v2.6.1

2.6.1 (Aug 14, 2025)

Bug Fixes and Improvements:

• Critical CLUSTENM(D) fixes
• Scipion fixes

Full Changelog: v2.6.0...v2.6.1

v2.6.0

2.6.0 (Jul 30, 2025)

New Features:

• Support for extended PDB IDs
• Trajectory wrapping
• py3Dmol visualization
• Expanded CIF file support
• Write long resnames
• RTB app

Bug Fixes and Improvements:

• Python 3.12 support
• NumPy 2 support
• KDTree extension fix
• Fixes for WatFinder, InSty, Scipion, ClustENM(D)
• pfam fixes
• Test fixes

Full Changelog: v2.5.0...v2.6.0

v2.5.0

2.5.0 (Aug 14, 2024)

New Features:

• InSty module prody/proteins/interactions.py for protein interactions and stability
• WatFinder module prody/proteins/waterbridges.py for analysing water bridges, chains and clusters
• Membrane exANM and exGNM apps
• kmedoid clustering
• Logistic regression for differences between sub-ensembles
• MMTF Parser by @vratins
• Protein-ligand interactions including calcSminaBindingAffinity by @karolamik13
• New support for Interpro Pfam
• New modules for accessing Bioexcel cv19 simulation database (precursor to MDDB)

Bug Fixes and Improvements:

• add weights to showProjection and fix colors
• fix catdcd frame selection
• fix showAtomicLines gaps
• update pyproject.toml and setup.py to limit scipy
• fix clustenm saving and loading
• fix adp matrix by @jamesmkrieger
• several fixes related to fetching, parsing and writing pdb and cif files
• limit pyparsing<=3.1.1

Full Changelog: v2.4.1...v2.5.0

v2.4.1

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: v2.4.0...v2.4.1

v2.4.0

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:

• @changephilip made their first contribution in #1618
• @odcambc made their first contribution in #1634
• @hrnciar made their first contribution in #1372

Full Changelog: v2.3.1...v2.4.0

v2.3.1

2.3.1 (Nov 15, 2022)

Bug Fixes and Improvements:

• use of 4-char hybrid36 (residue version) for biomol segnames
• remove pfam tests
• remove python 3.5 support

Full Changelog: v2.3.0...v2.3.1

v2.3.0

2.3.0 (Nov 12, 2022)

New Features:

• new Gamma function class from GOdMD
• added prody energy app based on ClustENM

Bug Fixes and Improvements:

• restored matrix option to dfi and dci
• pfam migrated to pfam-legacy
• fix to apps for broken imp.find_module
• various other fixes including to mmCIF parsing and alignments

Full Changelog: v2.2.0...v2.3.0

v2.2.0

2.2.0 (May 19, 2022)

Bug Fixes and Improvements:

• Updates to :function:`.parseScipionModes`` to use sqlite and xmd metadata files
  and handle eigenvalues

• Actual fix to logging so LOGGER.progress doesn't override logging level

• Updates to the PCA app to better handle number of modes for Scipion

• New arguments sparse, kdtree and turbo for :class:.ClustENM, allowing
  better control of ANM calculations.

• Another bug fix for mmCIF header parsing

• Bug fix for parsing CONECT bond records from PDB files

Full Changelog: v2.1.2...v2.2.0

v2.1.2

What's Changed

• New :function:.showRMSFlucts and :function:.calcRMSFlucts for root-mean-square fluctuations
• fix to :function:.showAtomicLines for overlaying multiple chains

Full Changelog: v2.1.1...v2.1.2

v2.1.1

2.1.1 (April 18, 2022)

Bug Fixes and Improvements:

• :function:.parseScipionModes can handle having a pdb file or not

• fix to mmCIF header parsing for chemicals in blocks not loops