ProDy 1.3 Series
===============================================================================

.. contents::
   :local:


1.3.1 (Nov 6, 2012)
-------------------------------------------------------------------------------

**New Features**:

  * Added :func:`.fetchPDBviaHTTP` and :func:`.fetchPDBviaFTP` functions.

  * Added :func:`.copyFile` function to :mod:`.utilities`.

  * Added ``prody test`` command for convenient testing of ProDy package.

**Improvements**:

  * Improved :func:`.gunzip` function to handle :file:`.gz` extensions and
    string buffers.

**Changes**:

  * :func:`.getWWPDBFTPServer` and :func:`.setWWPDBFTPServer` are deprecated
    for removal in v1.4, use :func:`.wwPDBServer` instead.

  * :func:`.getPDBLocalFolder` and :func:`.setPDBLocalFolder` are deprecated
    for removal in v1.4, use :func:`.pathPDBFolder` instead.

  * :func:`.getPDBMirrorPath` and :func:`.setPDBMirrorPath` are deprecated
    for removal in v1.4, use :func:`.pathPDBMirror` instead.

  * :func:`.getPDBCluster` is deprecated for removal in v1.4, use
    :func:`.listPDBCluster` instead.

  * :func:`.getReservedWords` is deprecated for removal in v1.4, use
    :func:`.listReservedWords` instead.

  * :func:`.getNonstdProperties` is deprecated for removal in v1.4, use
    :func:`.listNonstdAAProps` instead.

**Bugfix**:

  * Fixed a bug in :class:`.HierView` that would cause wrong assignment of
    residue/chain indices to atoms when residue or chain atoms are separated
    by atoms of other entities.  This would also caused problems when making
    keyword selections, such as :term:`protein`.

  * Added dummy atom check in :meth:`.Ensemble.setAtoms` and
    :meth:`.Trajectory.setAtoms` methods to avoid indexing problems.

1.3 (Sep 30, 2012)
-------------------------------------------------------------------------------

**Improvements**:

  * :mod:`~.atomic.select` module and its documentation are completely
    rewritten.  :class:`.Select` class uses simplest possible parser
    to evaluate selection strings and achieves more than 25% speed-up
    on average.

  * :ref:`selections` become more forgiving of small typos, but will issue
    warning messages when they are detected via :exc:`.SelectionWarning`.
    These messages can be turned of using :func:`.confProDy`

  * Functions used in :ref:`prody-apps` have been refactored to allow for using
    them directly.  See :mod:`.apps` for their documentation.

**Bugfix**:

  * A problem in :ref:`prody-catdcd` command that was introduced when
    refactoring :mod:`~prody.trajectory` classes is fixed.


