Ensure no modifications whilst iterating.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Encoding the existing aromaticity model from CDKHueckelAromaticityDetector and DoubleBondAcceptingAromaticityDetector as a new interface ElectronDontation. This separation makes it easier to use different (or a custom) aromaticity model within the CDK.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Rename ExoCyclicAtomTypeModelTest.java to ExocyclicAtomTypeModelTest.java

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
A simple aromaticity model for MDL/Mol2 file formats.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correct name for compound being tested.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correct check for cyclic bonds.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
The Daylight model for how many electrons are donated when computing aromaticity.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Including other aromaticity models in the 'standard' module suite.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Not enough electrons - then it cannot participate.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
For the simple cyclic pi bonds aromaticity model - don't allow atoms which are next to two cyclic pi bonds. Documentation wording also improved.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Utility to simplify bond lookup from index endpoints of the edge.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing some complexity by using the new edge to bond mapping.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Use the edge to bond map for a small performance gain.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Adding a generator for the cycles/rings used by the CDKHueckelAromaticityDetector and DoubleBondAcceptingAromaticityDetector.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity perception using configurable electron donation models and cycles.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Improved documentation - any more suggestions welcome.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Don't remove atoms whilst iterating.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Mark cyclic atoms and bonds before removing non-aromatic atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Changing factory method names for the CDK models. The factory does not take any attributes.

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