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branch: 355-m-mopacCha…

Jan 31, 2012

  1. Egon Willighagen

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

    authored
  2. Egon Willighagen

    Added a unit test for charged entities

    authored

Jan 25, 2012

  1. Rajarshi Guha

    Merge branch 'mopac'

    rajarshi authored

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 rajarshi committed
  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
  3. Egon Willighagen

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

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

    Added a Mopac 7.10 test file

    vedina authored committed
  5. ngn

    Added code from Ambit2 for reading Mopac output files

    vedina authored committed
  6. ngn

    Added code from Ambit2 for writing Mopac input files

    vedina authored committed
  7. Egon Willighagen

    Added missing @TestMethod annotation, and two test methods

    authored
  8. Egon Willighagen

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

    …mats
    authored
  9. Egon Willighagen

    Fixed API: the setResourceFormat() should accept a IResourceFormat

    authored
  10. Egon Willighagen

    Added missing TestMethod annotations for the matching methods

    authored
  11. Egon Willighagen

    Added a missing and corrected two other test class annotations

    authored
  12. Egon Willighagen

    Fixed extending the most specific test class

    authored
  13. Egon Willighagen

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

    … than an actual object
    authored
  14. Egon Willighagen

    Removed two static fields that are already provided by RingSizeCompar…

    …ator
    authored

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 rajarshi committed
  2. Egon Willighagen

    Use an enum, instead of ints

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

    Updated the copyright range

    authored
  4. Egon Willighagen

    Merged cdk-1.4.x

    authored
  5. Egon Willighagen

    Ensure the OpenJavaDocCheck plugins are compiled

    authored
  6. Egon Willighagen

    In Eclipse, use the Eclipse way to find JUnit

    authored

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 rajarshi committed
  2. Rajarshi Guha

    Updates MDL readers to set symbol of pseudatoms to label. Ensures tha…

    …t writing such a molecule does not force the SDF writer to see all pseudoatoms as R groups. Added unit test and test cases for V2000 and V3000 readers as well as V2000 writer
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
    Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
    rajarshi authored

Jan 16, 2012

  1. Egon Willighagen

    Made the method static, to follow JUnit practices

    authored

Jan 03, 2012

  1. Egon Willighagen

    Release 1.5.0 versioned

    authored
  2. Egon Willighagen

    Merged cdk-1.4.x

    authored

Jan 02, 2012

  1. Rajarshi Guha

    Merge pull request #9 from danielszisz/patch-5

    This commit puts a single comment line for the molecule @param in placeA...
    rajarshi authored
  2. Daniel Szisz

    This commit puts a single comment line for the molecule @param in pla…

    …ceAliphaticHeavyChain() method.
    
    
    commited by danielszisz
    danielszisz authored

Dec 31, 2011

  1. Egon Willighagen

    Bumped version: branch open for more bug fixes

    authored
  2. Egon Willighagen

    Added Yap Chun Wei to the list of authors

    authored
  3. Egon Willighagen

    Bumped release version to 1.4.7

    authored

Dec 29, 2011

  1. Egon Willighagen

    Another hot fix: use @link with the full qualified class name, and re…

    …moved the import, to fix a dependency issue
    authored
  2. Egon Willighagen

    Added a @deprecated tag on the nonotify data classes, pointing to the…

    … silent implementation
    
    Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
    authored rajarshi committed
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