v0.4.6: Add more options for protenix predict command

• Add more options for 'protenix predict' command
• Show a demo for ddp inference for 'inference_demo.sh'

Full Changelog: v0.4.5...v0.4.6

v0.4.5: Update output CIF file format and Fix typo of USE_DEEPSPEED_EVO_ATTENTION

What's Changed

• [Feat] Enhanced MSA Scripts by @popfido in #76
• Add the "_entity" field to the output CIF file
• Fix typo of USE_DEEPSPEED_EVO_ATTENTION

New Contributors

• @popfido made their first contribution in #76

Full Changelog: v0.4.4...v0.4.5

v0.4.4: Update the server domain name

What's Changed

• Enable precommit by @thalahors in #72
• Update the server domain name
• Convert MSE to MET in the atom array

Full Changelog: v0.4.3...v0.4.4

v0.4.3: Add cpu installation

What's Changed

• Add cpu installation by @thalahors in #71

New Contributors

• @thalahors made their first contribution in #71

Full Changelog: v0.4.2...v0.4.3

v0.4.2: update deepspeed version to solve vulnerability tips

What's Changed

• Update CONTRIBUTING.md by @NinoRisteski in #59
• Create scorecard.yml by @willem-bd in #64
• Update deepspeed version to solve vulnerability tips

New Contributors

• @NinoRisteski made their first contribution in #59
• @willem-bd made their first contribution in #64

Full Changelog: v0.4.1...v0.4.2

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