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>
CFP does not correctly implement count fingerprints. The similarity measures (see Tanimoto class) expect the bits in sorted order. Without this invariant the CFP similarity is way off par. (Spotted by Roger)

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Flip around the implementation and the default (we're going to switch them and use method2).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Make method2 of the continuous tanimoto the default. It provides better discrimination.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Tidy up Lingos similarity implementation and ensure aromatic SMILES are generated.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ideally aromaticity would be done outside of the fingerprint. Since it is already there we don't want to take it out but we can avoid the need to do atom typing by using a different aromaticity model.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Utils for creating bit and count fingerprints from feature maps.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Produce bit and count fingerprints in Lingos.

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