Camelia, the Perl 6 bug

IRC log for #cdk, 2009-12-19

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

All times shown according to UTC.

Time Nick Message
02:56 slyrus joined #cdk
07:20 egonw joined #cdk
07:42 Asad joined #cdk
07:42 Asad HI
07:42 zarah oh hai Asad
08:06 jbrefort joined #cdk
08:08 Guest27970 is Egon around?
08:08 Guest27970 left #cdk
08:21 asad_ joined #cdk
08:26 Asad joined #cdk
08:29 Guest28384 left #cdk
08:29 Asad joined #cdk
08:30 Asad left #cdk
08:30 Asad joined #cdk
08:31 Guest73743 left #cdk
08:31 s9asad joined #cdk
08:45 egonw asad_: ping
08:45 asad_ Hi
08:45 zarah hi asad_
08:46 egonw just saw your email
08:46 egonw sorry, i think I messed up in that email...
08:46 asad_ Oh
08:46 egonw you had to fix things *again* ...
08:46 egonw because the smsd branch was the old copy
08:46 egonw and *not* master
08:47 egonw the instructions should have been:
08:47 egonw git checkout master
08:47 egonw git branch -m smsd smsdOld
08:47 asad_ Oh!
08:47 egonw git checkout -b smsd master
08:47 egonw and then the merge with:
08:47 egonw git merge 102...
08:47 egonw really sorry about that :(
08:47 asad_ so let me try again and see what happens
08:47 asad_ np
08:47 asad_ we are human
08:48 egonw we'll, on the upside... it's educational for you :)
08:48 asad_ git checkout master
08:48 asad_ error: Entry 'build.xml' would be overwritten by merge. Cannot merge.
08:48 egonw git does git branch tell ?
08:48 asad_ 101-smsdRebase
08:48 asad_ 102-smsdRebase
08:48 asad_ master
08:48 asad_ * smsd
08:49 egonw ah, ok, that's good
08:49 egonw ok, just remove the build.xml file then
08:49 egonw it will be readded with the 'git checkout master'
08:49 egonw in fact...
08:49 egonw that checkout will overwrite the file...
08:49 egonw oh wait...
08:49 egonw there must be an option to allow overwriting of files...
08:49 egonw that would be much easier...
08:49 egonw mom
08:49 egonw checking docs
08:50 asad_ hmm
08:50 asad_ but I just deleted build.xml
08:50 asad_ anyways
08:50 egonw OK, try the -f option:
08:50 asad_ lets check the boc
08:50 egonw git checkout -f master
08:50 egonw asad_: yeah, that's fine...
08:50 asad_ git checkout -f master
08:50 asad_ Switched to branch 'master'
08:50 egonw ok, cool :)
08:51 asad_ now git branch -m smsd smsdOld :-)
08:51 asad_ now git checkout -b smsd master
08:51 asad_ git checkout -b smsd master
08:51 asad_ Switched to a new branch 'smsd'
08:51 egonw good
08:52 asad_ Updating 6d453a1..bdd0918
08:52 asad_ Fast forward
08:52 asad_ AUTHORS                                            |    1 +
08:52 asad_ Part 1.3                                           |   11 +
08:52 asad_ build.xml                                          |   10 +-
08:52 asad_ doc/refs/cheminf.bibx                              |   12 +
08:52 asad_ javadoc.xml                                        |    1 +
08:52 asad_ manifest.mf                                        |    3 +
08:52 asad_ nbbuild.xml                                        |  113 ++
08:52 asad_ nbproject/build-impl.xml                           |  739 ++++++++++
08:52 egonw yes, perfect
08:52 asad_ nbproject/genfiles.properties                      |    8 +
08:52 asad_ nbproject/project.properties                       |   98 ++
08:52 asad_ nbproject/project.xml                              |   15 +
08:52 egonw that will be a very long list
08:52 asad_ pmd-migrating.xml                                  |    2 +
08:53 asad_ pmd-unused.xml                                     |    2 +
08:53 asad_ pmd.xml                                            |    2 +
08:53 asad_ src/META-INF/smsd.cdkdepends                       |    8 +
08:53 asad_ src/META-INF/smsd.libdepends                       |    2 +
08:53 asad_ src/META-INF/test-smsd.cdkdepends                  |   12 +
08:53 asad_ src/META-INF/test-smsd.devellibdepends             |    1 +
08:53 asad_ src/META-INF/test-smsd.libdepends                  |    4 +
08:53 asad_ src/main/org/openscience/cdk/AminoAcid.java        |   28 +-
08:53 asad_ src/main/org/openscience/cdk/Association.java      |   99 +-
08:53 asad_ src/main/org/openscience/cdk/Atom.java             |  629 +++++-----
08:53 asad_ src/main/org/openscience/cdk/AtomContainer.java    |  141 +-
08:53 asad_ src/main/org/openscience/cdk/AtomContainerSet.java |   15 +-
08:53 asad_ src/main/org/openscience/cdk/AtomParity.java       |   46 +-
08:53 asad_ src/main/org/openscience/cdk/AtomType.java         |   39 +-
08:53 asad_ src/main/org/openscience/cdk/BioPolymer.java       |  402 +++---
08:53 asad_ src/main/org/openscience/cdk/Bond.java             |   61 +-
08:53 asad_ src/main/org/openscience/cdk/CDKConstants.java     |   35 +-
08:53 asad_ src/main/org/openscience/cdk/ChemFile.java         |  297 ++---
08:53 asad_ src/main/org/openscience/cdk/ChemModel.java        |   29 +-
08:53 asad_ src/main/org/openscience/cdk/ChemObject.java       |  692 +++++-----
08:53 asad_ src/main/org/openscience/cdk/ChemSequence.java     |  305 ++---
08:53 asad_ .../org/openscience/cdk/ConformerContainer.java    |   65 +-
08:53 asad_ src/main/org/openscience/cdk/Crystal.java          |   37 +-
08:53 asad_ .../openscience/cdk/DefaultChemObjectBuilder.java  |   77 +-
08:53 asad_ .../org/openscience/cdk/ElectronContainer.java     |   60 +-
08:53 asad_ src/main/org/openscience/cdk/Element.java          |   51 +-
08:53 asad_ .../org/openscience/cdk/EnzymeResidueLocator.java  |   11 +-
08:53 asad_ src/main/org/openscience/cdk/FragmentAtom.java     |   82 +-
08:53 asad_ .../cdk/IImplementationSpecification.java          |   19 +-
08:53 asad_ src/main/org/openscience/cdk/Isotope.java          |  296 ++--
08:54 asad_ src/main/org/openscience/cdk/LonePair.java         |   59 +-
08:54 asad_ src/main/org/openscience/cdk/Mapping.java          |   46 +-
08:54 asad_ src/main/org/openscience/cdk/Molecule.java         |   62 +-
08:54 asad_ src/main/org/openscience/cdk/MoleculeSet.java      |  123 +-
08:54 asad_ src/main/org/openscience/cdk/Monomer.java          |  141 +-
08:54 asad_ .../org/openscience/cdk/PhysicalConstants.java     |    4 +-
08:54 asad_ src/main/org/openscience/cdk/Polymer.java          |  188 ++--
08:54 asad_ src/main/org/openscience/cdk/PseudoAtom.java       |   25 +-
08:54 asad_ src/main/org/openscience/cdk/Reaction.java         |  210 ++--
08:54 asad_ src/main/org/openscience/cdk/ReactionScheme.java   |  134 +-
08:54 asad_ src/main/org/openscience/cdk/ReactionSet.java      |  270 ++--
08:54 asad_ src/main/org/openscience/cdk/Ring.java             |  194 ++--
08:54 asad_ src/main/org/openscience/cdk/RingSet.java          |  270 ++--
08:54 asad_ src/main/org/openscience/cdk/SingleElectron.java   |   61 +-
08:54 asad_ src/main/org/openscience/cdk/Strand.java           |  358 +++---
08:54 asad_ src/main/org/openscience/cdk/Vibration.java        |   15 +-
08:54 asad_ .../org/openscience/cdk/io/cml/CDKConvention.java  |   11 +-
08:54 asad_ .../org/openscience/cdk/io/cml/CMLCoreModule.java  |  736 +++++-----
08:54 asad_ .../openscience/cdk/io/cml/CMLReactionModule.java  |  120 +-
08:54 asad_ .../cdk/io/cml/JMOLANIMATIONConvention.java        |   12 +-
08:54 asad_ .../org/openscience/cdk/io/cml/QSARConvention.java |  135 +-
08:54 asad_ .../cdk/isomorphism/IsomorphismTester.java         |  209 ++--
08:54 asad_ .../cdk/isomorphism/matchers/IQueryAtom.java       |   16 +-
08:54 asad_ .../isomorphism/matchers/IQueryAtomContainer.java  |    3 +-
08:54 asad_ .../cdk/isomorphism/matchers/IQueryBond.java       |   15 +-
08:54 asad_ .../matchers/InverseSymbolSetQueryAtom.java        |   14 +-
08:54 asad_ .../cdk/isomorphism/matchers/OrderQueryBond.java   |   18 +-
08:54 asad_ .../matchers/OrderQueryBondOrderOnly.java          |   14 +-
08:54 asad_ .../isomorphism/matchers/QueryAtomContainer.java   |   53 +-
08:54 asad_ .../matchers/QueryAtomContainerCreator.java        |   77 +-
08:55 asad_ .../matchers/SymbolAndChargeQueryAtom.java         |   36 +-
08:55 asad_ .../matchers/SymbolChargeIDQueryAtom.java          |   38 +-
08:55 asad_ .../cdk/isomorphism/matchers/SymbolQueryAtom.java  |   51 +-
08:55 asad_ .../isomorphism/matchers/SymbolSetQueryAtom.java   |   13 +-
08:55 asad_ .../isomorphism/matchers/smarts/AliphaticAtom.java |   40 +-
08:55 asad_ .../cdk/isomorphism/matchers/smarts/AnyAtom.java   |    8 +-
08:55 asad_ .../matchers/smarts/AnyOrderQueryBond.java         |   19 +-
08:55 asad_ .../isomorphism/matchers/smarts/AromaticAtom.java  |    9 +-
08:55 asad_ .../matchers/smarts/AromaticOrSingleQueryBond.java |   22 +-
08:55 asad_ .../matchers/smarts/AromaticQueryBond.java         |   31 +-
08:55 asad_ .../matchers/smarts/HybridizationNumberAtom.java   |   38 +-
08:55 asad_ .../matchers/smarts/ImplicitHCountAtom.java        |   29 +-
08:55 asad_ .../matchers/smarts/LogicalOperatorAtom.java       |   88 +-
08:55 asad_ .../matchers/smarts/LogicalOperatorBond.java       |   58 +-
08:55 asad_ .../cdk/isomorphism/matchers/smarts/MassAtom.java  |    5 +-
08:55 asad_ .../matchers/smarts/NonCHHeavyAtom.java            |    5 +-
08:55 asad_ .../matchers/smarts/OrderQueryBond.java            |   28 +-
08:55 asad_ .../matchers/smarts/PeriodicGroupNumberAtom.java   |   47 +-
08:55 asad_ .../cdk/isomorphism/matchers/smarts/RingAtom.java  |   67 +-
08:55 asad_ .../matchers/smarts/RingMembershipAtom.java        |   42 +-
08:55 asad_ .../matchers/smarts/SmallestRingAtom.java          |   44 +-
08:55 asad_ .../isomorphism/matchers/smarts/StereoBond.java    |   11 +-
08:55 asad_ .../matchers/smarts/TotalConnectionAtom.java       |   56 +-
08:55 asad_ .../matchers/smarts/TotalRingConnectionAtom.java   |   71 +-
08:55 asad_ .../matchers/smarts/TotalValencyAtom.java          |   16 +-
08:55 asad_ .../openscience/cdk/isomorphism/mcss/RNode.java    |  186 ++--
08:55 asad_ .../reaction/type/parameters/IParameterReact.java  |   53 +-
08:55 asad_ .../reaction/type/parameters/ParameterReact.java   |   90 +-
08:55 asad_ .../type/parameters/SetReactionCenter.java         |    6 +-
08:55 asad_ .../cdk/renderer/GraphRendererModel.java           |  394 +++---
08:56 asad_ .../org/openscience/cdk/renderer/JCPAction2D.java  |    2 +-
08:56 asad_ .../org/openscience/cdk/similarity/Cosine.java     |   88 ++
08:56 asad_ src/main/org/openscience/cdk/similarity/Dice.java  |   87 ++
08:56 asad_ src/main/org/openscience/cdk/smsd/SMSD.java        |  323 +++++
08:56 asad_ .../openscience/cdk/smsd/algorithm/cdk/CDKMCS.java | 1148 ++++++++++++++++
08:56 asad_ .../cdk/smsd/algorithm/cdk/CDKMCSHandler.java      |  299 ++++
08:56 asad_ .../cdk/smsd/algorithm/cdk/CDKRGraph.java          |  575 ++++++++
08:56 asad_ .../cdk/smsd/algorithm/cdk/CDKRMap.java            |  113 ++
08:56 asad_ .../cdk/smsd/algorithm/cdk/CDKRMapHandler.java     |  444 ++++++
08:56 asad_ .../cdk/smsd/algorithm/cdk/CDKRNode.java           |  132 ++
08:56 asad_ .../cdk/smsd/algorithm/mcgregor/McGregor.java      |  937 +++++++++++++
08:56 asad_ .../smsd/algorithm/mcgregor/McGregorChecks.java    |  643 +++++++++
08:56 asad_ .../smsd/algorithm/mcgregor/McgregorHelper.java    |  183 +++
08:56 asad_ .../smsd/algorithm/mcgregor/QueryProcessor.java    |  430 ++++++
08:56 asad_ .../smsd/algorithm/mcgregor/TargetProcessor.java   |  404 ++++++
08:56 asad_ .../cdk/smsd/algorithm/mcsplus/BKKCKCF.java        |  489 +++++++
08:56 asad_ .../cdk/smsd/algorithm/mcsplus/ExactMapping.java   |   86 ++
08:56 asad_ .../mcsplus/GenerateCompatibilityGraph.java        |  417 ++++++
08:56 asad_ .../cdk/smsd/algorithm/mcsplus/MCSPlus.java        |  125 ++
08:56 asad_ .../cdk/smsd/algorithm/mcsplus/MCSPlusHandler.java |  248 ++++
08:56 asad_ .../cdk/smsd/algorithm/single/SingleMapping.java   |  157 +++
08:56 asad_ .../algorithm/single/SingleMappingHandler.java     |  231 ++++
08:56 asad_ .../cdk/smsd/algorithm/vflib/VFlibHandler.java     |  201 +++
08:56 asad_ .../cdk/smsd/algorithm/vflib/VFlibMCSHandler.java  |  335 +++++
08:56 asad_ .../smsd/algorithm/vflib/VFlibTurboHandler.java    |  192 +++
08:56 asad_ .../smsd/algorithm/vflib/builder/EdgeBuilder.java  |   64 +
08:56 asad_ .../smsd/algorithm/vflib/builder/NodeBuilder.java  |   81 ++
08:56 asad_ .../algorithm/vflib/builder/VFQueryBuilder.java    |  176 +++
08:56 asad_ .../cdk/smsd/algorithm/vflib/interfaces/IEdge.java |   62 +
08:56 asad_ .../smsd/algorithm/vflib/interfaces/IMapper.java   |   87 ++
08:57 asad_ .../cdk/smsd/algorithm/vflib/interfaces/INode.java |   96 ++
08:57 asad_ .../smsd/algorithm/vflib/interfaces/IQuery.java    |  109 ++
08:57 asad_ .../algorithm/vflib/interfaces/IQueryCompiler.java |   60 +
08:57 asad_ .../smsd/algorithm/vflib/interfaces/IState.java    |  123 ++
08:57 asad_ .../cdk/smsd/algorithm/vflib/map/VFMCSMapper.java  |  200 +++
08:57 asad_ .../cdk/smsd/algorithm/vflib/map/VFMCSState.java   |  260 ++++
08:57 asad_ .../cdk/smsd/algorithm/vflib/map/VFMapper.java     |  217 +++
08:57 asad_ .../cdk/smsd/algorithm/vflib/map/VFState.java      |  292 ++++
08:57 asad_ .../algorithm/vflib/query/TemplateCompiler.java    |  137 ++
08:57 asad_ .../algorithm/vflib/validator/VFAtomMatcher.java   |  284 ++++
08:57 asad_ .../algorithm/vflib/validator/VFBondMatcher.java   |  123 ++
08:57 asad_ .../smsd/algorithm/vflib/validator/VFMatch.java    |   87 ++
08:57 asad_ .../cdk/smsd/factory/FragmentMatcher.java          |  243 ++++
08:57 asad_ .../smsd/factory/SubStructureSearchAlgorithms.java |  620 +++++++++
08:57 asad_ .../cdk/smsd/filters/ChemicalFilters.java          |  791 +++++++++++
08:57 asad_ .../openscience/cdk/smsd/filters/PostFilter.java   |   91 ++
08:57 asad_ .../org/openscience/cdk/smsd/global/BondType.java  |   72 +
08:57 asad_ .../org/openscience/cdk/smsd/global/TimeOut.java   |   65 +
08:57 asad_ .../openscience/cdk/smsd/helper/BinaryTree.java    |   60 +
08:57 asad_ .../openscience/cdk/smsd/helper/BondEnergy.java    |   93 ++
08:57 asad_ .../openscience/cdk/smsd/helper/FinalMappings.java |   92 ++
08:57 asad_ .../cdk/smsd/helper/LabelContainer.java            |  149 ++
08:57 asad_ .../openscience/cdk/smsd/helper/MolHandler.java    |  232 ++++
08:57 asad_ .../cdk/smsd/interfaces/IFinalMapping.java         |   71 +
08:57 asad_ .../org/openscience/cdk/smsd/interfaces/IMCS.java  |  161 +++
08:57 asad_ .../cdk/smsd/interfaces/IMCSAlgorithm.java         |   77 ++
08:57 asad_ .../openscience/cdk/smsd/interfaces/IMCSBase.java  |   58 +
08:57 asad_ .../openscience/cdk/smsd/interfaces/ISubGraph.java |   76 +
08:57 asad_ .../openscience/cdk/smsd/tools/BondEnergies.java   |  428 ++++++
08:57 asad_ .../smsd/tools/ExtAtomContainerManipulator.java    |  529 +++++++
08:58 asad_ .../openscience/cdk/smsd/tools/MDLFileReader.java  |  200 +++
08:58 asad_ .../cdk/smsd/tools/MoleculeSanityCheck.java        |  146 ++
08:58 asad_ .../openscience/cdk/smsd/tools/TimeManager.java    |  109 ++
08:58 asad_ .../tools/BremserOneSphereHOSECodePredictor.java   | 1441 ++++++++++----------
08:58 asad_ .../org/openscience/cdk/tools/CDKUtilities.java    |  504 ++++----
08:58 asad_ .../openscience/cdk/tools/HOSECodeAnalyser.java    |   71 +-
08:58 asad_ .../org/openscience/cdk/tools/LoggingTool.java     |  122 +-
08:58 asad_ src/main/org/openscience/cdk/tools/Normalizer.java |  119 +-
08:58 asad_ .../openscience/cdk/tools/ProteinBuilderTool.java  |   37 +-
08:58 asad_ .../cdk/tools/diff/AtomContainerDiff.java          |   30 +-
08:58 asad_ .../org/openscience/cdk/tools/diff/AtomDiff.java   |   24 +-
08:58 asad_ .../openscience/cdk/tools/diff/AtomTypeDiff.java   |   12 +-
08:58 asad_ .../org/openscience/cdk/tools/diff/BondDiff.java   |   26 +-
08:58 asad_ .../openscience/cdk/tools/diff/ChemObjectDiff.java |    9 +-
08:58 asad_ .../cdk/tools/diff/ElectronContainerDiff.java      |   24 +-
08:58 asad_ .../openscience/cdk/tools/diff/ElementDiff.java    |   12 +-
08:58 asad_ .../openscience/cdk/tools/diff/IsotopeDiff.java    |    8 +-
08:58 asad_ .../openscience/cdk/tools/diff/LonePairDiff.java   |   24 +-
08:58 asad_ .../cdk/tools/diff/SingleElectronDiff.java         |   24 +-
08:58 asad_ .../cdk/tools/diff/tree/AbstractDifference.java    |    4 +-
08:58 asad_ .../tools/diff/tree/AbstractDifferenceList.java    |   10 +-
08:58 asad_ .../cdk/tools/periodictable/PeriodicTable.java     |   99 +-
08:58 asad_ src/test/data/mdl/ADP.mol                          |   61 +
08:58 asad_ src/test/data/mdl/ADP_H.mol                        |   91 ++
08:58 asad_ src/test/data/mdl/ATP.mol                          |   69 +
08:58 asad_ src/test/data/mdl/ATP_H.mol                        |  101 ++
08:58 asad_ src/test/data/mdl/C03374.mol                       |  119 ++
08:58 asad_ src/test/data/mdl/C05787.mol                       |  144 ++
08:58 asad_ src/test/data/mdl/frag5.mol                        |   32 +
08:58 asad_ src/test/data/mdl/het5.mol                         |   60 +
08:59 asad_ .../openscience/cdk/coverage/SmsdCoverageTest.java |   40 +
08:59 asad_ .../cdk/isomorphism/IsomorphismTesterTest.java     |    1 -
08:59 asad_ .../openscience/cdk/modulesuites/MsmsdTests.java   |   46 +
08:59 asad_ .../org/openscience/cdk/similarity/CosineTest.java |   72 +
08:59 asad_ .../org/openscience/cdk/similarity/DiceTest.java   |   72 +
08:59 asad_ src/test/org/openscience/cdk/smsd/SMSDTest.java    |  846 ++++++++++++
08:59 asad_ .../cdk/smsd/algorithm/cdk/CDKMCSTest.java         |  410 ++++++
08:59 asad_ .../cdk/smsd/algorithm/vflib/VFLibTest.java        |  267 ++++
08:59 asad_ .../cdk/smsd/tools/BondEnergiesTest.java           |   41 +
08:59 asad_ .../cdk/smsd/tools/TimeManagerTest.java            |   41 +
08:59 asad_ store/CDK-SMSD.jar                                 |  Bin 0 -> 12699916 bytes
08:59 asad_ 203 files changed, 24252 insertions(+), 5725 deletions(-)
08:59 asad_ create mode 100644 Part 1.3
08:59 asad_ create mode 100644 manifest.mf
08:59 asad_ create mode 100644 nbbuild.xml
08:59 asad_ create mode 100644 nbproject/build-impl.xml
08:59 asad_ create mode 100644 nbproject/genfiles.properties
08:59 asad_ create mode 100644 nbproject/project.properties
08:59 asad_ create mode 100644 nbproject/project.xml
08:59 asad_ create mode 100644 src/META-INF/smsd.cdkdepends
08:59 asad_ create mode 100644 src/META-INF/smsd.libdepends
08:59 asad_ create mode 100644 src/META-INF/test-smsd.cdkdepends
08:59 asad_ create mode 100644 src/META-INF/test-smsd.devellibdepends
08:59 asad_ create mode 100644 src/META-INF/test-smsd.libdepends
08:59 asad_ mode change 100755 => 100644 src/main/org/openscience/cdk/Association.java
08:59 asad_ mode change 100755 => 100644 src/main/org/openscience/cdk/Vibration.java
08:59 asad_ create mode 100644 src/main/org/openscience/c​dk/similarity/Cosine.java
08:59 asad_ create mode 100644 src/main/org/openscience/cdk/similarity/Dice.java
08:59 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/SMSD.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/s​msd/algorithm/cdk/CDKMCS.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd​/algorithm/cdk/CDKMCSHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/sm​sd/algorithm/cdk/CDKRGraph.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/s​msd/algorithm/cdk/CDKRMap.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/​algorithm/cdk/CDKRMapHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/sm​sd/algorithm/cdk/CDKRNode.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd​/algorithm/mcgregor/McGregor.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/mcgregor/McGregorChecks.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/mcgregor/McgregorHelper.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/mcgregor/QueryProcessor.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/alg​orithm/mcgregor/TargetProcessor.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/sms​d/algorithm/mcsplus/BKKCKCF.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/a​lgorithm/mcsplus/ExactMapping.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algorith​m/mcsplus/GenerateCompatibilityGraph.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/sms​d/algorithm/mcsplus/MCSPlus.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/mcsplus/MCSPlusHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/a​lgorithm/single/SingleMapping.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algo​rithm/single/SingleMappingHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/​algorithm/vflib/VFlibHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/a​lgorithm/vflib/VFlibMCSHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/vflib/VFlibTurboHandler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/alg​orithm/vflib/builder/EdgeBuilder.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/alg​orithm/vflib/builder/NodeBuilder.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algor​ithm/vflib/builder/VFQueryBuilder.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/vflib/interfaces/IEdge.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/alg​orithm/vflib/interfaces/IMapper.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/vflib/interfaces/INode.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/vflib/interfaces/IQuery.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algori​thm/vflib/interfaces/IQueryCompiler.java
09:00 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/vflib/interfaces/IState.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/a​lgorithm/vflib/map/VFMCSMapper.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/a​lgorithm/vflib/map/VFMCSState.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/​algorithm/vflib/map/VFMapper.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd​/algorithm/vflib/map/VFState.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algor​ithm/vflib/query/TemplateCompiler.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algor​ithm/vflib/validator/VFAtomMatcher.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/algor​ithm/vflib/validator/VFBondMatcher.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/al​gorithm/vflib/validator/VFMatch.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/sm​sd/factory/FragmentMatcher.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/smsd/fact​ory/SubStructureSearchAlgorithms.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/sm​sd/filters/ChemicalFilters.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk/​smsd/filters/PostFilter.java
09:01 asad_ create mode 100644 src/main/org/openscience/cd​k/smsd/global/BondType.java
09:01 asad_ create mode 100644 src/main/org/openscience/cd​k/smsd/global/TimeOut.java
09:01 asad_ create mode 100644 src/main/org/openscience/cdk​/smsd/helper/BinaryTree.java
09:03 s9asad joined #cdk
09:03 egonw s9asad: :)
09:03 egonw so, it worked allright :)
09:03 s9asad :-)
09:03 s9asad yes
09:03 s9asad but don't know then next step
09:04 s9asad git push origin master
09:04 s9asad git push origin :smsd
09:04 s9asad git push origin smsd
09:04 s9asad should I try them
09:04 egonw yes
09:05 s9asad git push origin master
09:05 s9asad To git@github.com:asad/cdk-smsd.git
09:05 s9asad ! [rejected]        master -> master (non-fast forward)
09:05 s9asad error: failed to push some refs to 'git@github.com:asad/cdk-smsd.git'
09:05 s9asad To prevent you from losing history, non-fast-forward updates were rejected
09:05 s9asad Merge the remote changes before pushing again.  See the 'non-fast forward'
09:05 s9asad section of 'git push --help' for details.
09:05 s9asad :-(
09:05 egonw ok, try the same thing there: remove master first by adding the ':', as in:
09:05 egonw git push origin :master
09:05 egonw and then add it again with:
09:06 egonw git push origin master
09:06 s9asad git push origin :master
09:06 s9asad To git@github.com:asad/cdk-smsd.git
09:06 s9asad - [deleted]         master
09:07 s9asad git push origin master
09:07 s9asad Counting objects: 1946, done.
09:07 s9asad Delta compression using up to 2 threads.
09:07 s9asad Compressing objects: 100% (381/381), done.
09:07 s9asad Writing objects: 100% (1540/1540), 1.45 MiB, done.
09:07 s9asad Total 1540 (delta 960), reused 1510 (delta 940)
09:07 s9asad To git@github.com:asad/cdk-smsd.git
09:07 s9asad * [new branch]      master -> master
09:07 s9asad now
09:07 s9asad should I git push origin master
09:08 s9asad or git push origin :smsd
09:14 egonw second
09:14 egonw git push origin :smsd
09:14 egonw git push origin smsd
09:14 egonw that should do it
09:17 s9asad its uploading smsd
09:18 egonw excellent
09:19 s9asad git push origin smsd
09:19 s9asad Counting objects: 4259, done.
09:19 s9asad Delta compression using up to 2 threads.
09:19 s9asad Compressing objects: 100% (2155/2155), done.
09:19 s9asad Writing objects: 100% (4133/4133), 12.20 MiB | 56 KiB/s, done.
09:19 s9asad Total 4133 (delta 2470), reused 1857 (delta 1379)
09:19 s9asad To git@github.com:asad/cdk-smsd.git
09:19 s9asad * [new branch]      smsd -> smsd
09:19 s9asad Done
09:19 s9asad Awesome :-)
09:19 egonw I'll rerun nightly now then
09:19 s9asad sure!
09:20 s9asad so is there a ways to automatically update my master with cdk master (auto sync and auto track)
09:20 s9asad :-)
09:20 egonw no, rebasing cannot be automated
09:20 s9asad ic
09:21 s9asad then we should have a written standard protocol of doing it and if we get stuck....then u r the saviour!
09:24 s9asad Thanks alot Egom
09:24 s9asad Egon*
09:27 egonw OK, nightly is rerunning now
09:28 s9asad great
09:28 s9asad will see what comes up!
09:29 s9asad by the way I can see alot of error in core CDK test regarding super.getBondOrderSum(atom)
09:30 s9asad example
09:30 s9asad org/openscience/cdk/validat​e/BasicValidator.java:320: warning: [deprecation] getBondOrderSum(org.opensci​ence.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated
09:30 s9asad [javac]             int bos = (int)molecule.getBondOrderSum(atom);
09:30 s9asad [javac]                                    ^
09:32 egonw ah, yes
09:32 egonw yeah, these are abundant...
09:32 egonw file a bug report...
09:32 egonw it needs to be fixed before 1.4.0
09:32 s9asad okay
09:41 s9asad https://sourceforge.net/tracker/?func=detail&amp​;aid=2917547&group_id=20024&atid=120024
09:41 s9asad done
09:41 egonw tack!
09:41 egonw nightly is still running
09:42 s9asad hmm
09:42 s9asad how about this
09:42 s9asad V2M.VectorToMatrix(r2, ncase, npvar);
09:43 s9asad org/openscience/cdk/qsar/model/R​/PLSRegressionModelFit.java:148: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated
09:43 s9asad [javac]         this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar);
09:43 s9asad [javac]                      ^
09:43 s9asad even these are in abundance
09:43 egonw indeed
09:43 egonw please ask Rajarshi on cdk-devel about that...
09:44 s9asad okay
09:44 egonw i think those deprecated classes should be removed from 1.3.x
09:44 egonw and thanx for the peer review :)
09:44 egonw I wish more people were doing that
09:44 s9asad no problem, my pleasure :-)
10:01 s9asad I can see more Variables should start with a lowercase character warnings
10:01 s9asad may be the criteria has changes ;-)
10:02 s9asad more work for the weekennds
10:03 egonw I might have updated the PMD version...
10:03 egonw that is, I did...
10:03 egonw and it seems after we branched your initial smsd branch
10:04 egonw s9asad: never mind the complexity warnings...
10:05 egonw those do not need to be fixed... not necessarily at least...
10:05 egonw more important are warnings like:
10:05 egonw Avoid catching NullPointerException; consider removing the cause of the NPE
10:05 s9asad Oh
10:05 egonw Avoid empty if statements
10:05 egonw These nested if statements could be combined
10:06 s9asad and
10:06 egonw JUnit 4 tests that execute tests should use the @Test annotation
10:06 egonw because these *may* result from coding errors...
10:06 s9asad I see I will do so
10:06 egonw yeah, check them...
10:06 s9asad just wondering about this
10:06 s9asad Avoid catching NullPointerException; consider removing the cause of the NPE
10:07 egonw yeah, it's better to handle that inline:
10:07 egonw if (foo != null) foo.bla()
10:07 egonw because then it is much more clear what can be null...
10:07 s9asad private Integer getUnsaturation(IAtom atom) {
10:07 s9asad Integer value = 0;
10:07 s9asad try {
10:07 s9asad value = atom.getValency() - atom.getFormalNeighbourCount();
10:07 s9asad } catch (NullPointerException nep) {
10:07 s9asad value = -1;
10:07 s9asad }
10:07 s9asad return value;
10:07 s9asad }
10:07 egonw also, exception handling is quite time consuming
10:07 s9asad how to set this one
10:07 egonw so, it badly hurts performance
10:08 egonw yeah, make that:
10:08 egonw Integer value = atom.getValency() == null ? -1 : atom.getValency() - atom.getFormalNeighbourCount();
10:08 egonw (with 120 char line wrapping)
10:09 egonw unused code is also suspicious: http://pele.farmbio.uu.se/nigh​tly-smsd/pmd-unused/smsd.html
10:09 zarah egonw's link is also http://tinyurl.com/ybcnh7b
10:09 egonw the method may have actual purpose, but accidentally not called...
10:09 egonw again: could be...
10:09 s9asad sure
10:09 egonw I actually found many bugs in the CDK because of these warnings...
10:10 s9asad great I will go at it and get back to you
11:43 Chrom_ joined #cdk
11:44 Chrom_ left #cdk
14:18 s9asad joined #cdk
14:51 egonw joined #cdk
15:25 carsten joined #cdk
16:46 egonw joined #cdk
17:51 slyrus joined #cdk
19:19 s9asad joined #cdk
19:20 s9asad Hello everyone
20:50 s9asad joined #cdk
20:51 CIA-74 cdk: annulen * r15212 /jchempaint/trunk/src/main/org/openscien​ce/jchempaint/action/ExportAction.java: i18n
20:53 CIA-74 cdk: annulen * r15213 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (5 files): added menuTextMaker as member of AbstarctJChemPaintPanel
21:17 CIA-74 cdk: annulen * r15214 /jchempaint/trunk/po/ (keys.pot ru.po): Russian

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