v0.2.7

• Bugs in domain splitting with a blank chain ID and Mac multithreading are fixed.

v0.2.6

• Python packaging issues are fixed.

v0.2.5

• Structures can now be split into domains with Chainsaw before searching, with each domain searched separately. This makes Progres suitable for use with multi-domain structures.
• The whole PDB split into domains with Chainsaw is made available to search against.
• Hetero atoms are now ignored during file reading.
• Example files are added for searching and database embedding.

v0.2.4

• The score mode is added to calculate the Progres score between two structures.

v0.2.3

• Incomplete downloads are handled during setup.

v0.2.2

• The environmental variable PROGRES_DATA_DIR can be used to change where the downloaded data is stored.
• A Docker file is added.
• Searching on GPU is made more memory efficient.
• Bugs when running on Windows are fixed.

v0.2.1

• The AlphaFold database TED domains are made available to search against, with FAISS used for fast searching.
• Pre-embedded databases are stored as Float16 to reduce disk usage.
• Datasets and scripts for benchmarking (including for other methods), FAISS index generation and training are made available.

v0.2.0

• Change model architecture to use 6 EGNN layers and tau torsion angles, making it faster and SE(3)-invariant rather than E(3)-invariant.
• The AlphaFold models for 21 model organisms are made available to search against.
• The trained model and pre-embedded databases are downloaded from Zenodo rather than GitHub when first running the software.

v0.1.3

• Fix data download.

v0.1.2

• Add ECOD database.
• Use versioned model directory.