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