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branch: 366-m-newIDesc…
Commits on Feb 21, 2012
  1. Removed the IAtomicDescriptor, IBondDescriptor, and IAtomPairDescriptor

    authored
    Change-Id: I2ff6a505f1f290d309135b7f401355defeb5a51c
  2. Extracted the new helper method into a separate class

    authored
    Change-Id: I18ddf99e44f2887b24ff76e45733b45bd52d8b10
  3. Use reflection to see if some descriptor is an atomic, bond, or other…

    authored
    … descriptor type
    
    Change-Id: I4c26730322462d603e9d9812fc1ab793ef5673cb
  4. Added test to ensure that the descriptor implements a parameterized I…

    authored
    …MoleculePartDescriptor<?>
    
    Change-Id: I9e134099bdeceba40e6f1a5f588367141888caf5
Commits on Feb 20, 2012
  1. Used the new QSAR API to merge the AbstractBondDescriptor and Abstrac…

    authored
    …tAtomicDescriptor classes
    
    Change-Id: I0ff2311aadaa12d05635da7fffa3e6900352aa8d
  2. Used the new IAtomPair interface in the QSAR API

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    Change-Id: I0fd0ca7b78a6fcd6c339dc645b56399ff6984ae1
  3. Added the IAtomPair interface

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    Change-Id: Ibb4bfce441f421ffe94cf3d8e17d7501b1ba4fba
Commits on Feb 3, 2012
  1. @rajarshi

    Merge branch 'foo'

    rajarshi authored
  2. @johnmay

    Corrected JUnit version

    johnmay authored committed
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Commits on Jan 31, 2012
  1. @rajarshi

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

    authored rajarshi committed
  2. @rajarshi

    Added a unit test for charged entities

    authored rajarshi committed
Commits on Jan 25, 2012
  1. @rajarshi

    Merge branch 'mopac'

    rajarshi authored
Commits on Jan 24, 2012
  1. @rajarshi

    Removed two static fields that are already provided by RingSizeCompar…

    authored rajarshi committed
    …ator
    
    Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
  2. Updated to CDK coding standards:

    authored
    * 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
  3. Updated to match the CDK hierarchy and classes; LEGO building block s…

    authored
    …tyle: no processing, just writing
  4. @vedina

    Added a Mopac 7.10 test file

    vedina authored committed
  5. @vedina

    Added code from Ambit2 for reading Mopac output files

    vedina authored committed
  6. @vedina

    Added code from Ambit2 for writing Mopac input files

    vedina authored committed
Commits on Jan 23, 2012
  1. @rajarshi

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

    authored rajarshi committed
    …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>
  2. @rajarshi

    Use an enum, instead of ints

    authored rajarshi committed
    Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
  3. Updated the copyright range

    authored
  4. Merged cdk-1.4.x

    authored
Commits on Jan 22, 2012
  1. @rajarshi

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

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