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  • 12 commits
  • 36 files changed
  • 3 contributors

Commits on Nov 1, 2012

  1. Added an alternative aromaticity perception model, which is happy abo… 

    …ut double bonds pointing outwards from aromatic rings

Change-Id: I631ffb26431d5c80d1eb6495dbdff30e7113722e
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
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  2. Because the placement of double bonds is not deterministic, we cannot… 

    … be sure we always get them at the same location. Better is to just test that all carbons are perceived as C.sp2 and that they are aromatic.

Change-Id: Ifc5e41a8378de3e6b22f698c77a36fa67b88cbc8
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
    @egonw
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  3. Testing that benzoquinone is perceived as aromatic using the alternat… 

    …ive detection method.

Change-Id: Ia64a05d62546f6bd055043e28da68e60c67b740e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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    johnmay authored and egonw committed Nov 1, 2012
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  4. Removed cdk.create dates, as suggested by the reviewer 

    Change-Id: I3fbef0fde1991e4c9f737450bacfefd37027c907
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  5. Removed SVN tags, as suggested by the reviewer 

    Change-Id: I25728722640b54d2ca3d65f6d8758ce2adf10df6
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  6. Documenting new method and extended unit test 

    Added documentation to method created to deal with N.planar.3 perception (S Beisken).
Added unit test to ensure that explicit hydrogens to do change the perception.
Included @cdk.inchi taglet

Change-Id: I4d43507be9357dc6fec0409e5628428202bd88cc
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    @johnmay @egonw
    johnmay authored and egonw committed Nov 1, 2012
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  7. Added missing test annotation 

    Change-Id: I66318bc6a324de0ed0bb42182e99238896bf2db8
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  8. Be more informative when the test fails 

    Change-Id: I1603134367a41849fa24da10da943f63850f35c0
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  9. add isEmpty() to classes/interfaces ChemModel, AtomContainerSet, Reac… 

    …tionSet, Crystal and AtomContainer

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
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  10. Added unit test and @TestMehtod annotaitons for new 'isEmpty' mehtods 

    Change-Id: If3ab0f5797345e40596762afd4f6fc9db80b76fb
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/ChemModel.java
	src/main/org/openscience/cdk/debug/DebugChemModel.java
	src/main/org/openscience/cdk/silent/ChemModel.java
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  11. s/Molecule/AtomContainer/ 

    Change-Id: I854763947af96b956c948967a131dfc32b7a53c6
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  12. Added the now requires isEmpty() method, copying the implementation f… 

    …rom AtomContainer

Change-Id: I5007b9e1438b83951d7b07d1a0d02f7e842db797
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