The rotatable bond count descriptor should not include C-N amides and terminal hydrogen- and hetero-atoms for the extended Lipinki's rule of five implementation (see Veber, D.F. et al., 2002. Journal of medicinal chemistry, 45(12), pp.2615–23). The parameters for the rotatable bond counts descriptor have been modified to that end and an option has been added to exclude simple C-N amides (ignoring tautomeric or charged constitutions).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
The Vertex Adjacency Magnitude descriptor requires the number of heavy atom - heavy atom bonds as input. The current incorrect calculation retrieves the number of heavy atoms instead. Correct bond number estimation and test cases have been added.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Storage and manipulation of an independent edge-set, a matching. A matching can be used to represent pi bond placement in conjugated/aromatic systems.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
DisjointSetForest generally useful - move to cdk-standard. Left in the same package for now.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Maximum matching using Edmond's blossom algorithm.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Utility in the Matching API provides simplified procedure to assigning a perfect matching.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
We can correctly define the descriptors exported by each module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move resources files required by cdh-hash to that module and eliminates dependence on testdata.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move the hash resources files to the same package as the test that needs them.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Dependencies that can be safely removed from cdk-group and cdk-hash.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
We can remove the dependence on cdk-extra and valency check by not use the MoleculeFactory. Using cdk-data (test) isn't ideal but is better than extra.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move test resources to be local to the test that requires them. These files in particularly have been reused in pcore/io so the originals have been left in place for the moment.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Pattern implementation for SMARTS queries.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Random test order causes failure now default option is to ignore aromaticity.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Check null hydrogen count [bug:1335]

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Similarity measure was modified (d1527c6) but value was not updated.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove language assertion that caused test error. The test assertions were passing and the lang assert was causing an error randomly. This class will be moved to a deprecated module shortly.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Triplet = 2 unpaired electrons, not currently represented.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Unpaired electrons affect hydrogen count.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Exceptions being thrown in functional fingerprint generation.