javadoc

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated the source URI for updates from the SF platform

Change-Id: I0d9d168e8207ccb0e0ae3599a565d688defc4e75
Added additional checks to fix NPE regressions

Change-Id: Ic1c54c000b22b27a776827a9e3ac8b0ff2a78c26
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added line separator for multiline extra data (when length < 80 chars).

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Don't change anything except the hydrogen count

Change-Id: I0933be18bef3cf9221d39a1485c6e396ec06d3cf
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removing long running test which did not have any assertions.
Fixed unit tests: now that the addEx|ImplicitHydrogens() doesn't change atom type names anymore, we have to do that explicitly

Change-Id: Ib954b80bea8b78bd4d8bf80970640ae210a9bea5
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Another NPE test: when the atomicNumber doesn't correspond to a isotope list

Change-Id: I9e25735117668c7c5e5b30336be39d0db2710816
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
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>