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