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>
Terminate SMARTS parsing on whitespace or EOF.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated the default value in the unit test

Change-Id: Ie5b55a72381fa3d447642fa5bef0a49362ffd5d5
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a PMD warning: final static vars should have fully capatalized names

Change-Id: Ife64671a946ffda202c35a79e94b0f5096a0fcf7

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed a private, unused variable

Change-Id: I60ebac75237655fcfe5ea553c92fe04f46449c4e

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a PMD warning: removed an underscore from a non-final var

Change-Id: I36bd56a172ae92259b6935aca6875f3db6f2026f

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed dead code

Change-Id: I52eeedcd2e3e15953d60d1abb6131c1bfadfb0da

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a PMD warning: final static vars should have fully capatalized names

Change-Id: I2404c85a8c5fe55ae7837da88363bd68a2a38a33

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a PMD warning: removed an underscore from a non-final var

Change-Id: I22f17b64ebb97b605402b6636bfa02be5fcb1ac9

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a PMD warning: removed an underscore from a non-final var

Change-Id: I1a7bdaec31884988b96ac4701eb1535ae73a948d

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