Bonds are bidirectional - resolves regression in smarts matching.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Changes to canon ranking means the ranks are now stable and the labels have changed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Hydrogen removal now requires non-null hydrogen counts.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Abstract test classes should be abstract.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test class should have 'Test' somewhere in the class name.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure stereo elements assertions are in the correct order.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Silent objects do not notify on these methods and the tests need to be overridden.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixing test errors (atom indices were wrong).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Wrong order of parameters.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
The test for vinylogous ester is not a bug but a limitation of the SMARTS used to match functional group. The test is now ignored as it will always fail. Additionally the fingerprint can not be used to filter substructures and we must override testBug706786 from the abstract superclass.
Correct tests for accepting IAtomContainers.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Annoyingly the AtomDiff reports there is a difference in the atom ID... when that's not what we are testing. As CML adds ids to atoms differences were being incorrectly reported. Adding an ID before we write the file resolves all but 1 failure.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
CML can't round trip exact mass at the moment.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
More readers that didn't correctly test of accepting IChemFile.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Access correct bond index.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Iterable list is immutable we need to wrap it in another instance.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Invoking correct method in test assertion.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
ElementRule needs a builder to create it's parameters. The parameter are null to start with and then created once a builder was available (i.e. when validated).

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