New Features:
- Added :func:`.fetchPDBviaHTTP` and :func:`.fetchPDBviaFTP` functions.
- Added :func:`.copyFile` function to :mod:`.utilities`.
- Added
prody testcommand 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.
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.