Empty targets are also a problem for the substructure search. Simple checks avoids the infinite loop.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Repository config to use RELEASE and LATEST.
Update README.md
Correcting typos.
Ignore aromatic bonds by default. The option has be deprecated but should be removed in future. Global state, therefore impossible to test reliably.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test that three valent nitrogen cations (radical) are not allow to be aromatic [bug:1332]

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Check for normal valence in aromatic model before anything else.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow five valent nitrogen for non-charge separated representation, see pyridinone test case.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Similarity measure was modified (d1527c6) but value was not updated.
Remove language assertion that caused test error. The test assertions were passing and the lang assert was causing an error randomly. This class will be moved to a deprecated module shortly.
Replacing usage of the SSSRFinder.
Using TripletCycles for PubChemFingerprinter. These better reflect the set of rings described in the documentation.
Remove import.
Removing SSSRFinder from SMARTSQueryTool - note it was not used.
fixup
Use the CDK based ShortestPaths.