If you are upgrading from ProDy v1.1, see also the below changes introduced in v1.2.
Bugfix:
- A problem in :mod:`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 :ref:`prody-anm`, :ref:`prody-gnm`, and :ref:`prody-fetch` related to writing output files.
Changes:
- The way that :ref:`prody-fetch` command handles files containing PDB identifiers has changed.
Important Changes:
Package folder :file:`prody` is moved into :file:`lib` folder to prevent exceptions related to importing compiled packages from the installation folder.
Some changes in :class:`.Trajectory` and :class:`.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:
- :class:`.AtomGroup` instances can be linked to a :class:`.Trajectory` using :meth:`.Trajectory.link` method and linking status of an instance can be checked using :meth:`.Trajectory.isLinked` medhod.
- :meth:`.Trajectory.setAtoms` method accepts :class:`.AtomGroup` and :class:`.Selection` instances and should be used to select a subset of atoms. This method will not link :class:`.AtomGroup` instance to the trajectory and also will not update the reference coordinates of the instance.
- :meth:`.Trajectory.select` and :meth:`.Ensemble.select` methods are removed and their functions are overloaded to :meth:`.Trajectory.setAtoms` and :meth:`.Ensemble.setAtoms` methods, respectively.
- :meth:`.Trajectory.getSelection` and :meth:`.Ensemble.getSelection` methods are removed, use :meth:`.Trajectory.getAtoms` and :meth:`.Ensemble.getAtoms` instead.
- :class:`.Trajectory` reference coordinates must be changed using :meth:`.Trajectory.setCoords` method.
For usage examples see :ref:`trajectory`, :ref:`trajectory2`, :ref:`frame`, and :ref:`outputtraj`.
New Features:
- :ref:`flags`, that are used in :ref:`selections`, is implemented. See its documentation for handy usage examples.
- :func:`.sortAtoms` function is implemented.
- :func:`.pickCentralConf` function is implemented to pick the conformation or the active coordinate set that is closest to the average of coordinate sets.
- :func:`.writePSF`, a simple PSF file writer, is implemented.
- :func:`.glob` utility function is implemented.
- :func:`.iterPDBFilenames` function is implemented, which can be used to iterate over all PDB files stored in a local mirror of Protein Data Bank.
- :func:`.findPDBFiles` function is implemented, which can be used to access PDB files in a path.
Improvements:
- :class:`.HierView` instances are built more efficiently. Two times speed-up is achieved by delaying instantiation of :class:`.Chain` and :class:`.Residue` instances until they are needed.
- Multiple :ref:`flags` can be used in :ref:`selections` without using
'and'operator, e.g.'sidechain carbon'is the same as'sidechain and carbon'.- :func:`.writePDB` accepts :class:`.Ensemble`, :class:`.Conformation`, and :class:`.Frame` instances as atoms argument.
- :func:`.writePDB` function is around 25% faster.
- :func:`.pickCentral` is extended to accept :class:`.Atomic` and :class:`.Ensemble` instances. Old function is now :func:`.pickCentralAtom`.
- :ref:`prody-align` command and :func:`.prody_align` function can handle non-protein atom selections (see examples for :ref:`prody-align`).
- :func:`.parsePDB` and :func:`.writePDB` supports 100K and more atoms.
Changes:
- :func:`.showOverlapTable` displays first set of modes along x axis of the plot.
- :meth:`.AtomGroup.setData` does not accept arrays with boolean data type, use :meth:`.AtomGroup.setFlags` instead.
- :func:`.writePDB` function argument model is changed to csets that indicates the coordinate set index of atoms argument.
- :meth:`.PackageLogger.timing` does not return elapsed time, only logs this information.
- :meth:`.PackageLogger.startLogfile` is deprecated for removal in v1.3, use :meth:`.PackageLogger.start` instead.
- :meth:`.PackageLogger.closeLogfile` is deprecated for removal in v1.3, use :meth:`.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.- :func:`.writePDB` appends :file:`.pdb` extension to filename when it is not present
- :ref:`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 :func:`.alignCoordsets` is removed, make selection outside of the function instead.
Deprecations:
- :meth:`.AtomGroup.getHeteros` method has been deprecated for removal in v1.3, use
getFlags('hetatm')instead.- :meth:`.AtomMap.getMappedFlags` and :meth:`.AtomMap.getDummyFlags` methods have been deprecated for removal in v1.3, use
getFlags('mapped')andgetFlags('dummy')instead.- :func:`.getVerbosity` and :func:`.setVerbosity` are deprecated for removal in v1.3, use :func:`.confProDy` instead which save changes permanently.
- :meth:`.NMA.getModes` and :meth:`.ModeSet.getModes` methods are deprecated for removal in v1.3, use :func:`list`, e.g.
list(model), instead.
Bugfixes:
- Fixed a bug in :ref:`prody-contacts` command that arose problems when when selecting a subset of the target atoms.
Improvements:
- :guilabel:`ProDy Interface` shows the size of the trajectory output file for PCA calculations.
- :guilabel:`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 :guilabel:`Protein Graphics Options` panel.