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  • 18 commits
  • 31 files changed
  • 1 contributor

Commits on Jan 18, 2014

  1. Convert implicit hydrogens to explicit in tetrahedral elements. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  2. Minor cleanup and comments on removeHydrogens(). 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  3. Use org/cpy to refer to the two structures. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  4. Remove hydrogens in stereoelements. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  5. Rather than blindly remove hydrogens we now only remove hydrogens we … 

    …can accurately represent as implicit. Previously with molecular hydrogen an empty structure was returned - molecular hydrogen is now preserved. This makes more sense as we can then convert to/from explicit hydrogen without losing atoms - an empty structure definitely doesn’t represent molecular hydrogen and so ‘add explicit hydrogens’ would not put back in the correct number of atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  6. Updating other hydrogen removal methods to check if the hydrogen can … 

    …actually be implicit. Also the removeNonChiralHydrogens now also checks double-bond stereo chemistry.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  7. Store stereo-elements in a set. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  8. When adding two containers - also add stereo elements. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  9. Friendlier atom cloning - still throws the exception but at least the… 

    … cast can be removed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  10. Friendlier bond cloning. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  11. Don’t clear the stereo elements - cloning messing things up here but … 

    …is fixed now.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  12. Objects atoms when adjusting clone methods. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  13. required dependency 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  14. Stereo elements are now in a set - swap if they are out of order. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  15. Hydrogen removal now correctly persists stereo chemistry. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  16. no longer need the timeout - default threshold is good enough. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  17. Not sure if this is correct - but there nether was a clone method for… 

    … QueryAtom but builder3d tests complain otherwise. I ‘think’ is okay but don’t quote me on that.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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  18. Fixing atom cloning. 

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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