Releases · prody/ProDy

17 Feb 19:36

v2.0.2

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

Assets 6

21 Dec 13:32

v2.0.1

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).