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>
Allow CFP of varied length.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure first bit is never negative and use a count list for the hash counts.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Delegate to the constructor of IntArrayCountFingerprint.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Check the classType is valid.

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