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base repository: cdk/cdk
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  • 17 commits
  • 37 files changed
  • 1 contributor

Commits on Aug 1, 2013

  1. Formatting AllRingsFinder to make changes more obvious.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  2. Helper class to allow us to quickly convert back to CDK 'Ring' object…

    …s - probably won't be needed in future and is private.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  3. Convert molecules to graphs and keeping track of bonds.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  4. Efficient conversion from int[] paths to rings.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  5. Removing old timeout (to be replaced with threshold) and deprecating …

    …methods modifying it. If a user attempts to set a timeout it will print to standard error prompt to use the non-deprecated method.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  6. Added threshold parameters enumeration.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  7. Allowing construction of AllRingsFinder using the new threshold values.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  8. Using new method for finding all rings of an isolated system.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  9. Ignoring timeout tests (threshold tests to be added in later) and inc…

    …luding guava.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  10. Adjusting timeout/threshold for bigRingSystem()

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  11. Using the newer RingSearch to partition rings and only process fused …

    …systems.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  12. Modify assertions to confirm output - the ring flags are already set …

    …by SMILES and to really test we need to unset.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  13. Correcting ring assembly - test changes showed that we forgot to put …

    …the atoms/bonds in the ring. Also the isolated rings can reach 'to' the ring size inclusive.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  14. Copyright update and removal of old implementation, Path is now repla…

    …ced by PathEdge.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  15. API documentation updated

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  16. Can't wait for dependency inheritance in maven...

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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  17. Fixing test regression that depended on the molecule having the same …

    …kekule form - i.e. order dependant. When the ring perception changed the order may not be exactly the same but nothing should rely on that fact. Setting the aromaticity fixes the test failure.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Aug 1, 2013
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