Comparing changes
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base repository: cdk/cdk
base: 5f0d0c61381c
head repository: cdk/cdk
compare: fdfbf5e8e092
- 17 commits
- 37 files changed
- 1 contributor
Commits on Aug 1, 2013
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Formatting AllRingsFinder to make changes more obvious.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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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>
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Convert molecules to graphs and keeping track of bonds.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Efficient conversion from int[] paths to rings.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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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>
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Added threshold parameters enumeration.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Allowing construction of AllRingsFinder using the new threshold values.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Using new method for finding all rings of an isolated system.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Ignoring timeout tests (threshold tests to be added in later) and inc…
…luding guava. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Adjusting timeout/threshold for bigRingSystem()
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Using the newer RingSearch to partition rings and only process fused …
…systems. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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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>
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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>
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Copyright update and removal of old implementation, Path is now repla…
…ced by PathEdge. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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Can't wait for dependency inheritance in maven...
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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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>
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