ProDy 0.7 Series

0.7.2 (Jun 21, 2011)

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.

0.7.1 (Apr 28, 2011)

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:

0.7 (Apr 4, 2011)

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”.

Normal Mode Wizard

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.