Foldcomp v0.0.7

Thank you for all the valuable feedback 😄

What's Changed

• version bump by @vagkaratzas in #46

Contributors

• Thanks to @valentynbez for active feedbacks
• Thanks to @vagkaratzas for the contribution in #46

Full Changelog: v0.0.6...v0.0.7

Foldcomp v0.0.6

Full Changelog: v0.0.5...v0.0.6

Foldcomp v0.0.5

Bug fix

We have fixed these errors

• #30 OXT b-factor
• #33 Compressing multiple chains in python API
• DB key reset for every input

Full Changelog: v0.0.4...v0.0.5

Foldcomp v0.0.4-1

Bug fix

We have fixed errors from these issues

• #25, #29 Memory leakage in Python api
• #28 Errors in decompressing database subset

Great thanks to @Oxer11, @kad-ecoli and @milot-mirdita

Foldcomp v0.0.4

Bug fix

We have fixed errors from these issues

• #25, #29 Memory leakage in Python api
• #28 Errors in decompressing database subset

Great thanks to @Oxer11, @kad-ecoli and @milot-mirdita

Full Changelog: v0.0.3...v0.0.4

Foldcomp v0.0.3

Foldcomp v0.0.3

We have much improved Foldcomp since its first release

Features

Foldcomp CLI

• Multiple input file types including tarball, gzipped tar, and file lists
• Foldcomp now handles structure files with multiple chains or discontinous fragments.
• Reduced RMSD to ~0.08Å with default parameter
• Overwriting is forbidden by default and can be enabled with --overwrite or -y
• Reduced copying data by applying span range

Foldcomp Python API

• get_data is now available
• Given ids are checked when opening foldcomp database

Foldcomp Databases

• Added ESMatlas v2023_02: esmatlas_v2023_02
• Added AlphaFold DB cluster representatives (AlphaFold database clustering)
  • afdb_rep_v4: All cluster representatives
  • afdb_rep_dark_v4: Dark cluster representatives

What's Changed

• Sync dev with master by @khb7840 in #10
• Sync with master by @khb7840 in #12
• Add recursive directory read-in mode by @milot-mirdita in #13
• Sync master with dev by @khb7840 in #16
• Input processor wip by @khb7840 in #21
• Updated to handle database input by @khb7840 in #22

Full Changelog: v0.0.2...v0.0.3

Foldcomp v0.0.2

First release of Foldcomp

Foldcomp compresses protein structures with torsion angles effectively. It compresses the backbone atoms to 8 bytes and the side chain to additional 4-5 bytes per residue, thus an averaged-sized protein of 350 residues requires ~6kb.

Features

• Multithreading using OpenMP
• Python interface
• Supports CIF & gzipped input using gemmi
• Reduced RMSD by saving inner atoms (~0.1Å by default)
• TAR and MMseqs database format support