Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: cdk/cdk
base: 93036136efb8
Choose a base ref
...
head repository: cdk/cdk
compare: 3e63a7513c3e
Choose a head ref
  • 12 commits
  • 5 files changed
  • 1 contributor

Commits on Sep 17, 2013

  1. Remove global bond length.

    Change-Id: Ibe46c3ecdbf824bd972b88c65af7f2af54d7499e
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    dbc1b3d View commit details
    Browse the repository at this point in the history
  2. Use the average bond length of the molecule.

    Change-Id: Ib059077fb100b8512017df6f6d702148cac83e22
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    6f25d47 View commit details
    Browse the repository at this point in the history
  3. Overlap cutoff to 1/4th average bond length rather than 1/10th.

    Change-Id: I9959152fcc9b0d840c6044de70d609dc82e8ff9e
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    3eb97e1 View commit details
    Browse the repository at this point in the history
  4. Reusing utilities for RecursiveTests

    Change-Id: I06767388a19467a3614eef7847b3d0677a08bb62
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    aea2dcc View commit details
    Browse the repository at this point in the history
  5. Demonstrating that the recursive mismatch of the test is due to Dayli…

    …ght/CDK aromatic differences - testRecursive28.
    
    Change-Id: I260b0c4f7853bf4c9f7a5aa6547c6b1a2b20073e
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    ccb82bd View commit details
    Browse the repository at this point in the history
  6. Demonstrating that the recursive mismatch of the test is due to Dayli…

    …ght/CDK aromatic differences - testRecursive29.
    
    Change-Id: I941a22270a034d437ac36d6d2ad803c40ea583c6
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    2815d39 View commit details
    Browse the repository at this point in the history
  7. Demonstrating that the recursive mismatch of the test is due to Dayli…

    …ght/CDK aromatic differences - testRecursive26.
    
    Change-Id: I3c45286eba829036f0a051203b1260a64e52b59e
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    c85c215 View commit details
    Browse the repository at this point in the history
  8. Demonstrating that the recursive mismatch of the test is due to Dayli…

    …ght/CDK aromatic differences - testRecursive27.
    
    Change-Id: I2f68e3fd23637a1a5d4c706940d62b99eec7ec36
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    547014d View commit details
    Browse the repository at this point in the history
  9. There are 142 lines in 'data/smiles/drugs.smi' but only 141 non-empty…

    … lines. Technically according to the OpenSMILES specification an empty string is a valid SMILES string but the current IteratingSMILESReader skips empty molecules (a good thing).
    
    Change-Id: Iec648a7a39d7e868620623599bc80213d3442e5d
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    63ab46d View commit details
    Browse the repository at this point in the history
  10. Altering assertions for what CDK perceives as aromatic.

    Change-Id: Ia5996de81114e3ded907ac620955cc6031e9a66d
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    900e676 View commit details
    Browse the repository at this point in the history
  11. Test that when the aromaticity is preserve the expected number matche…

    …s are found.
    
    Change-Id: I00eb477ead115dc6057e396d0e3e10d0066ad66f
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    d10db9e View commit details
    Browse the repository at this point in the history
  12. Correct assertion in atomic tsar descriptor. Assertion was likely inc…

    …orrect due using the number instead of the index. Using the index '12' to access atom 13 provides the expected result. The assertions were altered to test all added hydrogens - for which two are adjacent to an aromatic system.
    
    Change-Id: I84a15de8348cb10407e91edc0cefe9462d7e0a00
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    johnmay authored and egonw committed Sep 17, 2013
    Copy the full SHA
    3e63a75 View commit details
    Browse the repository at this point in the history