipation of removal.
17:02 bag joined #cdk
17:04 CIA-23 cdk: miguelrojasch * r11359 /cdk/trunk/src/ (2 files in 2 dirs):
17:04 CIA-23 cdk: The rule RDBE is not only based on the lower valence states. It will check all possible combinations. So for CHS we will have:
17:04 CIA-23 cdk: CHS(II),CHS(IV),CHS(VI) which for the last one with a RDBE of 0, can be accept
19:16 rojasm joined #cdk
21:03 CIA-23 cdk: miguelrojasch * r11360 /cdk/trunk/src/ (2 files in 2 dirs): added negative score when the experimental m/z is not found in the spectra
22:28 CIA-23 jmol: hansonr * r9485 /trunk/Jmol/src/org/jmol/ (shapespecial/Draw.java viewer/Jmol.properties):
22:28 CIA-23 jmol: 11.5.40 VERSION (d)
22:28 CIA-23 jmol: # (with corrected 40_dev draw scale)

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary