New Features:
- :func:`.parseDCD` is implemented for parsing coordinate sets from DCD files.
Improvements:
- :func:`.parsePDB` parses
SEQRESrecords in header sections.
Changes:
- Major classes can be instantiated without passing a name argument.
- Default selection in NMWiz ProDy interface is changed to ensure selection only protein Cα atoms.
Bug Fixes:
- A bug in :func:`.writeNMD` function causing problems when writing a single mode is fixeed.
- Other bugfixes in :mod:`~prody.dynamics` module functions.
Highlights:
- :class:`.Atomic` :meth:`__getattribute__` is overloaded to interpret atomic selections following the dot operator. For example,
atoms.calphais interpreted asatoms.select('calpha'). See :ref:`` for more details.- :class:`.AtomGroup` class is integrated with :class:`.HierView` class. Atom group instances now can be indexed to get chains or residues and number of chains/residues can be retrieved. A hierarchical view is generated and updated when needed. See :ref:`` for more details.
New Features:
- :func:`.matchAlign` is implemented for quick alignment of protein structures. See :ref:`extract-ligands` usage example.
- :meth:`~.AtomGroup.setAttribute`, :meth:`~.AtomGroup.getAttribute`, :meth:`~.AtomGroup.delAttribute`, and :meth:`~.AtomGroup.isAttribute` functions are implemented for :class:`.AtomGroup` class to facilitate storing user provided atomic data. See :ref:`attributes` example.
- :func:`.saveAtoms` and :func:`.loadAtoms` functions are implemented to allow for saving atomic data and loading it This saves custom atomic attributes and much faster than parsing data from PDB files.
- :func:`.calcCollectivity` function is implemented to allow for calculating collectivity of deformation vectors.
Improvements:
- :func:`.parsePDB` can optionally return biomolecule when
biomol=Truekeyword argument is passed.- :func:`.parsePDB` can optionally make secondary structure assignments when
secondary=Truekeyword argument is passed.- :func:`.calcSqFlucts` function is changed to accept :class:`.Vector` instances, e.g. deformation vectors.
Changes:
- Changes were made in :func:`.calcADPAxes` function to follow the conventions in analysis ADPs. See its documentation.
Bug Fixes:
- A in :class:`.Ensemble` slicing operations is fixed. Weights are now copied to the new instances obtained by slicing.
- Bug fixes in :mod:`~prody.dynamics` plotting functions :func:`.showScaledSqFlucts`, :func:`.showNormedSqFlucts`,
New Features:
- Regular expressions can be used in atom selections. See :mod:`~prody.select` module for details.
- User can define selection macros using :func:`~select.defSelectionMacro` function. Macros are saved in ProDy configuration and loaded in later sessions. See :mod:`~prody.select` module for other related functions.
- :func:`.parseSparseMatrix` function is implemented for parsing matrices in sparse format. See the usage example in :ref:`external-matrix`.
- :func:`.deform` function is implemented for deforming coordinate sets along a normal mode or linear combination of multiple modes.
- :func:`.sliceModel` function is implemented for slicing normal mode data to be used with functions calculating atomic properties using normal modes.
Improvements:
- Atom selections using bare keyword arguments is optimized. New keyword definitions are added. See :mod:`~prody.select` module for the complete list.
- A new keyword argument for :func:`.calcADPAxes` allows for comparing largest axis to the second largest one.
Changes:
- There are changes in function used to alter definitions of selection keywords. See :mod:`~prody.select` for details.
- :func:`.assignSecondaryStructure` function assigns SS identifiers to all atoms in a residue. Residues with no SS information specified is assigned coil conformation.
- When :class:`.Ensemble` and :class:`.NMA` classes are instantiated with an empty string, instances are called "Unnamed".
- :func:`.sliceMode`, :func:`.sliceVector` and :func:`.reduceModel` functions return the atom selection in addition to the sliced vector/mode/model instance.
Bug Fixes:
- Default selection for :func:`.calcGNM` function is set to "calpha".
New Features:
- NMWiz supports GNM data and can use ProDy for GNM calculations.
- NMWiz can gather normal mode data from molecules loaded into VMD. This allows NMWiz to support all formats supported by VMD.
- User can write data loaded into NMWiz in NMD format.
- An Arrow Graphics option allows the user to draw arrows in both directions.
- User can select Licorice representation for the protein if model is an all atom mode.
- User can select Custom as the representation of the protein to prevent NMWiz from chancing a user set representation.
- Trace is added as a protein backbone representation option.
Improvements:
- NMWiz remembers all adjustments on arrow graphics for all modes.
- Plotting :guilabel:`Clear` button clears only atom labels that are associated with the dataset.
- Removing a dataset removes all associated molecule objects.
- Selected atom representations are turned on based on atom index.
- Padding around interface button has been standardized to provide a uniform experience between different platforms.