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.
1.1.8 - 2024-06-26
- 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
- hetero atom bug introduced by Ruff (c044a158)
- MacOS CI/CD bug connected to Foldcomp binary
1.1.7 - 2024-06-10
- resolved old naming issues (closes #84)
1.1.6 - 2024-06-04
- MMSeqs2 API + tests
- rudimentary documentation website
- fixed bugs of v1.1.5
1.1.5 - 2024-04-01
- improved logging
- support for ESM databases (closes #80)
- corrected structures retrieval from PDB (closes #81, #83)
- correct non-standard amino acids
- remove base pairs
- 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
--skip-pdbflag in case of unexpected PDB bugs- user parameter for allowed protein lengths
--min-lengthand--max-length
- 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%)
- cases are reported via
v1.1.3 - 2024-03-13
- bug where MMseqs2 returned empty results search #73
v1.1.2 - 2024-02-22
- chunked loading of MMSeqs2 preselected targets - improves runtime
- C++17 lowered to C++14 for compatibility
- pyopal API v0.5 integrated
- removed
scipydistance calculation with function - replaced
biopythonwithbiotitefor structure manipulation - better runtime and easier deploy - tests fixed & added to CI/CD
v1.1.1 - 2024-03-01
- Automatic setup of the PDB database during the first run
- Automatic parsing of both mmCIF and PDB files
- Removed
torchdependency - significant improvement in startup times - added models of v1.1 - available for the download via
get-modelssubcommand - CI/CD