Formatting AllRingsFinder to make changes more obvious.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Helper class to allow us to quickly convert back to CDK 'Ring' objects - probably won't be needed in future and is private.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Convert molecules to graphs and keeping track of bonds.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Efficient conversion from int[] paths to rings.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing old timeout (to be replaced with threshold) and deprecating methods modifying it. If a user attempts to set a timeout it will print to standard error prompt to use the non-deprecated method.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added threshold parameters enumeration.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allowing construction of AllRingsFinder using the new threshold values.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using new method for finding all rings of an isolated system.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ignoring timeout tests (threshold tests to be added in later) and including guava.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Adjusting timeout/threshold for bigRingSystem()

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using the newer RingSearch to partition rings and only process fused systems.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Modify assertions to confirm output - the ring flags are already set by SMILES and to really test we need to unset.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correcting ring assembly - test changes showed that we forgot to put the atoms/bonds in the ring. Also the isolated rings can reach 'to' the ring size inclusive.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Copyright update and removal of old implementation, Path is now replaced by PathEdge.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Can't wait for dependency inheritance in maven...

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixing test regression that depended on the molecule having the same kekule form - i.e. order dependant. When the ring perception changed the order may not be exactly the same but nothing should rely on that fact. Setting the aromaticity fixes the test failure.

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