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>
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>
Added a field to the bond order enumeration allow access to the numeric 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
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
Updated the @cdk.bugs taglet to support the new SourceForge project pages

Change-Id: I080fe6433b361a22a054f1d92724ee10291c9679
Added accessor for the bond length in StructureDiagramGenerator

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
A few unit tests uncovering some issues with == comparisons

Change-Id: Ib013c284e1f742a6d7655ec2c81ae01ca2757b07
Added a method to order the cells of a partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a method to check that two elements are in the same cell of a partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a bug in the fromString static method of Partition, and test for the case that caused it

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
The second half of the group module, containing the majority of the important stuff : The key classes are the Atom and Bond Discrete Partition Refiners.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Additional patch for aromatic support, and test cases borowed from bug 1250

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Additional patch that calls refine before returning the automorphism partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Post-review fixes; javadocs, making permutation final, improvement to partition refiner

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Alter the data representation in the refiners, and fix some test cases for the Bond Refiner

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a missing dependency

Change-Id: I02c34ec7e205186868cab24fd28418535b556eca
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>
Revert "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."

This reverts commit e3b1c8e8b75325b8fd72cfcfda49fa5176ff60d9.
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>
Proper modules (wasn't this fixed earlier already??)

Change-Id: I5598c9f4b68699081958e257e3062affe820f40b