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base repository: cdk/cdk
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  • 11 commits
  • 9 files changed
  • 1 contributor

Commits on Dec 11, 2014

  1. CFP does not correctly implement count fingerprints. The similarity m…

    …easures (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>
    johnmay authored and egonw committed Dec 11, 2014
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  2. 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>
    johnmay authored and egonw committed Dec 11, 2014
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  3. Make method2 of the continuous tanimoto the default. It provides bett…

    …er discrimination.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  4. Tidy up Lingos similarity implementation and ensure aromatic SMILES a…

    …re generated.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  5. Ideally aromaticity would be done outside of the fingerprint. Since i…

    …t 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>
    johnmay authored and egonw committed Dec 11, 2014
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  6. Utils for creating bit and count fingerprints from feature maps.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  7. Produce bit and count fingerprints in Lingos.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  8. Allow CFP of varied length.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  9. Ensure first bit is never negative and use a count list for the hash …

    …counts.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  10. Delegate to the constructor of IntArrayCountFingerprint.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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  11. Check the classType is valid.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Dec 11, 2014
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