Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-16

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All times shown according to UTC.

Time Nick Message
07:12 jbrefort joined #cdk
09:51 edrin joined #cdk
10:15 CIA-37 cdk: miguelrojasch * r13119 /cdk/branches/cdk-1.2.x/src/main/org/openscie​nce/cdk/formula/IsotopePatternGenerator.java: Removed duplicate method
10:16 CIA-37 cdk: miguelrojasch * r13120 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/formula/rules/RDBERuleTest.java: added missed test
10:20 CIA-37 cdk: miguelrojasch * r13121 /cdk/branches/cdk-1.2.x/src/ (3 files in 3 dirs): Added in MolecularFormulaManipulator the option to choose for set the integer value 1 or not in the character formula when a chemical formula contains an element with one atom.
10:42 egonw joined #cdk
11:36 carsten joined #cdk
11:46 thomasku joined #cdk
11:50 egonw hi thomasku
11:50 egonw all: I found a grave bug in reading aromaticity info for bonds in CDK 1.1.1
11:50 thomasku hi egonw
11:51 thomasku oh that's not good
11:53 egonw will check in a moment if it is present in CDK 1.1.x too...
11:56 CIA-37 cdk: egonw * r13122 /cdk/branches/cdk-1.2.x/src/test/ (5 files in 4 dirs): Added unit test for a file where atom typing failed
11:56 CIA-37 cdk: egonw * r13123 /cdk/branches/cdk-1.2.x/src/main​/org/openscience/cdk/Bond.java: Fixed missing output of ElectronContainer
11:56 CIA-37 cdk: egonw * r13124 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/io/cml/CMLCoreModule.java: Fixed grave bug in reading of bond aromaticity and dict refs
12:00 egonw yes, present in CDK 1.0.4 too :(
12:00 egonw grmp... that will mean a 1.0.5 release
12:00 egonw for which I don't really have time :(
13:52 edrin joined #cdk
16:21 shk3 joined #cdk
16:48 edr1n joined #cdk
16:58 egonw OK, big Sybyl atom type clean up commit batch coming up...
16:59 CIA-37 cdk: egonw * r13125 /cdk/branches/cdk-1.2.x/src/test/org/opensc​ience/cdk/config/AtomTypeFactoryTest.java:
16:59 CIA-37 cdk: Added assertions for missing info in OWL: so far, all I wanted to know was the
16:59 CIA-37 cdk: atom type name... but, deriving properties from Sybyl atom types is currently
16:59 CIA-37 cdk: not possible, and deriving them from CDK atom types neither, as we do not map
16:59 CIA-37 cdk: Sybyl to CDK atom types. I think it would be best to add neighborcount, formal
16:59 CIA-37 cdk: charge, etc to the Sybyl OWL too, which would then also allow us to use
16:59 CIA-37 cdk: reasoning to test the reasonableness of the CDK to Sybyl atom type mapping.
17:00 CIA-37 cdk: egonw * r13126 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added unit tests for the Sybyl atom types; currently fail, because the AbstractAtomTypeTest also tests neighbor counts, etc, which is information that is not yet available from the Sybyl OWL
17:01 CIA-37 cdk: egonw * r13127 /cdk/branches/cdk-1.2.x/src/main/org/opens​cience/cdk/dict/data/sybyl-atom-types.owl: Added many missing properties
17:02 CIA-37 cdk: egonw * r13128 /cdk/branches/cdk-1.2.x/src/tes​t/org/openscience/cdk/atomtype/ (AbstractAtomTypeTest.java SybylAtomTypeMatcherTest.java): Be happy with just atom types names
17:03 CIA-37 cdk: egonw * r13129 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added test method halogens
17:04 CIA-37 cdk: egonw * r13130 /cdk/branches/cdk-1.2.x/src/main/org/opens​cience/cdk/dict/data/sybyl-atom-types.owl: Removed duplicate definition
17:05 CIA-37 cdk: egonw * r13131 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Ignore 5 more meta types
17:06 CIA-37 cdk: egonw * r13132 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: countTestedAtomTypes must be the last method in the class (yes, dirty but it works
17:07 CIA-37 cdk: egonw * r13133 /cdk/branches/cdk-1.2.x/src/test/org/opensci​ence/cdk/atomtype/AbstractAtomTypeTest.java: Only test if the reference in not UNSET too
17:08 CIA-37 cdk: egonw * r13134 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added explicit tests
17:08 CIA-37 cdk: egonw * r13135 /cdk/branches/cdk-1.2.x/src/test/org/openscienc​e/cdk/atomtype/AbstractSybylAtomTypeTest.java: More relaxed atom type checking, as these are mapped types
17:08 CIA-37 cdk: egonw * r13136 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: C.ar is only detected with findMatchinAtomType(IAtomContainer)
17:09 CIA-37 cdk: egonw * r13137 /cdk/branches/cdk-1.2.x/src/main/org/opensc​ience/cdk/dict/data/cdk-sybyl-mappings.owl: Fixed missing mapping: CDK C.plus.[planar3|sp2] -> Sybyl C.cat
17:09 carsten joined #cdk
17:09 CIA-37 cdk: egonw * r13138 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added test for N.ar
17:10 CIA-37 cdk: egonw * r13139 /cdk/branches/cdk-1.2.x/src/main/org/opensci​ence/cdk/atomtype/SybylAtomTypeMatcher.java: An aromatic N.2 is a N.ar
17:10 CIA-37 cdk: egonw * r13140 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added perception testing for common inorganic kations
17:11 CIA-37 cdk: egonw * r13141 /cdk/branches/cdk-1.2.x/src/test/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcherTest.java: Added perception testing for most other atom types
18:32 CIA-37 cdk: egonw * r13142 /cdk/branches/cdk-1.2.x/src/test/org/opens​cience/cdk/config/IsotopeFactoryTest.java: Private helper methods should not have @Ignore and @Test annotation

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