ProDy 2.0 Series
===============================================================================

.. contents::
   :local:

2.0.2 (February 17, 2022)
------------------------------------------------------------------------------

**New Features**:
  
  * Added :function:`.realignModes` for comparing sets of modes calculated on unaligned 
  structures

  * New option *by_time* in :function:`.showProjection`, allowing projections onto 1 PC 
  and the frames sampled over the time course of a simulation or the conformers in an ensemble.

  * Updates to ClustENM(D) to use latest and more efficient OpenMM version, 7.6

  * New :function:`.parseGromacsModes` for parsing NMA and PCA modes calculated in Gromacs, 
  allowing the use of all-atom force fields and more efficient handling of large trajectories

**Bug Fixes and Improvements**:
  
  * Bug fixes to searchPfam and fetchPfamMSA, which no longer worked due to some security change.

  * Bug fix to Ensembles and Conformations for weights being indexed twice

  * Bug fix to --quiet option of apps that fixes the VMD ProDy interface

  * General documentation and error improvements

**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0.1...v2.0.2


2.0.1 (Dec 20, 2021)
------------------------------------------------------------------------------

**New Features**:
  
  * Added :function:`.calcRWSIP` for comparing sets of modes

  * New methods to convert :class:`.Atom`, :class:`.Atomic` and :class:`.EMDMAP` 
  to TEMPy objects, allowing calculations such as cross-correlation coefficient (CCC) 
  to EM maps.

  * Added :func:`.calcDynamicFlexibilityIndex` and :func:`.calcDynamicCouplingIndex`
  for further interpretation of PRS results.

  * Reinstated the option of using forces in PRS as in ProDy v1.8 (`turbo=**False**`)

  * Added GitHub Actions Continuous Integration in place of Travis. 

**Bug Fixes and Improvements**:
  
  * Compatibility and bug fixes for various functions, including pyparsing for selections.

  * Extended :class:`.AdaptiveANM` to work with other models including explicit membrane 
  ANM, :class:`.exANM`.

  * Improved capabilities for fetching and parsing mmCIF and EMD files.

  * Improved handling of residue and serial numbers including hexadecimal and hybrid36 formats.

  * Consistency fixes.

  * More non-standard amino acids (MEN, CSB, CME).

**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0...v2.0.1

2.0 (Dec 30, 2020)
------------------------------------------------------------------------------

**New Features**:

*ESSA*

  * New classes and functions for Essential Site Scanning Analysis (ESSA)

*Updates for CryoDy*

  * Finalised the :class:`.AdaptiveANM` (initially added in v1.10.11) for exploring transitions between conformations.

  * Improved domain decomposition 

*Expanded database module*

  * New interfaces including for QuartataWeb

*New compounds module*

  * New modules for fetching and parsing compound data from 
    the PDB including Biologically Interesting Reference Dictionary (BIRD) 
    and Chemical Component Dictionary (CCD) CIF files

  * New functions module including 2D chemical similarity calculations 
    using Morgan Fingerprint Similarity.

*Improved membrane ENMs*

  * New implementation of exANM based on iterative Schur complements and 
    block-wise inversion

  * New exGNM based on improved exANM

**Bug Fixes and Improvements**:

  * New function :func:`.inferBonds` in :class:`.AtomGroup` for inferring bonds 
    based on distances without information from :file:`PSF` files.
