ProDy 1.3 Series

1.3.1 (Nov 6, 2012)

New Features:

• Added fetchPDBviaHTTP() and fetchPDBviaFTP() functions.
• Added copyFile() function to utilities.
• Added prody test command for convenient testing of ProDy package.

Improvements:

• Improved gunzip() function to handle .gz extensions and string buffers.

Changes:

• getWWPDBFTPServer() and setWWPDBFTPServer() are deprecated for removal in v1.4, use wwPDBServer() instead.
• getPDBLocalFolder() and setPDBLocalFolder() are deprecated for removal in v1.4, use pathPDBFolder() instead.
• getPDBMirrorPath() and setPDBMirrorPath() are deprecated for removal in v1.4, use pathPDBMirror() instead.
• getPDBCluster() is deprecated for removal in v1.4, use listPDBCluster() instead.
• getReservedWords() is deprecated for removal in v1.4, use listReservedWords() instead.
• getNonstdProperties() is deprecated for removal in v1.4, use listNonstdAAProps() instead.

Bugfix:

• Fixed a bug in 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 protein.
• Added dummy atom check in Ensemble.setAtoms() and Trajectory.setAtoms() methods to avoid indexing problems.

1.3 (Sep 30, 2012)

Improvements:

• select module and its documentation are completely rewritten. Select class uses simplest possible parser to evaluate selection strings and achieves more than 25% speed-up on average.
• Atom Selections become more forgiving of small typos, but will issue warning messages when they are detected via SelectionWarning. These messages can be turned of using confProDy()
• Functions used in ProDy Applications have been refactored to allow for using them directly. See apps for their documentation.

Bugfix:

• A problem in prody catdcd command that was introduced when refactoring trajectory classes is fixed.