ProDy 0.2 Series
===============================================================================

.. contents::
   :local:


0.2 (Nov 16, 2010)
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**Important Changes**:


  * Single word keywords *not* followed by "and" logical operator are not
    accepted, e.g. "protein within 5 of water" will raise a
    :class:`.SelectionError`, use "protein and within 5 of water" instead.

  * :func:`findMatchingChains` is renamed to  :func:`.matchChains`.

  * :func:`showOverlapMatrix` is renamed to :func:`.showOverlapTable`.

  * Modules are reorganized.

**New Features**:

  * :class:`.Atomic` for easy type checking.

  * :class:`.Contacts` for faster intermolecular contact identification.

  * :class:`.Select` can identify intermolecular contacts. See :ref:`contacts`
    for an examples and details.

  * :func:`.sampleModes` implemented for sampling conformations along normal
    modes.

**Improvements**:

  * :mod:`.proteins.compare` functions are improved. Now they perform sequence
    alignment if simple residue number/identity based matchin does not work,
    or if user passes ``pwalign=True`` argument. This impacts the speed
    of X-ray ensemble analysis.

  * :class:`.Select` can cache data optionally. This results in speeds up from
    2 to 50 folds depending on number of atoms and selection operations.

  * Implementation of :func:`.showProjection` is completed.

Normal Mode Wizard
^^^^^^^^^^^^^^^^^^

**Release 0.2.3**

  * For each mode a molecule for drawing arrows and a molecule for showing
    animation is formed in VMD on demand. NMWiz remembers a color associated
    with a mode.

  * Deselecting a residue by clicking on a plot is possible.

  * A bug causing incorrect parsing of NMD files from ANM server is fixed.


**Release 0.2.2**

  * Selection string option allows user to show a subset of arrows matching
    a VMD selection string. Optionally, this selection string may affect
    protein and animation representations.

  * A bug that caused problems when over plotting modes is removed.

  * A bug affecting line width changes in plots is removed.

  * Selected residue representations are colored according to the color of the
    plot.

**Release 0.2.1**

  * Usability improvements.

  * Loading the same data file more than once is prevented.

  * If a GUI window for a dataset is closed, it can be reloaded from the main
    window.

  * A dataset and GUI can be deleted from the VMD session via the main window.

**Release 0.2**

  * Instant documentation is improved.

  * Problem with clearing selections is fixed.

  * Plotting options frame is populated.

  * Multiple modes can be plotted on the same canvas.