New Features:
- parseDCD() is implemented for parsing coordinate sets from DCD files.
Improvements:
- parsePDB() parses SEQRES records 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 writeNMD() function causing problems when writing a single mode is fixeed.
- Other bugfixes in dynamics module functions.
Highlights:
- Atomic __getattribute__() is overloaded to interpret atomic selections following the dot operator. For example, atoms.calpha is interpreted as atoms.select('calpha'). See :ref:`` for more details.
- AtomGroup class is integrated with 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:
- matchAlign() is implemented for quick alignment of protein structures. See Ligand Extraction usage example.
- setAttribute(), getAttribute(), delAttribute(), and isAttribute() functions are implemented for AtomGroup class to facilitate storing user provided atomic data. See Storing data in AtomGroup example.
- saveAtoms() and 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.
- calcCollectivity() function is implemented to allow for calculating collectivity of deformation vectors.
Improvements:
- parsePDB() can optionally return biomolecule when biomol=True keyword argument is passed.
- parsePDB() can optionally make secondary structure assignments when secondary=True keyword argument is passed.
- calcSqFlucts() function is changed to accept Vector instances, e.g. deformation vectors.
Changes:
- Changes were made in calcADPAxes() function to follow the conventions in analysis ADPs. See its documentation.
Bug Fixes:
- A in Ensemble slicing operations is fixed. Weights are now copied to the new instances obtained by slicing.
- Bug fixes in dynamics plotting functions showScaledSqFlucts(), showNormedSqFlucts(),
New Features:
- Regular expressions can be used in atom selections. See select module for details.
- User can define selection macros using defSelectionMacro() function. Macros are saved in ProDy configuration and loaded in later sessions. See select module for other related functions.
- parseSparseMatrix() function is implemented for parsing matrices in sparse format. See the usage example in Using an External Matrix.
- deform() function is implemented for deforming coordinate sets along a normal mode or linear combination of multiple modes.
- 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 select module for the complete list.
- A new keyword argument for 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 select for details.
- assignSecondaryStructure() function assigns SS identifiers to all atoms in a residue. Residues with no SS information specified is assigned coil conformation.
- When Ensemble and NMA classes are instantiated with an empty string, instances are called “Unnamed”.
- sliceMode(), sliceVector() and reduceModel() functions return the atom selection in addition to the sliced vector/mode/model instance.
Bug Fixes:
- Default selection for 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 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.