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]

[Release]

[1.1.8] - 2024-06-26

Added

• fixed tests and added to CI/CD
• added function to download MMseqs2 binaries for full CI/CD runs
• removed Conda install - fully installable from PyPI

Fixed

• hetero atom bug introduced by Ruff (c044a158)
• MacOS CI/CD bug connected to Foldcomp binary

[1.1.7] - 2024-06-10

Fixed

• resolved old naming issues (closes #84)

[1.1.6] - 2024-06-04

Added

• MMSeqs2 API + tests
• rudimentary documentation website
• fixed bugs of v1.1.5

[1.1.5] - 2024-04-01

Added

• improved logging
• support for ESM databases (closes #80)
• corrected structures retrieval from PDB (closes #81, #83)
  • correct non-standard amino acids
  • remove base pairs

Changed

• retrieval of structures from PDB & FoldComp databases
• optimized contact map alignment via Cython - improved search in large databases (ESM)

[v1.1.4] - 2024-03-23

Added

• --skip-pdb flag in case of unexpected PDB bugs
• user parameter for allowed protein lengths --min-length and --max-length

Fixes

• installation of PDB database
• alignment of faulty PDB structures
  • cases are reported via logging, require case-by-case investigation
  • faulty structures are then aligned to a predicted database, which are consistent
  • around 130/1300 alignments to PDB fail (10%)

[v1.1.3] - 2024-03-13

Fixes

• bug where MMseqs2 returned empty results search #73

[v1.1.2] - 2024-02-22

Added

• chunked loading of MMSeqs2 preselected targets - improves runtime

Fixed

• C++17 lowered to C++14 for compatibility
• pyopal API v0.5 integrated
• removed scipy distance calculation with function
• replaced biopython with biotite for structure manipulation - better runtime and easier deploy
• tests fixed & added to CI/CD

[v1.1.1] - 2024-03-01

Added

• Automatic setup of the PDB database during the first run
• Automatic parsing of both mmCIF and PDB files
• Removed torch dependency - significant improvement in startup times
• added models of v1.1 - available for the download via get-models subcommand
• CI/CD