Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-15

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All times shown according to UTC.

Time Nick Message
01:00 jbrefort joined #cdk
06:40 jbrefort joined #cdk
07:00 CIA-31 jmol: nicove * r8417 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
07:04 CIA-31 jmol: nicove * r8418 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
07:29 jpansanel moin
08:15 jonalv joined #cdk
08:27 egonw joined #cdk
08:33 egonw moin
08:37 jonalv hi
08:49 rojasm joined #cdk
09:55 carsten joined #cdk
09:59 egonw lunch time
11:12 thomas_ku joined #cdk
11:12 thomas_ku moin
11:12 egonw hi thomas_ku
11:12 thomas_ku hi egonw
11:22 CIA-31 cdk: egonw * r9078 /branches/cdk-1.0.x/src/org/opens​cience/cdk/smiles/smarts/parser/: Ignore autogenerated files.
11:24 CIA-31 cdk: egonw * r9079 /branches/cdk-1.0.x/src/org/openscience/cdk/qs​ar/descriptors/atomic/IPAtomicDescriptor.java: Renamed container to localClone to clear up code. Fixed a bug where the uncloned atoms was searched in the cloned atomcontainer. More bugs like this are in the code. Miguel is contacted about this problem.
11:32 CIA-31 cdk: egonw * r9080 /trunk/cdk/src/org/openscience/cdk/qsar/de​scriptors/atomic/IPAtomicDescriptor.java: Merged r9079: Renamed container to localClone to clear up code. Fixed a bug where the uncloned atoms was searched in the cloned atomcontainer. More bugs like this are in the code.
11:32 CIA-31 cdk: egonw * r9081 /trunk/cdk/src/org/openscience/cdk/​test/smiles/SmilesParserTest.java: Kations instead of solids; CDK does not do solids.
11:48 CIA-31 cdk: egonw * r9082 /branches/cdk-1.0.x/src/org/opens​cience/cdk/qsar/descriptors/bond/ (IPBondDescriptor.java ResonancePositiveChargeDescriptor.java): Renamed container to localClone to clear up code. Fixed a bug where the uncloned atoms was searched in the cloned atomcontainer.
11:49 CIA-31 cdk: egonw * r9083 /trunk/cdk/src/org/openscienc​e/cdk/qsar/descriptors/bond/ (IPBondDescriptor.java ResonancePositiveChargeDescriptor.java): Merged r9082: Renamed container to localClone to clear up code. Fixed a bug where the uncloned atoms was searched in the cloned atomcontainer. Just like 9080.
12:00 CIA-31 cdk: egonw * r9084 /trunk/cdk/src/org/openscience/cdk/qsar/result/ (DoubleArrayResult.java IntegerArrayResult.java): Now uses generics.
12:01 CIA-31 cdk: egonw * r9085 /branches/cdk-1.0.x/patches.txt: Updated for current status.
12:17 CIA-31 bioclipse: egonw * r3978 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Fixed checking if IDs are empty: when getting column name, look at the column ids, not the row ids :)
12:27 CIA-31 bioclipse: egonw * r3979 /trunk/plugins/net.bioclipse.cdk/ (34 files in 2 dirs): Uploaded 1.0.2 pre
12:29 CIA-31 jmol: hansonr * r8419 /trunk/Jmol/src/org/jmol/ (10 files in 6 dirs): version=11.3.33 # povray for polyhedra, and crudely for mesh, single-color isosurface
12:33 CIA-31 bioclipse: egonw * r3980 /trunk/plugins/net.bioclipse.cdk.jchemp​aint/src/net/bioclipse/plugins/bc_jchem​paint/editors/JCPMultiPageEditor.java: Update with respect to CDK 1.0.2 prerelease.
14:11 carsten joined #cdk
15:48 CIA-31 jmol: hansonr * r8420 /branches/v11_2/Jmol/src/org/jmol/ (shapebio/RocketsRenderer.java viewer/Jmol.properties): 11.2.15 # bug fix: rockets color incorrect for head groups
16:11 CIA-31 jmol: gutow * r8421 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (8 files):
16:11 CIA-31 jmol: Modifications to Web Page Maker Dialog
16:11 CIA-31 jmol: Added Intro Tab
16:11 CIA-31 jmol: Added minilog at bottom
16:11 CIA-31 jmol: Replaces instructions on each tab with a help/instructions button. Instructions now open in a Jmol Help dialog.
16:11 CIA-31 jmol: Some refactoring and minor code cleanup
16:15 CIA-31 jmol: gutow * r8422 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: update to Jmol.properties to reflect web export changes
17:26 CIA-31 jmol: hansonr * r8423 /trunk/Jmol/src/org/jmol/ (15 files in 6 dirs):
17:26 CIA-31 jmol: version=11.3.33_dev # _PovrayExporter adds polyhedra, pmesh, backbone, cartoons,
17:26 CIA-31 jmol: # meshRibbon, ribbon, rockets, trace, dots, geosurface, molecular orbitals,
17:26 CIA-31 jmol: # LCAO cartoons, single-color isosurfaces
17:39 CIA-31 jmol: hansonr * r8424 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs):
17:39 CIA-31 jmol: version=11.3.33_dev
17:39 CIA-31 jmol: # _PovrayExporter adds polyhedra, vectors, pmesh, backbone, cartoons,
17:39 CIA-31 jmol: # meshRibbon, ribbon, rockets, trace, dots, geosurface, molecular orbitals,
17:39 CIA-31 jmol: # LCAO cartoons, single-color isosurfaces
17:56 CIA-31 jmol: hansonr * r8425 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs):
17:56 CIA-31 jmol: version=11.3.33_dev
17:56 CIA-31 jmol: # _PovrayExporter adds draw, vectors, polyhedra, backbone, cartoons,
17:56 CIA-31 jmol: # meshRibbon, ribbon, rockets, trace, dots, geosurface, molecular orbitals,
17:56 CIA-31 jmol: # LCAO cartoons, pmesh, single-color isosurfaces
18:05 CIA-31 jmol: nicove * r8426 /trunk/Jmol-FAH/projects/ (p3739.xyz.gz p3740.xyz.gz): Folding@Home
18:10 egonw_ joined #cdk
18:14 carsten joined #cdk
18:46 CIA-31 jmol: hansonr * r8427 /trunk/Jmol/src/org/jmol/ (9 files in 5 dirs):
18:46 CIA-31 jmol: version=11.3.33_dev
18:46 CIA-31 jmol: # _PovrayExporter adds draw, halos, stars, dipoles, vectors, polyhedra,
18:46 CIA-31 jmol: # backbone, cartoons, meshRibbon, ribbon, rockets, strands, trace,
18:46 CIA-31 jmol: # dots, geosurface, molecular orbitals, LCAO cartoons, pmesh,
18:46 CIA-31 jmol: # single-color isosurfaces
19:06 CIA-31 jmol: hansonr * r8428 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties JmolConstants.java): version=11.2.15_dev # adds "OP1" and "OP2" as backbone designators (new PDB designation)
19:07 CIA-31 jmol: hansonr * r8429 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: version=11.3.33_dev # adds "OP1" and "OP2" as backbone designators (new PDB designation)
19:07 CIA-31 jmol: hansonr * r8430 /branches/v11_2/Jmol/src/org/jmol/viewer/ (Jmol.properties JmolConstants.java): version=11.2.15_dev # adds "OP1" and "OP2" as backbone designators (new PDB designation)
21:33 CIA-31 jmol: hansonr * r8431 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs): (log message trimmed)
21:33 CIA-31 jmol: version=11.3.33_dev # new feature: site_ support for PDB and CIF
21:33 CIA-31 jmol: #
21:33 CIA-31 jmol: # loading of PDB and CIF files containing site information
21:33 CIA-31 jmol: # automatically defines variables site_xxx and defines selections site_xxx and site_n
21:33 CIA-31 jmol: # where xxx is the site identifier and n is the site number.
21:33 CIA-31 jmol: # These settings are reset each time a file is loaded.
21:45 CIA-31 jmol: hansonr * r8432 /trunk/Jmol/src/org/jmol/adapter/sm​arter/AtomSetCollectionReader.java: (log message trimmed)
21:45 CIA-31 jmol: version=11.3.33_dev # new feature: site_ support for PDB and CIF
21:45 CIA-31 jmol: #
21:45 CIA-31 jmol: # loading of PDB and CIF files containing site information
21:45 CIA-31 jmol: # automatically defines variables site_xxx and defines selections site_xxx and site_n
21:45 CIA-31 jmol: # where xxx is the site identifier and n is the site number.
21:45 CIA-31 jmol: # These settings are reset each time a file is loaded.
22:08 CIA-31 jmol: hansonr * r8433 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties):
22:08 CIA-31 jmol: version=11.3.33_dev # new feature: inline scripting allows math
22:08 CIA-31 jmol: #
22:08 CIA-31 jmol: # script INLINE "select " + site_list[2]
23:58 CIA-31 jmol: hansonr * r8434 /trunk/Jmol/src/org/jmol/adapter/sm​arter/AtomSetCollectionReader.java:
23:58 CIA-31 jmol: version=11.3.33_dev # new feature: inline scripting allows math
23:58 CIA-31 jmol: #
23:58 CIA-31 jmol: # script INLINE "select " + site_list[2]
23:58 CIA-31 jmol: adding protection against non-alphanumeric characters in site_ids.

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