Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-12

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All times shown according to UTC.

Time Nick Message
04:10 CIA-23 jmol: hansonr * r9476 /trunk/Jmol/src/org/jmol/ (27 files in 5 dirs): (log message trimmed)
04:10 CIA-23 jmol: version=11.5.40_dev draw/axes [x y]
04:10 CIA-23 jmol: # new feature: draw Vector [x y] or [x y %] {x' y' z'}
04:10 CIA-23 jmol: # new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows
04:10 CIA-23 jmol: # bug fix: set picking center should not zoom -- just too annoying
04:10 CIA-23 jmol: # new feature: set echo myecho [x y] and set echo myecho [x y %]
04:10 CIA-23 jmol: # new feature: axes position [x y] and axes position [x y %]
04:11 CIA-23 jmol: hansonr * r9477 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: version=11.5.40_dev # new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental]
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07:14 thomas_ku moin
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08:05 jpansanel moin
09:28 CIA-23 cdk: ospjuth * r11326 /cdk/trunk/META-INF/MANIFEST.MF: Updated manifest to export new packages for other Eclipse plugins.
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14:53 CIA-23 cdk: rajarshi * r11327 /cdk/trunk/src/ (5 files in 3 dirs): (log message trimmed)
14:53 CIA-23 cdk: Updated core Bond class to support multi-center bonds. Right now the class will
14:53 CIA-23 cdk: handle multiple atoms in a bond and the related semantics of checking for
14:53 CIA-23 cdk: connectedness, containing atom, iterating etc are all updated for multi-center
14:53 CIA-23 cdk: bonds. However at this point, the bond orders available (single, double etc) may
14:53 CIA-23 cdk: not make sense for multi-center bonds. As a result, more work may be required to
14:53 CIA-23 cdk: provide comprehenive support. The update is backwards cmpatible and code that
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14:55 CIA-23 cdk: rajarshi * r11328 /cdk/trunk/src/main/org/ope​nscience/cdk/pharmacophore/ (PharmacophoreAngleBond.java PharmacophoreQueryAngleBond.java): Updated to use the new multi-center bond constructor
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15:35 CIA-23 cdk: rajarshi * r11329 /cdk/trunk/src/main/org/openscien​ce/cdk/interfaces/IIsotope.java: Fixed a Javadoc
15:43 CIA-23 cdk: rajarshi * r11330 /cdk/trunk/src/main/org/openscienc​e/cdk/config/IsotopeFactory.java: Updated Javadocs
15:55 CIA-23 cdk: rajarshi * r11331 /cdk/trunk/src/main/org/openscience/cdk​/renderer/old/AbstractRenderer2D.java: Updated renderer to check that mass number has been set - if not, then isotopic labels will not be used
16:06 CIA-23 cdk: rajarshi * r11332 /cdk/trunk/src/main/org/openscience/cdk/debug/ (DebugBond.java DebugChemObjectBuilder.java): Updated debug versions of the bond class for the new multi-center constructors
16:20 CIA-23 cdk: rajarshi * r11333 /cdk/trunk/src/main/org/openscience/cdk/nonotify/ (NNBond.java NoNotificationChemObjectBuilder.java): Updated NN versions of the bond class for the new multi-center constructors
16:26 CIA-23 cdk: rajarshi * r11334 /cdk/trunk/src/main/org/openscience/​cdk/formula/MassToFormulaTool.java: Removed erroneous imports
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17:27 egonw hi rguha
17:29 rguha hi egonw
17:29 rguha hows the ummer going?
17:29 rguha summer
17:29 egonw bit colder now :)
17:29 rguha aah, hitting 30C here :)
17:30 egonw yeah, that's bad...
17:30 egonw it's not been that hot here yet...
17:30 egonw but I expect that this summer again
17:30 rguha good for cycling as long as there is a breeze
17:30 egonw true
17:33 rguha did you see my post regarding VdW radii?
17:34 egonw yes, but not read it yet :)
17:34 egonw browsing todays email
17:34 rguha aah ok
17:34 rguha btw, nice CDK usage in Scripps, FL
17:35 egonw oh?
17:35 egonw I missed that...
17:35 egonw details?
17:35 rguha on cdk-user
17:35 rguha relatedto strctre depiction
17:35 egonw oh, that export email?
17:35 rguha some nice helper classes which I think could be merged into trunk
17:35 rguha yes
17:35 egonw did not read it properly yet
17:39 rguha btw, are yo and/or Christoph going to make it to the ACS in August?
17:40 egonw I will not
17:40 egonw not sure about Christoph
17:40 egonw being in metabolomics now, it's more difficult to go to chemo conferecnes
17:40 rguha aah
17:42 egonw that nonotify thing in MassToFormula is now fixed, right?
17:44 rguha yes - just an unused import messing things up
17:45 egonw ok, good
17:47 * egonw feels he has to soon leave for dinner
17:49 egonw rguha: will do some more OWL work tonite
17:49 rguha ok
17:49 * egonw has had a nasty cold the last 48-ish hours
17:49 egonw which should include the OWL mapping stuff
17:49 rguha ok
18:14 CIA-23 cdk: rajarshi * r11335 /cdk/trunk/src/main/org/openscience​/cdk/config/ElementPTFactory.java: Updated to provide access to all the elements loaded from the config file
18:19 CIA-23 cdk: rajarshi * r11336 /cdk/trunk/src/main/org/openscien​ce/cdk/config/data/radii-vdw.txt: Added the VdW radii from the BODR. This seems more reliable than the Jmol derived radii since it is referenced
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19:24 CIA-23 cdk: rajarshi * r11337 /cdk/trunk/src/main/org/openscience/cd​k/config/data/electroneg-pauling.txt: Added Pauling electroneg values for use in the Periodic Table class
19:41 CIA-23 cdk: rajarshi * r11338 /cdk/trunk/src/main/org/openscien​ce/cdk/PeriodicTableElement.java: Updated to provide getters and setters for vdw radii and pauling eneg values
19:46 CIA-23 cdk: rajarshi * r11339 /cdk/trunk/src/ (3 files in 3 dirs):
19:46 CIA-23 cdk: Added a class and associated test representing the periodic table. Allows the
19:46 CIA-23 cdk: user to retireve element propertis that are independent of atom types.
19:46 CIA-23 cdk: Properties include group, phase, at num, VdW radii and Pauling
19:46 CIA-23 cdk: electronegativity. This is essentially a wrapper round PeriodicTableElement, but
19:46 CIA-23 cdk: does not require any explicit object instantitation. All methods are static and
19:46 CIA-23 cdk: lookup is based on element symbol
19:50 CIA-23 cdk: rajarshi * r11340 /cdk/trunk/src/main/org/openscience/cdk/​geometry/surface/NumericalSurface.java: Updated surface area code to use the VdW values from the Periodic table class rather than via configuration derived from Jmol types
19:53 CIA-23 cdk: rajarshi * r11341 /cdk/trunk/src/main/org/openscience/cdk/​geometry/surface/NumericalSurface.java: Updated surface area code to use the VdW values from the periodic table class
20:01 CIA-23 cdk: rajarshi * r11342 /cdk/trunk/src/main/org/ope​nscience/cdk/AtomType.java: Marked the getter for VdW as deprectated since these values should now come from the PeriodicTable class
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20:58 CIA-23 cdk: rajarshi * r11343 /cdk/trunk/src/main/org/ope​nscience/cdk/pharmacophore/ (PharmacophoreQueryAngleBond.java PharmacophoreQueryBond.java): Added getter for the lower and upper values of the constraints. Required for serialization of a pcore query
21:33 CIA-23 cdk: rajarshi * r11344 /cdk/trunk/src/ (2 files in 2 dirs): Added a helper method to write out pharmacophore queries to disk using the CDK XML format
21:50 CIA-23 cdk: rajarshi * r11345 /cdk/trunk/src/main/org/openscien​ce/cdk/tools/PeriodicTable.java: Minor modification to ensure that we only initialize on the first usage of this class

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