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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

0.4.1 - 2025-02-19

Added

  • Better error messages and flag documentations

Fixed

  • Create parent directories if the output directory does not exist
  • Only interactions within the same model of the input file is considered
  • Rows in the output of contacts are now sorted more naturally
  • Use one thread by default, as using more rarely gives any gains in performance
  • Use a distance cutoff of 6.5Å for searching neighbor atoms by default, as the previous 4.5Å could miss certain Pi interactions

0.4.0 - 2025-02-17

Added

  • Detection of repulsion between like charges
  • Support of parquet, json, and ndjson output formats
  • Added a -name flag in the CLI to rename the output file of contacts and sasa commands

Fixed

  • Checks for polar contacts were skipped when hydrogen bond criteria are not satisfied
  • Better error messages when rings have missing atoms for finding the center and normal vector
  • Nomenclature mix of residue insertion codes and alternative locations; the two are now stored under separate columns (*_insertion and *_altloc) in the output files

Changed

  • Distance cutoff for T-shaped Pi-stacking lowered from 6Å to 5Å
  • Added hydrogen bond distance check to better differentiate Hbonds and polar contacts
  • Performance/memory footprint improvement by switching from 64-bit numbers to 32-bit
  • Logging is now less verbose

0.3.1

Fixed

  • Wrong theta angle specification for pi-pi interactions
  • Reduced unnecessary cloning of objects and strings

Changed

  • Defaults to searching for all intra- and inter-chain interactions when -g '/' is passed to contacts

0.3.0 - 2024-08-14

Added

  • sasa command to calculate the atom level SASA
  • seq command to extract protein sequences from PDB files

Fixed

  • Only report chains that are part of the ligand or receptor for contacts

Changed

  • Moved previous top-level command to contacts sub-command
  • Better path parsing

0.2.0 - 2024-08-08

Added

  • Separate CLI and core methods to prepare for future Python tooling
  • Dump results to CSV file

Fixed

  • Use pdbtbx version that can deal with non-standard PDB rows

Changed

  • As a consequence of the pdbtbx update, only atomic coordinates are now parsed

0.1.0 - 2024-05-09

Added

  • Initial release
  • Detection of common protein-protein interactions in a PDB or mmCIF file