🚀 Release Notes – Version 1.0.0 🎉

Major Changes & Breaking Updates

New Default Cutoff: 4.5 Å

• The default contact cutoff has been increased from 4.0 Å to 4.5 Å.
• Affects all throughout API, CLI and notebooks.

aGPCR GAIN Domain Support

• New GAIN domain generic residue labeling for adhesion GPCRs
• Integrated seamlessly in the existing LabelerGPCR

API Breaking Changes

• Sorting Option Change

  • sort_by_freq → sort_by across:
    • ContactGroup.plot_frequency_sums_as_bars
    • ContactGroup.frequency_sum_per_residue_names
    • ContactGroup.plot_neighborhood_freqs
    • There's still some sort_by_freq optargs missing but they're mostly in methods where you either sort by freq or you don't.

• Fragment Naming

  • Auto-generating fragment names now requires the "auto" keyword.
  • Passing None or "" disables fragment naming.

New Methods & Options (among others)

• New GPCR Fragment Methods:

  • LabelerGPCR.top2domains to break a continuous GPCR into GAIN domain and TM domain

• Improved PDB Handling:

  • .cif file support via Biopython in pdb.pdb2traj (fallback when .pdb is unavailable).

• New residuemap option for ContactGroup.frequency_delta, allows deltas between different topologies if a map is available

• fragments.fragment_slice now supports string-based fragment selection.

Performance & Accuracy

• Improved speed in assert_no_intersection by eliminating pair-wise loops.
• Better handling of GLY and non-proteins via residue_sidechain_membership.
• Faster residue selection in ContactGroup.select_by_residues.
• Faster ContactGroup creation by comparing tops by using id(top) at first

Documentation Updates

• Updated documentation and images to reflect the new 4.5 Å cutoff.
• Added aGPCR and GAIN domain nomenclature references.
• Restored missing images in the notebook gallery.

Infrastructure & Compatibility

• Unofficial Python 3.13 Support:

• CI Improvements:

  • Improved macOS workflows with better parallelization.
  • Increased test stability across Python versions.

Miscellaneous

• Improved error messages and handling for ContactGroup.
• Numerous typo fixes in docstrings and comments.
• Removed outdated TODOs from the README.

What's Changed

• Change ctc_cutoff_val to 4.5 Ang by @gph82 in https://github.com/gph82/mdciao/pull/53

Full Changelog: https://github.com/gph82/mdciao/compare/0.0.9...1.0.0