Changed saturation conditional to also check that a bond is not aromatic.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added unit test and annotation for moment generation (3D Similarity)

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added missing literature reference, and minimal additional information requested in bug #1285

Change-Id: Id4b46baf50130af657cf1c28cd7ce24b96a240aa
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Expanded explanation of Sigma Electronegativity Descriptor

Change-Id: Ic37241a6a3d161f873b3d2290c41be7c86ab99c3
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Now also has a task to create a source distrib that includes the unit tests (per user request)

Change-Id: I6e47a18d2084ce5cf83efc731e2b3db95acbb6b5
Fixed null condition to ensure that null values get pushed back in the array.
replacing full array sort with a range sort
unit tests ensure broken comparators don't put null to the start of the set and than an empty set is never sorted
renamed variable 'minimum' and added explanation as to why it is used.
updated sort to also sort multiplier values - bug:1291
a faster ring search to identify the atoms and bonds which are members of rings.

Conflicts:
	src/test/org/openscience/cdk/modulesuites/McoreTests.java

Change-Id: I044a11b41ad170dac31db0d541a2a9da63616f26
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added new tests for equivalent class partitioning of aromatic systems (bug:3562476) Added test class to extra modules test suite

Signed-off-by: maclean <gilleain.torrance@gmail.com>
The adjacency matrix was corrected in order to account for aromatic bonds. There was also other corrections to the condition statements to set the node priorities. This corrections fix bug 3562476.

Signed-off-by: maclean <gilleain.torrance@gmail.com>
Reformatting patch

Change-Id: Id835e0260bac0092ba2e6306fa817fb4a2e457bd
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added a wavy bond type for unset stereobonds.

Change-Id: Ied54df213317d58d19f5e9c56b78ecbc18c16f8b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added an option to define a maximum drawable ring size for
the aromatic ring representation. Added dynamic scaling
based on the ring size for inner bond elements.

Change-Id: I33cacb2a898fdcfa35fd634f175a36dfbb1dc909
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Made QueryChemObject require a IChemObject builder when being constructed. This has a knock on effect that all the SMARTs atoms require the builder also. Although there are a lot of changes there's little front end API changes - the SMARTSQueryTool and PubChemFingerprinter now require a builder but other methods (e.g. descriptors and QueryAtomContainerCreator) could make use of the builder from other IChemObjects.

Change-Id: I64a6d7a3450ad1ad9b684d3679a11ace293e58fa
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
allow DescriptorEngine to load the two descriptors that require an IChemObjectBuilder injection. DescriptorTest was updated and generiffied to allow testing of the modified descriptors.
Added a unit test for the sorting of the multiplier

Change-Id: If572a12da7e89e80d2e986035c57acff928aeaa8
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Test to ensure that the atom type name is returned with IAtomType.toString()

Change-Id: I83ec328f025aabf0915a17ef04dcff5299690498
Signed-off-by: John May <john.wilkinsonmay@gmail.com>