Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-11

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

All times shown according to UTC.

Time Nick Message
02:39 jbrefort joined #cdk
02:46 CIA-32 jmol: hansonr * r9474 /trunk/Jmol/src/org/jmol/ (15 files in 7 dirs): (log message trimmed)
02:46 CIA-32 jmol: version=11.5.40_dev axes, echo
02:46 CIA-32 jmol: # new feature: axes position x [%] y [%]
02:46 CIA-32 jmol: # sets the axes to the x y screen position or percent indicated.
02:46 CIA-32 jmol: # bug fix: echos with active script and a model designation
02:46 CIA-32 jmol: # and multiple models select even if not displayed because it is not their model
02:46 CIA-32 jmol: # that is displayed.
04:04 egonw joined #cdk
06:23 thomas_ku_ joined #cdk
06:29 thomas_ku_ moin
06:51 rojasm joined #cdk
07:07 jonalv joined #cdk
07:34 CIA-32 cdk: miguelrojasch * r11310 /cdk/trunk/src/test/org/openscience/cdk​/formula/MolecularFormulaSetTest.java: test checking if is setting correctly the ID of ChemModel and MoleculeSet objects
07:38 CIA-32 cdk: miguelrojasch * r11311 /cdk/trunk/src/ (2 files in 2 dirs): Correction of the algorithm extracting EC. It was a bug losing information. Added test.
08:17 egonw joined #cdk
08:17 thomas_ku moin
08:50 egonw joined #cdk
09:10 jbrefort joined #cdk
09:35 steinbeck joined #cdk
09:37 steinbeck egonw: around?
09:38 egonw yes
09:38 steinbeck we at some time had a folding@home group. Was it jmol?
09:38 egonw yes
09:38 egonw mom
09:39 steinbeck the team is also just called "jmol"? Upper/lower case important?
09:39 egonw http://wiki.jmol.org:81/index.​php/Folding_At_Home_Community
09:39 steinbeck cool.
09:39 steinbeck Are you still "folding" yourself?
09:40 egonw no
09:42 egonw never took time to install it on my new machines
10:07 egonw steinbeck: how was noordwijkerhout?
10:08 steinbeck quite ok. A bit of a step down in terms of food, as compared to Bozen the week ago :-)
10:13 egonw :)
10:13 egonw did you blog about it?
10:16 egonw not yet, at least
10:28 steinbeck will probably not do it
10:28 * steinbeck is off for lunch now
10:29 steinbeck left #cdk
11:14 CIA-32 cdk: egonw * r11312 /cdk/trunk/src/main/org/openscie​nce/cdk/dict/data/elements.owl: Added an OWL version of a template chemical element ontology
11:14 CIA-32 cdk: egonw * r11313 /cdk/trunk/src/main/org/openscie​nce/cdk/dict/data/elements.xml: Removed thought experiment
11:46 CIA-32 cdk: miguelrojasch * r11314 /cdk/trunk/src/ (2 files in 2 dirs): Added the nitrogen rule to validate Elemental composition and tests
14:04 CIA-32 cdk: rajarshi * r11315 /cdk/trunk/src/main/org/openscie​nce/cdk/qsar/descriptors/atomic/ (12 files): Updated atomic descriptors to use the non-deprecated version of the DescriptorValue constructor
14:29 CIA-32 cdk: rajarshi * r11316 /cdk/trunk/src/main/org/openscie​nce/cdk/io/MDLV2000Reader.java:
14:29 CIA-32 cdk: Updated code to handle extra spaces at the end of the file. Addresses bug
14:29 CIA-32 cdk: 1974826. The idea is that if the atom/bond count line is 0 length we are eiter
14:29 CIA-32 cdk: at a malformed molecule (so read on till the next $$$$) or else we have a bunch
14:29 CIA-32 cdk: of empty space at the end of the SD file. The fix handles both cases
15:08 rojasm egonw can I obtain the valence of a atom without using CDKAtomTypeMatch? is it only with AtomValenceTool method possible?
15:09 egonw isn't there always atom type info involved?
15:09 egonw e.g. oxidation state?
15:09 rojasm not! it is only to apply the lewis rule from EC
15:11 egonw ummm... what makes you see atom type perception is involved?
15:11 rojasm not it is not
15:12 rojasm It was the only method that I remembered extracting this information
15:12 egonw so, what is the problem/question exactly>
15:12 egonw ?
15:12 rojasm but I see now that iin SMARTSQueryTool
15:13 rojasm is creating a Map with Elements vs valence
15:13 egonw that should/could be reusing AtomValenceTool
15:13 egonw feel free to file a bug report
15:13 rojasm but atomValenceTool is qsar modul
15:14 egonw ok, will fix that
15:14 egonw no need for that
15:16 rojasm In what module will you put?
15:16 rojasm valencycheck?
15:16 CIA-32 cdk: egonw * r11317 /cdk/trunk/src/main/org/openscien​ce/cdk/qsar/AtomValenceTool.java: Moving to standard; TODO: move to better package; add unit tests
15:16 egonw standard
15:16 rojasm ok perfect
15:19 rojasm thanks
15:19 rojasm egonw
15:24 egonw yes?
15:36 carsten joined #cdk
15:57 jpansanel moin
16:05 CIA-32 cdk: rajarshi * r11318 /cdk/trunk/src/ (2 files in 2 dirs): Added support for simple angle constraints between 3 pharmacophore groups
16:24 CIA-32 cdk: rajarshi * r11319 /cdk/trunk/src/ (2 files in 2 dirs): Added angle c onstraint support for the pcore query bond types
16:50 CIA-32 cdk: rajarshi * r11320 /cdk/trunk/src/data/pcore/pcoreangle.xml: Added an example definiton for the pcore angle constraints
16:58 jpansane1 joined #cdk
17:17 jbrefort joined #cdk
17:22 jpansanel joined #cdk
17:42 CIA-32 cdk: miguelrojasch * r11321 /cdk/trunk/src/ (2 files in 2 dirs): Nitrogen rule adapted to EC with charge
18:03 CIA-32 joined #cdk
18:04 CIA-23 joined #cdk
19:18 CIA-23 joined #cdk
19:29 rojasm joined #cdk
19:31 CIA-23 jmol: nicove * r9475 /trunk/Jmol-FAH/projects/p784.xyz.gz: Folding@Home
19:52 rojasm joined #cdk
19:55 CIA-23 cdk: rajarshi * r11323 /cdk/trunk/src/data/pcore/pcoreangle.xml: Fixed a typo
20:44 CIA-23 cdk: rajarshi * r11324 /cdk/trunk/src/ (2 files in 2 dirs): Added support for handling and mathcing angle constraints
21:35 CIA-23 cdk: rajarshi * r11325 /cdk/trunk/src/ (2 files in 2 dirs):
21:35 CIA-23 cdk: Updated code so that the when retrieving matching constraints we return all the
21:35 CIA-23 cdk: different types of matching constraints (distance and angle). Clients should
21:35 CIA-23 cdk: coerce the IBond objects to the appropriate pharmacophore bond classes
23:01 azeem joined #cdk

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