Removed obsolete meta files for the nonotify module

Change-Id: Ib05fdbdc097519199d3bf63b6303d42b7dddee63
Removed an obsolete dependency

Change-Id: I1fef4ca7e8b4c43ca967570ed71773a051afd117
Be happy with more than one assert in each test method

Change-Id: Idc0f7ffcd871ecc9d53d735a116b099c06cecc33

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
We're happy for abstract classes to be named differently

Change-Id: I9533e4cad790542eac0f75721e8afb14f49fcbdc

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing @cdk.githash annotation

Change-Id: Ie89fafdf1f8665a248b6a9f8a57fde50eefd43bc

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing end-of-first-line periods to the JavaDoc

Change-Id: I7862b007beb255b463d1727bde55a1294cb47fe3

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Reformatting MDLV2000Reader in preparation for patching.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolves warnings in the MDLV2000Reader class including, redundant assignment, redundant casts, using for int loops when for each can be used and using StringBuilder instead of StringBuffer. Unchecked casts have also been suppressed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow direct provision of the adjacent list to the cycle finder. This will allow us to apply some optimisations in aromaticity.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test the number of cycles found is the same when using the new method.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Avoid re-conversion of the CDK container.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Reinstates the behaviour of the CDKHueckelAromaticityDetector in that all atoms that can not be in an aromatic system are removed before finding the rings. This has little performance gain but it does allow us to exactly mimic the behaviour of the CDKHueckelAromaticityDetector for backwards compatibility.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removed the dependency on the data module, by adding the IChemObjectBuilder to the API

Change-Id: I05dc82cee22450879bec44bbbd8c98c58c9b7d75
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removing ignored CVS files, version control is currently using git.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing change log - still available on wiki: https://github.com/cdk/cdk/wiki

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
doxygen doesn’t appear to be used for any CDK doc - being such a small configuration this could easily be written if required.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
10+ year old scripts no longer run - the new way for running tests is ‘ant test-all’

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