v0.4.1

What's Changed

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

Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's New

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

Full Changelog: v0.3.1...v0.4.0

v0.3.1

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

Full Changelog: v0.3.0...v0.3.1

v0.3.0

What's Changed

• Feat/sasa by @y1zhou in #9

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

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

Full Changelog: v0.2.0...v0.3.0

v0.2.0

What's Changed

• Separate the cli and the core methods by @y1zhou in #8

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

Full Changelog: v0.1.0...v0.2.0

v0.1.0

This is the initial release with the goal of detecting common protein-protein interactions in a PDB or mmCIF file.

What's Changed

• Van der Waals contacts and steric clashes by @y1zhou in #1
• feat(ionic): find ionic bonds by @y1zhou in #2
• Docs and some tests by @y1zhou in #3
• feat(hphobic): detect hydrophobic contacts by @y1zhou in #4
• feat(intxn): search for disulfides by @y1zhou in #5
• feat(rings): identify aromatic interactions by @y1zhou in #6
• GitHub ci to build targets by @y1zhou in #7

New Contributors

• @y1zhou made their first contribution in #1

Full Changelog: https://github.com/y1zhou/arpeggia/commits/v0.1.0