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.
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.