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Dec 11, 2012

  1. gilleain torrance

    Merge branch 'master' of git://github.com/cdk/cdk

    authored

Dec 06, 2012

  1. John May

    Corrected comparator in InvPair sorting. The current comparison was i…

    …n violation of the comparable contract which was throwing an IllegalArgumentException on JRE 7.
    
    Change-Id: I5d3753a51afcb38585f2f17dac0c769c564ebac8
    Signed-off-by: maclean <gilleain.torrance@gmail.com>
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored egonw committed
  2. Egon Willighagen

    Proper modules (wasn't this fixed earlier already??)

    Change-Id: I5598c9f4b68699081958e257e3062affe820f40b
    egonw authored

Dec 02, 2012

  1. John May

    Added more unit tests for the MDLV2000Writer - including corner cases…

    … such as multiline RGPs, atom aliases, truncated atom aliases and pseudo atoms with null labels. The MDLV2000Writer can now handle all of these cases correctly.
    
    Change-Id: I3d134d23fc6252d7425fa2a8c50fb308d058ec7d
    Signed-off-by: Stephan Beisken <beisken@ebi.ac.uk>
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored egonw committed
  2. Egon Willighagen

    Revert "Added more unit tests for the MDLV2000Writer - including corn…

    …er cases such as multiline RGPs, atom aliases, truncated atom aliases and pseudo atoms with null labels. The MDLV2000Writer can now handle all of these cases correctly."
    
    This reverts commit e3b1c8e.
    egonw authored
  3. Stephan Beisken

    Added more unit tests for the MDLV2000Writer - including corner cases…

    … such as multiline RGPs, atom aliases, truncated atom aliases and pseudo atoms with null labels. The MDLV2000Writer can now handle all of these cases correctly.
    
    Change-Id: I3d134d23fc6252d7425fa2a8c50fb308d058ec7d
    Signed-off-by: Stephan Beisken <beisken@ebi.ac.uk>
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    SBeisken authored egonw committed
  4. Egon Willighagen

    Added a missing dependency

    Change-Id: I02c34ec7e205186868cab24fd28418535b556eca
    egonw authored
  5. gilleain torrance

    Alter the data representation in the refiners, and fix some test case…

    …s for the Bond Refiner
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed
  6. gilleain torrance

    Post-review fixes; javadocs, making permutation final, improvement to…

    … partition refiner
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed

Nov 29, 2012

  1. gilleain torrance

    Additional patch that calls refine before returning the automorphism …

    …partition
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed
  2. gilleain torrance

    Additional patch for aromatic support, and test cases borowed from bu…

    …g 1250
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed
  3. gilleain torrance

    The second half of the group module, containing the majority of the i…

    …mportant stuff : The key classes are the Atom and Bond Discrete Partition Refiners.
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed
  4. gilleain torrance

    Fixed a bug in the fromString static method of Partition, and test fo…

    …r the case that caused it
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed
  5. gilleain torrance

    Added a method to check that two elements are in the same cell of a p…

    …artition
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed
  6. gilleain torrance

    Added a method to order the cells of a partition

    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    authored egonw committed

Nov 18, 2012

  1. gilleain torrance

    Merge remote-tracking branch 'origin/master'

    authored

Nov 15, 2012

  1. Egon Willighagen

    A few unit tests uncovering some issues with == comparisons

    Change-Id: Ib013c284e1f742a6d7655ec2c81ae01ca2757b07
    egonw authored
  2. rwst

    Added accessor for the bond length in StructureDiagramGenerator

    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    rwst authored egonw committed
  3. Egon Willighagen

    Updated the @cdk.bugs taglet to support the new SourceForge project p…

    …ages
    
    Change-Id: I080fe6433b361a22a054f1d92724ee10291c9679
    egonw authored

Nov 12, 2012

  1. John May

    Replaced IBond.Order.ordinal() usages with IBond.Order.numeric()

    Conflicts:
    	src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
    	src/test/org/openscience/cdk/smiles/FixBondOrdersToolTest.java
    
    Change-Id: I53a0e74dfbc138e49f7fc85ce6fd226444608f0b
    johnmay authored egonw committed
  2. John May

    Added a field to the bond order enumeration allow access to the numer…

    …ic value for that order.
    
    Change-Id: I69b108218a127dad9ca73994de76558f977a304d
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    
    Conflicts:
    	src/main/org/openscience/cdk/interfaces/IBond.java
    johnmay authored egonw committed

Nov 11, 2012

  1. Egon Willighagen

    Added perception of N.sp2 and N.planar3 when SINGLE_OR_DOUBLE is used

    Change-Id: Ib2b045f6801bfd23479d89d148dae7b777067079
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored
  2. Egon Willighagen

    Fixed a big goof up: 1. IBond.Order.UNSET was not considered; 2. when…

    … SINGLE_OR_DOUBLE the type bond order can also be SINGLE, and in fact must be SINGLE or DOUBLE, as the flag name suggests
    
    Change-Id: Ifa960198b15737c3a51e8bee8858ff6d2303262f
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored

Nov 10, 2012

  1. Egon Willighagen

    Added a missing dependency

    Change-Id: I5ff09850deefad62f8e927adced4462ba2c3218e
    egonw authored
  2. Egon Willighagen

    Merged in cdk-1.4.x patches: s/IMolecule/IAtomContainer/ an s/Nonotif…

    …ication/Silent/
    
    Change-Id: I642a9b12b4f90baf9b61f0e33b8157c7de38d20d
    egonw authored
  3. rwst

    unit test

    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    rwst authored egonw committed
  4. rwst

    unit test

    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    rwst authored egonw committed
  5. rwst

    unit test for bug 1269 (atom... not placed by SDG, causing NPE), remo…

    …ve catch statements, set expected
    
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    rwst authored egonw committed

Nov 09, 2012

  1. Egon Willighagen

    Added a unit test for C.sp2 perception with SINGLE_OR_DOUBLE bonds

    Change-Id: Ic1de95e700e6d52adc3b89f97dc2caf78d07ddac
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored
  2. Egon Willighagen

    Added detection of C.sp2 atom types with SINGLE_OR_DOUBLE bonds

    Change-Id: Ia25ce5449e70922ece571c0b02f97ab86ff806a7
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored
  3. Egon Willighagen

    Accept that bonds are sometimes unset (and except them to have a SING…

    …LE_OR_DOUBLE flag then), and no longer use IBond.Order ordinals for comparison, but do it the proper way.
    
    Change-Id: I87a20792ae6249bf1f06d57e11e3b44defef2311
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored
  4. Egon Willighagen

    Fixed a bug present in many readers: it would not accept a subclass i…

    …f ChemFile (e.g. NNChemFile) even if ChemFile itself was accepted
    
    Change-Id: Ic8c00d63d9b11ebdda27198588b25293f97c1d86
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored
  5. Egon Willighagen

    Fixed loading of the right class when reporting possible alternative …

    …constructors
    
    Change-Id: I91c1682c8a46dcd520616d381ca365ad2c74dbf4
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    egonw authored
  6. John May

    [bug:1275] added check to ensure that when String.substring is called…

    … the string is long enough
    johnmay authored egonw committed
  7. John May

    [bug:1274] added conditional to ensure that when multiple bond stereo…

    … is specified as attributes and characters only one is used. This is achieved by using the existing flag to determine if a stereo bond value has already been provided.
    
    Change-Id: I2a4e64b1df2cbfdc5a3dfe5d8ff9a13c11f94e98
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored egonw committed
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