ProDy 2.4 Series

2.4.1 (Aug 11, 2023)

New Features:

  • New function writeBILD to write modes in BILD format for viewing in Chimera/ChimeraX
  • New function addMissingAtoms based on PDBFixer or OpenBabel
  • Added Seaborn kernel density estimator (KDE) options to showProjection like Kaynak et al., 2022
  • Added options to control adjust_text for showProjection
  • Added unite_chains option to parseMMCIF to handle splitting over segments
  • New function interpolateModel based on SITUS ModeHunter
  • New ClustENM app
  • New module for analysing water bridges (only for Python 3)
  • New option nproc as a number of processors limit for solveEig, ANM, GNM and PCA calcModes

Bug Fixes and Improvements:

  • Fixed Trajectory next frame overwriting with atoms linked
  • Important fixes to alignBioPairwise
  • Update to blastpdb to account for changes to on the NCBI side
  • Improvements to apps including writing matrices
  • Improved handling of mmCIF files including those from PDB-REDO

Full Changelog: https://github.com/prody/ProDy/compare/v2.4.0...v2.4.1

2.4.0 (Feb 2, 2023)

New Features:

  • New function alignBioPairwise to address Biopython deprecation
  • Added gromos rmsd clustering
  • New data_type option for refineEnsemble to use seqid instead of rmsd
  • New ignore_ids option for mergeMSA to use different ids for interacting proteins

Bug Fixes and Improvements:

  • Fixed error during writeout PQR file
  • Proper handling of fragments when bonds are absent
  • Setting the atoms for ensemble even if the atoms is a subset
  • Allowing setFlags to take scalar values
  • Transpose princ axes matrix to get columns
  • New flag selpdbter to keep ter lines in selections
  • No sorting of strands in writing
  • Add cif datafiles to setup
  • Select app help fix
  • Fixes to mmcif parsing
  • Improvements to cutoffs in Dali filtering
  • Fix to protein definition
  • Set matrix interactive to false and fix to axes3d usage for matplotlib 3.6
  • Improved requirements
  • Fix to fetchPDB for files with two dots but not gz ending

New Contributors:

Full Changelog: https://github.com/prody/ProDy/compare/v2.3.1...v2.4.0