ProDy 1.2 Series

1.2.1 (Sep 6, 2012)

If you are upgrading from ProDy v1.1, see also the below changes introduced in v1.2.

Bugfix:

• A problem in select module regarding Numpy numeric types is fixed. Problem would emerge on platforms which do not offer some numeric types, e.f. np.float16.
• Fixed problems in prody anm, prody gnm, and prody fetch related to writing output files.

Changes:

• The way that prody fetch command handles files containing PDB identifiers has changed.

1.2 (Aug 30, 2012)

Important Changes:

Package folder prody is moved into lib folder to prevent exceptions related to importing compiled packages from the installation folder.

Some changes in Trajectory and Ensemble methods related to linking, setting, and selecting atoms were made to make the interface more intuitive. These changes, which may break your code, are as follows:

• AtomGroup instances can be linked to a Trajectory using Trajectory.link() method and linking status of an instance can be checked using Trajectory.isLinked() medhod.
• Trajectory.setAtoms() method accepts AtomGroup and Selection instances and should be used to select a subset of atoms. This method will not link AtomGroup instance to the trajectory and also will not update the reference coordinates of the instance.
• Trajectory.select() and Ensemble.select() methods are removed and their functions are overloaded to Trajectory.setAtoms() and Ensemble.setAtoms() methods, respectively.
• Trajectory.getSelection() and Ensemble.getSelection() methods are removed, use Trajectory.getAtoms() and Ensemble.getAtoms() instead.
• Trajectory reference coordinates must be changed using Trajectory.setCoords() method.

For usage examples see Trajectory Analysis, Trajectory Analysis II, Frames and Atom Groups, and Trajectory Output.

New Features:

• Atom Flags, that are used in Atom Selections, is implemented. See its documentation for handy usage examples.
• sortAtoms() function is implemented.
• pickCentralConf() function is implemented to pick the conformation or the active coordinate set that is closest to the average of coordinate sets.
• writePSF(), a simple PSF file writer, is implemented.
• glob() utility function is implemented.
• iterPDBFilenames() function is implemented, which can be used to iterate over all PDB files stored in a local mirror of Protein Data Bank.
• findPDBFiles() function is implemented, which can be used to access PDB files in a path.

Improvements:

• HierView instances are built more efficiently. Two times speed-up is achieved by delaying instantiation of Chain and Residue instances until they are needed.
• Multiple Atom Flags can be used in Atom Selections without using 'and' operator, e.g. 'sidechain carbon' is the same as 'sidechain and carbon'.
• writePDB() accepts Ensemble, Conformation, and Frame instances as atoms argument.
• writePDB() function is around 25% faster.
• pickCentral() is extended to accept Atomic and Ensemble instances. Old function is now pickCentralAtom().
• prody align command and prody_align() function can handle non-protein atom selections (see examples for prody align).
• parsePDB() and writePDB() supports 100K and more atoms.

Changes:

• showOverlapTable() displays first set of modes along x axis of the plot.
• AtomGroup.setData() does not accept arrays with boolean data type, use AtomGroup.setFlags() instead.
• writePDB() function argument model is changed to csets that indicates the coordinate set index of atoms argument.
• PackageLogger.timing() does not return elapsed time, only logs this information.
• PackageLogger.startLogfile() is deprecated for removal in v1.3, use PackageLogger.start() instead.
• PackageLogger.closeLogfile() is deprecated for removal in v1.3, use PackageLogger.close() instead.
• from prody.utilities import * will not work anymore due to potential name conflicts with Python standard library functions. Import required functions explicitly.
• writePDB() appends .pdb extension to filename when it is not present
• prody select command positional argument order is changed to allow for handling multiple PDBs at a time. Old older will be supported until v1.4, but a warning message will be issued.
• select argument in alignCoordsets() is removed, make selection outside of the function instead.

Deprecations:

• AtomGroup.getHeteros() method has been deprecated for removal in v1.3, use getFlags('hetatm') instead.
• AtomMap.getMappedFlags() and AtomMap.getDummyFlags() methods have been deprecated for removal in v1.3, use getFlags('mapped') and getFlags('dummy') instead.
• getVerbosity() and setVerbosity() are deprecated for removal in v1.3, use confProDy() instead which save changes permanently.
• NMA.getModes() and ModeSet.getModes() methods are deprecated for removal in v1.3, use list(), e.g. list(model), instead.

Bugfixes:

• Fixed a bug in prody contacts command that arose problems when when selecting a subset of the target atoms.

Normal Mode Wizard

Improvements:

• ProDy Interface shows the size of the trajectory output file for PCA calculations.
• Mode Graphics Options allows for copying arrows settings from one mode to another.
• Color scale method and midpoint for protein coloring based on mobility and bfactors can be adjusted from Protein Graphics Options panel.