Allow SMARTS expressions of the form [h0] and [!h0] analogous to [H0] and [!H0]. Previously this was not possible to null handling semantics.
Make the CDK 2D atom colors modifiable and simplar with a map instance.

Change-Id: Ic22c6a731c56217ded2ca6e43f8df9b96ddb5d19
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Extend CDK 2D atom coloring.

Change-Id: I7e897c9a9b35a7e972350bc6accd60b580163b8a
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correct handling of empty reactions.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow SMARTS expressions of the form [h0] and [!h0] analogous to [H0] and [!H0]. Previously this was not possible to null handling semantics.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Make it possible to obtain an atom-atom and bond-bond map all in one. This is more useful then either the atom-atom or bond-bond maps alone.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Make sure array index is now called out of range. We only sort by low atomic number elements to minimise ring double bonds flipping between.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Add info on creating a Jar of sources.
Tell eclipse to run JavaCC on import (i.e. before the module is built).
Merge branch 'master' of github.com:cdk/cdk
Unit tests for bug reports by Yannick on the cdk-user@ mailing list

Change-Id: I20cdb8e7f9c0c25be4fbcf344e3dddfaf4e93794
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Already okay in the CDK but needed fixing in BEAM.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Update beam to 0.7. Minor fixes to Kekulisation, reset Ring Numbering between components (fragments are now canonical C1CC1.C1CC1 instead of C1CC1.C2CC2).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Avoid NPE due to implicit bond.

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