Removing duplicate dependency.
Junit should have test scope.
Added recognition of MOPAC 2007, 2009 and 2012 output files.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
includes suggestions from John May

https://github.com/cdk/cdk/pull/36

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
added unit tests for MopacFormats 2007,2009 & 2012

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
updated older Mopac formats and unit tests

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Migrating FiguerasSSSRFinder to 'cdk-legacy' and the helper 'Queue' class.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Replace SSSRFinder usage with the more recent 'Cycles' impl.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Migrate SSSRFinder to 'cdk-legacy' along with helper classes.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Minor optimisation - shortest path only needs to computed once.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move BFSShortestPath to 'cdk-legacy' module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move over SSSRFinder helper classes (we have alternatives for these). BiconnectivityInspector = RingSearch, MinimalPathIterator = ShortestPaths.pathsTo().

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
jgrapht is now only required by the 'cdk-legacy' module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure canonical labelling can still be computed with explicit hydrogens. This was broken in a previous patch.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test the CIFReader can read input. Some guards have been added to prevent this.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated to use Map and Iterator instead of Hashtable and Enumeration

Change-Id: I92e1fba528371f1253a708a24823f2fe66690f0e

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Use IAtom instead of Atom

Change-Id: If7752313311039a29b3af0b6d88a811f13972832

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed a needless String variable

Change-Id: I767b2d6e464a300d36193e34d91924ae38ce0ca4

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added closing of many IO resources, fixing PMD warnings

Change-Id: I4fbaf0b9eb9c3f4e2f9fb226ee46dc5e12a10126

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