ProDy 1.1 Series
===============================================================================

.. contents::
   :local:


1.1 (June 1, 2012)
-------------------------------------------------------------------------------


**New Features**:

  * :func:`.iterFragments` function is added.

  * :func:`.findNeighbors` function is added.

  * :func:`.calcMSF` and :func:`.calcRMSF` functions are added.

  * :func:`.wrapAtoms` functions is added.

  * :func:`.extendMode` and :func:`.extendVector` functions are added.

  * :ref:`prody-contacts` command is added.

**Improvements**:

  * :func:`.moveAtoms` function is improved to move atoms to a specified
    location.

  * :class:`.DCDFile` and :func:`.parseDCD` take *astype* keyword argument for
    automatic type recasting for coordinate arrays.  This option can be used
    to convert 32-bit coordinate arrays to 64-bit automatically for higher
    precision calculations.

  * Commands :ref:`prody-anm`, :ref:`prody-gnm`, and :ref:`prody-pca` can
    extend a coarse grained model to backbone or all atoms of the residues.
    See their documentation pages.

**Changes**:

  * Color scale used by :func:`.showOverlapTable` is normalized by default.

  * :mod:`.tools` module is deprecated for removal, use :mod:`.utilities`
    instead.

  * *array* argument in :func:`.moveAtoms` is replaced with *by* keyword
    argument.

  * *which* argument in :meth:`.AtomGroup.copy` method is deprecated for
    removal in version 1.2.

  * :class:`.DCDFile` does not log information for most common type of DCD
    file, i.e. 32-bit CHARMM format.

  * :meth:`.Trajectory.getNextIndex` method is deprecated for removal in v1.2,
    use :meth:`~.Trajectory.nextIndex` instead.

**Bugfixes**:

  * Fixed several problems in :func:`.iterNeighbors` function and
    :class:`.Contacts` class that were introduced after transition to new
    :class:`.KDTree` interface.

  * Fixed a problem in setting selection strings of fragments identified using
    :func:`.findFragments`.

  * Fixed a problem in :func:`.calcCenter` related to weighted center
    calculation.

  * Fixed a problem of in copying :class:`.AtomMap` instances, which would
    emerge when bond information was present in unusual mappings, such as
    when atom orders are changed or an atom is present multiple times in the
    mapping.

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

**Improvements**:

  * Mode scaling options are improved.

  * Options added for extending coarse grained NMA models to residue backbone
    or all atoms.


