v0.4.1: Reset unique chain id

Changed

• old chain id: [A, B, A, B, C] -> [A, B, A.1, B.1, C]
  new chain id: [A, B, A, B, C] -> [A0, B0, A1, B1, C0]

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

v0.4.0: training data pipeline release and msa server pairing fix

Changed

• Add open-source code for the training data processing pipeline.
• Include documentation for the data processing scripts in the docs/prepare.
• Add MSA pipeline for generating MSAs for training and inference.
• Add local colabfold_search demo to generate Protenix compatible MSA.
• Fix MSA post processing bug about the pairing MSA.

Full Changelog: v0.3.9...v0.4.0

v0.3.9: fix minor bugs of local inference if MSA is provided

Changed

• Fix minor bugs of local inference if MSA is provided

Full Changelog: v0.3.8...v0.3.9

v0.3.8: add occupancy to output CIF file

Changed

• Add occupancy to output CIF file
• Update citation information

Full Changelog: v0.3.7...v0.3.8

v0.3.7: fix copy_id in json and conformer generation

Changed

• Fix copy_id type in json
• Generate random reference conformer if failed

Full Changelog: v0.3.6...v0.3.7

v0.3.6: More readable directory of MSA search result

Changed

• Modified "covalent_bonds" field of json
• Ranking compatible with multi-GPU inference
• More readable directory of MSA search result

Full Changelog: v0.3.5...v0.3.6

v0.3.5: fix predicted cif name ranking

Changed

• fix predicted cif name ranking

Full Changelog: v0.3.4...v0.3.5

v0.3.4: Set deterministic to false to accelerate

Changed

• Set deterministic to false to acceralate

Full Changelog: v0.3.3...v0.3.4

v0.3.3: modification for Protenix server and fix inplace bug

Changed

• Add visualization for confidence head in protenix server
• Other modification for Protenix server
  • Add some main functions to facilitate the server to call through the command line
  • When searching for msa, add an optional parameter email. Used to distinguish the inference traffic of the web server with login status and the traffic of the user's local inference
• Fix inplace-safe bug in confidence head, which will affect the ranking

Full Changelog: v0.3.2...v0.3.3

v0.3.2: Fix checkpoint cache dir bug

Changed

• Fix checkpoint cache dir bug

Full Changelog: v0.3.1...v0.3.2