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branch: 366-m-newIDesc…

Feb 21, 2012

  1. Egon Willighagen

    Removed the IAtomicDescriptor, IBondDescriptor, and IAtomPairDescriptor

    Change-Id: I2ff6a505f1f290d309135b7f401355defeb5a51c
    authored February 21, 2012
  2. Egon Willighagen

    Extracted the new helper method into a separate class

    Change-Id: I18ddf99e44f2887b24ff76e45733b45bd52d8b10
    authored February 21, 2012
  3. Egon Willighagen

    Use reflection to see if some descriptor is an atomic, bond, or other…

    … descriptor type
    
    Change-Id: I4c26730322462d603e9d9812fc1ab793ef5673cb
    authored February 21, 2012
  4. Egon Willighagen

    Added test to ensure that the descriptor implements a parameterized I…

    …MoleculePartDescriptor<?>
    
    Change-Id: I9e134099bdeceba40e6f1a5f588367141888caf5
    authored February 21, 2012

Feb 20, 2012

  1. Egon Willighagen

    Used the new QSAR API to merge the AbstractBondDescriptor and Abstrac…

    …tAtomicDescriptor classes
    
    Change-Id: I0ff2311aadaa12d05635da7fffa3e6900352aa8d
    authored February 20, 2012
  2. Egon Willighagen

    Used the new IAtomPair interface in the QSAR API

    Change-Id: I0fd0ca7b78a6fcd6c339dc645b56399ff6984ae1
    authored February 20, 2012
  3. Egon Willighagen

    Added the IAtomPair interface

    Change-Id: Ibb4bfce441f421ffe94cf3d8e17d7501b1ba4fba
    authored February 20, 2012

Feb 03, 2012

  1. Rajarshi Guha

    Merge branch 'foo'

    authored February 03, 2012
  2. Egon Willighagen

    Added a bit of missing test method annotation

    authored February 03, 2012
  3. John May

    Corrected JUnit version

    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    authored February 01, 2012 egonw committed February 03, 2012
  4. Egon Willighagen

    Renamed the IteratingMDLReader to a IteratingSDFReader, matching the …

    …format name
    authored February 03, 2012

Jan 31, 2012

  1. Egon Willighagen

    Write a CHARGE command when the entity has a non-zero charge

    authored January 31, 2012 rajarshi committed January 31, 2012
  2. Egon Willighagen

    Added a unit test for charged entities

    authored January 31, 2012 rajarshi committed January 31, 2012

Jan 25, 2012

  1. Rajarshi Guha

    Merge branch 'mopac'

    authored January 25, 2012

Jan 24, 2012

  1. Egon Willighagen

    Removed two static fields that are already provided by RingSizeCompar…

    …ator
    
    Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
    authored January 16, 2012 rajarshi committed January 24, 2012
  2. Egon Willighagen

    Updated to CDK coding standards:

    * Added the new MOPAC7 input format
    * CDK email in copyright header as contact; updated JavaDoc
    * Added test classes
    * Populated the getFormat() methods
    * Fixed accepting of other implementations of IAtomContainer
    * Added TestMethod annotation
    * JavaDoc fixes: missing JavaDoc, @inheritDoc, and a few methods that should be private
    * Reworked existing options as IOSettings
    * Made field private that do not need to be exposed
    * Implemented the setReader() methods, and test of a Reader is already buffered
    * better readable and longer var names
    * replace .equals("") with .isEmpty()
    * indexOf(char) is faster
    * less general Exception use
    authored December 19, 2011
  3. Egon Willighagen

    Updated to match the CDK hierarchy and classes; LEGO building block s…

    …tyle: no processing, just writing
    authored December 19, 2011
  4. ngn

    Added a Mopac 7.10 test file

    authored December 20, 2011 egonw committed January 24, 2012
  5. ngn

    Added code from Ambit2 for reading Mopac output files

    authored December 19, 2011 egonw committed January 24, 2012
  6. ngn

    Added code from Ambit2 for writing Mopac input files

    authored December 19, 2011 egonw committed January 24, 2012
  7. Egon Willighagen

    Added missing @TestMethod annotation, and two test methods

    authored January 16, 2012
  8. Egon Willighagen

    Added missing test classes for the POVRay, SVG, and CDKSourceCode for…

    …mats
    authored January 16, 2012
  9. Egon Willighagen

    Fixed API: the setResourceFormat() should accept a IResourceFormat

    authored January 16, 2012
  10. Egon Willighagen

    Added missing TestMethod annotations for the matching methods

    authored January 16, 2012
  11. Egon Willighagen

    Added a missing and corrected two other test class annotations

    authored January 16, 2012
  12. Egon Willighagen

    Fixed extending the most specific test class

    authored January 16, 2012
  13. Egon Willighagen

    Updated unit test for commit #3093241, where null's are always larger…

    … than an actual object
    authored January 16, 2012
  14. Egon Willighagen

    Removed two static fields that are already provided by RingSizeCompar…

    …ator
    authored January 16, 2012

Jan 23, 2012

  1. Egon Willighagen

    Very basic tests for the setWriter() methods (it cannot test if somet…

    …hing is really written, as we do not know what objects are supported by a random reader; therefore, we just expect that no exception is thrown)
    
    Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
    authored January 23, 2012 rajarshi committed January 23, 2012
  2. Egon Willighagen

    Use an enum, instead of ints

    Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
    authored January 23, 2012 rajarshi committed January 23, 2012
  3. Egon Willighagen

    Updated the copyright range

    authored January 23, 2012
  4. Egon Willighagen

    Merged cdk-1.4.x

    authored January 23, 2012
  5. Egon Willighagen

    Ensure the OpenJavaDocCheck plugins are compiled

    authored January 23, 2012
  6. Egon Willighagen

    In Eclipse, use the Eclipse way to find JUnit

    authored January 23, 2012

Jan 22, 2012

  1. Egon Willighagen

    Fixes for the pseudo atom patch backporting: allow reading of IAtomCo…

    …ntainer where IMolecule was already supported, fixed imports. Also removes an redundant, incorrect accepts() method
    
    Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
    authored January 22, 2012 rajarshi committed January 22, 2012
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