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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 Guha

    Merge branch 'foo'

    rajarshi authored
  2. John May

    Corrected JUnit version

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

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

    authored rajarshi committed
  2. Rajarshi Guha

    Added a unit test for charged entities

    authored rajarshi committed
Commits on Jan 25, 2012
  1. Rajarshi Guha

    Merge branch 'mopac'

    rajarshi authored
Commits on Jan 24, 2012
  1. Rajarshi Guha

    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…

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    …tyle: no processing, just writing
  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
Commits on Jan 23, 2012
  1. Rajarshi Guha

    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 Guha

    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 Guha

    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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