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base repository: cdk/cdk
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  • 8 commits
  • 12 files changed
  • 1 contributor

Commits on Sep 24, 2013

  1. Including the beam library in the SMILES module.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  2. Conversion of the CDK object model to Beam.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  3. Conversion from Beam to CDK objects.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  4. Iodine only belongs to the aliphatic and not the aromatic subset - it…

    … can not be lower case and this test does not work as intended. A correct example is to have an aliphatic carbon and an aromatic oxygen which make the symbol of Cobalt (non organic subset atom).
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  5. Removing redundant bracket. Generally such an error indicates somethi…

    …ng deeper is wrong. This test was checking hydrogen counts though so we can safely remove it.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  6. Noticeable performance improvement by avoiding invoking the factory e…

    …ach time. We cache a template atom/bond/container and then clone these when we need them. On large datasets provides a noticeable difference.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  7. Missing license headers and removal of a duplicate line.

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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  8. Only set aromatic flags if the atoms are aromatic AND the bond was im…

    …plicit.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 24, 2013
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