Camelia, the Perl 6 bug

IRC log for #cdk, 2008-07-08

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All times shown according to UTC.

Time Nick Message
01:04 Conrad joined #cdk
03:43 egonw joined #cdk
05:04 thomas_ku moin
05:41 rojasm joined #cdk
06:00 jbrefort joined #cdk
07:11 egonw joined #cdk
07:34 rojasm joined #cdk
07:55 jonalv joined #cdk
09:03 shk3 joined #cdk
11:44 jonalv joined #cdk
12:11 egonw joined #cdk
13:46 egonw thomas_ku: did your commit messages show up here?
14:24 thomas_ku no
14:24 thomas_ku they did not shown up
14:30 egonw ack
14:30 egonw will look into that
15:43 carsten joined #cdk
15:55 rojasm joined #cdk
15:59 CIA-33 jmol: hansonr * r9573 /trunk/Jmol/src/org/ (11 files in 6 dirs): version=11.5.46_dev # new feature: isosurface functionXY can be used for mapping.
17:49 CIA-33 cdk: rajarshi * r11516 /cdk/trunk/src/test/org/openscience/cdk/char​ges/GasteigerMarsiliPartialChargesTest.java: Added a unit test (currently fails) to check that partial charges on the atoms for a molecule derived from different (kekule and aromatic) SMILES match.
17:51 CIA-33 cdk: rajarshi * r11517 /cdk/trunk/src/test/org/openscience/cdk/qsar/d​escriptors/molecular/BCUTDescriptorTest.java:
17:51 CIA-33 cdk: Added a unit test (currently fails) to check that desc values for a molecule
17:51 CIA-33 cdk: derived from different (kekule and aromatic) SMILES match. The reason it fails
17:51 CIA-33 cdk: now is due to a problem in partial charge and polarizabilty calculations
18:32 bag joined #cdk
18:34 CIA-33 jmol: hansonr * r9574 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs): version=11.5.46_dev # new feature: isosurface functionXY can be used for mapping.
18:43 CIA-33 cdk: rajarshi * r11518 /cdk/trunk/src/test/org/openscience/cdk/char​ges/GasteigerMarsiliPartialChargesTest.java: Removed the test for aromatic systems since this class is not meant for pi systems
18:45 CIA-33 cdk: rajarshi * r11519 /cdk/trunk/src/test/org/openscience/cdk/cha​rges/GasteigerPEPEPartialChargesTest.java: Added a unit test to check that partial charges for a molecule derived from two different SMILES, matches
19:34 CIA-33 cdk: rajarshi * r11520 /cdk/trunk/src/test/org/openscience/cdk/cha​rges/GasteigerPEPEPartialChargesTest.java: Added a unit test (that currently fails) which checks whether the bond orders are mainaned after a call to get the pi partial charges
19:50 CIA-33 cdk: rajarshi * r11521 /cdk/trunk/src/ (2 files in 2 dirs):
19:50 CIA-33 cdk: Updated PEPE partial charge code so that the aromaticity flags on the atoms and
19:50 CIA-33 cdk: bonds are maintained on return from the function (since the code appears to wipe
19:50 CIA-33 cdk: out these flags). This fixes bug 2013754. Also modified the code to make the
19:50 CIA-33 cdk: gasteiger iterations variable an integer rather than double
20:02 CIA-33 cdk: rajarshi * r11522 /cdk/trunk/src/main/org/openscienc​e/cdk/charges/Polarizability.java: (log message trimmed)
20:02 CIA-33 cdk: Updated code for the KJ factors so that we first check whether an atom is
20:02 CIA-33 cdk: aromatic rather than check its max bond order. This is because depending on the
20:02 CIA-33 cdk: how the molecule was represented (say a kekule SMILES or an aromatic SMILES) the
20:02 CIA-33 cdk: max bond order might be different for the same atom in the two versions of the
20:02 CIA-33 cdk: molecule. However, assuming aromaticity was detected properly, the given atom in
20:02 CIA-33 cdk: the two versions will be flagged as aromatic. Hence we check for aromaticity
20:07 CIA-33 cdk: rajarshi * r11523 /cdk/trunk/src/main/org/openscience/cdk/qsar/de​scriptors/molecular/ZagrebIndexDescriptor.java: Updated to Java 1.5 idioms
20:17 CIA-33 cdk: rajarshi * r11524 /cdk/trunk/src/test/org/openscience/cdk/qsar/desc​riptors/molecular/ZagrebIndexDescriptorTest.java:
20:17 CIA-33 cdk: Added a unit test to check that if a molecule is derived from SMILES or from a
20:17 CIA-33 cdk: 3D version, they give the same result assuming that explicit h's are added to
20:17 CIA-33 cdk: the SMILES version and typing and aromaticity is performed on both
20:26 CIA-33 cdk: rajarshi * r11525 /cdk/trunk/src/test/org/openscience/cdk/qsar/d​escriptors/molecular/BCUTDescriptorTest.java: Added a test to check that BCUT values for molecules derived from SMILES (aromatic or kekule) will match
20:59 CIA-33 jmol: hansonr * r9575 /trunk/Jmol/src/org/jmol/ (adapter/readers/xml/XmlCmlReader.java viewer/Jmol.properties): version=11.5.46_dev # new feature: spacegroup/symmetry for CML files with <module> tags
21:00 CIA-33 jmol: hansonr * r9576 /trunk/Jmol-datafiles/cml/nacl.cml: NACL cml example
21:01 CIA-33 jmol: hansonr * r9577 /trunk/Jmol-datafiles/adf/adf-2007.out: adf 2007 example
21:02 CIA-33 jmol: hansonr * r9578 /trunk/Jmol-datafiles/tests/scripts/check/ (README.txt monster_script.spt): monster_script.spt should be the same here as in ../run

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