New Features:
- :meth:`~.PCA.performSVD` function is implemented for faster and more memory efficient principal compoment analysis.
- :func:`.extrapolateModel` function is implemented for extrapolating a coarse-grained model to an all atom model. See the usage example :ref:`extendmodel`.
- :func:`plog` is implemented for enabling users to make log entries.
Improvements:
- :mod:`~prody.compare` functions are improved to handle insertion codes.
- :class:`.HierView` allows for indexing using chain identifier and residue numbers. See usage example :ref:`hierview`.
- :class:`.Chain` allows for indexing using residue number and insertion code. See usage example :ref:`hierview`.
- :meth:`~.AtomGroup.addCoordset` function accepts :class:`.Atomic` and :class:`.Ensemble` instances as coords argument.
- New method :meth:`.HierView.getAtoms` is implemented.
- :class:`.AtomGroup` set functions check the correctness of dimension of data arrays to prevent runtime problems.
- :program:`prody pca` script is updated to use the faster PCA method that uses SVD.
Changes:
- "backbone" definition now includes the backbone hydrogen atom (Thanks to Nahren Mascarenhas for pointing to this discrepancy in the keyword definition).
Bug Fixes:
- A bug in :class:`.PCA` allowed calculating covariance matrix for less than 3 coordinate sets is fixed.
- A bug in :func:`.mapOntoChain` function that caused problems when mapping all atoms is fixed.
New Features:
- :func:`.setWWPDBFTPServer` and :func:`.getWWPDBFTPServer` functions allow user to change or learn the WWPDB FTP server that ProDy uses to download PDB files. Default server is RCSB PDB in USA. User can change the default server to one in Europe or Japan.
- :func:`.setPDBMirrorPath` and :func:`.getPDBMirrorPath` functions allow user to specify or learn the path to a local PDB mirror. When specified, a local PDB mirror is preferred for accessing PDB files, over downloading them from FTP servers.
- :func:`.mapOntoChain` function is improved to map backbone or all atoms.
Improvements:
- :class:`WWPDB_PDBFetcher` can download PDB files from different WWPDB FTP servers.
- :class:`WWPDB_PDBFetcher` can also use local PDB mirrors for accessing PDB files.
Changes:
- :class:`RCSB_PDBFetcher` is renamed as :class:`WWPDB_PDBFetcher`.
- :func:`.mapOntoChain` and :func:`.matchChains` functions accept
"ca"and"bb"as subset arguments.- Definition of selection keyword "protein" is updated to include some non-standard amino acid abbreviations.
Bug Fixes:
- A bug in :class:`WWPDB_PDBFetcher` causing exceptions when non-string items passed in a list is fixed.
- An important bug in :func:`.parsePDB` is fixed. When parsing backbone or Cα atoms, residue names were not checked and this caused parsing water atoms with name
"O"or calcium ions with name"CA".
New Features:
- Biopython module pairwise2 and packages KDTree and Blast are incorporated in ProDy package to make installation easier. Only NumPy needs to be installed before ProDy can be used. For plotting, Matplotlib is still required.
- :ref:`nmwiz` is distributed with ProDy source. On Linux, if VMD is installed, ProDy installer locates VMD plugins folder and installs NMWiz. On Windows, user needs to follow a separate set of instructions (see :ref:`nmwiz`).
- :class:`.Gamma` class is implemented for facilitating use of force constants based on atom type, residue type, or property. An example derived classes are :class:`.GammaStructureBased` and :class:`.GammaVariableCutoff`.
- :func:`.calcTempFactors` function is implemented to calculate theoretical temperature factors.
- 5 new :ref:`prody-apps` are implemented, and existing scripts are improved to output figures.
- :meth:`~.NMA.getModel` method is implemented to make function development easier.
- :func:`.resetTicks` function is implemented to change X and/or Y axis ticks in plots when there are discontinuities in the plotted data.
Improvements:
- :meth:`.ANM.buildHessian` and :meth:`.GNM.buildKirchhoff` classes are improved to accept :class:`.Gamma` instances or other custom function as gamma argument. See also :ref:`gamma`.
- :class:`.Select` class is changed to treat single word keywords differently, e.g. "backbone" or "protein". They are interpreted 10 times faster and in use achieve much higher speed-ups when compared to composite selections. For example, using the keyword "calpha" instead of the
name CA and protein, which returns the same selection, works >20 times faster.- Optimizations in :class:`~select.Select` class to increase performance (Thanks to Paul McGuire for providing several Pythonic tips and Pyparsing specific advice).
- :func:`.applyBiomolecularTransformations` function is improved to handle large biomolecular assemblies.
- Performance optimizations in :func:`.parsePDB` and other functions.
- :class:`.Ensemble` class accepts :class:`.Atomic` instances and automatically adds coordinate sets to the ensemble.
Changes:
- :class:`PDBlastRecord` is renamed as :class:`.PDBBlastRecord`.
- :class:`.NMA` instances can be index using a list or tuple of integers, e.g.
anm[1,3,5].- "ca", "bb", and "sc" keywords are defined as short-hands for "calpha", "backbone", and "sidechain", respectively.
- Behavior of :func:`.calcANM` and :func:`.calcGNM` functions have changed. They return the atoms used for calculation as well.
Bug Fixes:
- A bug in :func:`.assignSecondaryStructure` function is fixed.
- Bug fixes in :ref:`prody-anm` and :ref:`prody-gnm`.
- Bug fixes in :func:`.showSqFlucts` and :func:`.showProjection` functions.
- NMWiz can be used as a graphical interface to ProDy. ANM or PCA calculations can be performed for molecules that are loaded in VMD.
- User can set default color for arrow graphics and paths to ANM and PCA scripts.
- Optionally, NMWiz can preserve the current view in VMD display window when loading a new dataset. Check the box in the NMWiz GUI main window.
- A bug that prevented selecting residues from plot window is fixed.