Multiline SD value joined with non OS newline [bug:1337]

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Mask hydrogens in canonical labelling.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Symmetry of heavy atoms (skeleton) independent of explicit hydrogens.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Include unpaired electrons sooner to catch negative hydrogen count in existing conditionals [Fixes:1343].

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Encapsulate CML stack and make package private.

Change-Id: I79dbc0b2477f4504ac7f49cfd51f884026f6f30d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move new resource file to the module where it is used.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Mechanism for marking slow running tests with JUnit groups/categories.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Marking several slow running tests across various modules.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Formatting pom.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Run slow tests by invoking 'mvn test -Pslow-tests'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure atomic number is set when reading Mol2.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Improved Mol2 atom type handling.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added command to build source jars.
Added two missing bond order types

Change-Id: I889a6cce3ed75f68f56cbc53659dd5a7ab64eed4
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Configuring jacoco code coverage plugin. Due to separate prod/test modules some extra config is required and the setup cannot be bound to a build phase. When invoked, it is important that the report is built separately, example - 'mvn jacoco:prepare-agent test; mvn jacoco:report'.
Use the @cdk.cite mechanism of citing papers

Change-Id: I9cf52837cf6a2936eb6e9f6f3c99bbf4ef9ed549
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed unused imports and code

Change-Id: I9a3428fe2c0004bc87f632daf423611d118bfd45
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Very minor JavaDoc improvements

Change-Id: I4f639ecd400d4b84db7ed6d8a487ba8ec61c1c66
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
These atoms need to be recognised for creating extended tetrahedral (allene) stereo elements.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Additional commit to fix still failing test. The previous example was hitting a heuristic in the code, where there is more than one hydrogen the type is automatically set to non-stereogenic. This was the case for the terminal atoms in this extended tetrahedral example.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>