ProDy 2.0 Series

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 Atom, Atomic and EMDMAP

to TEMPy objects, allowing calculations such as cross-correlation coefficient (CCC) to EM maps.

Added calcDynamicFlexibilityIndex() and 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 AdaptiveANM to work with other models including explicit membrane

ANM, 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 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 inferBonds() in AtomGroup for inferring bonds based on distances without information from PSF files.