mdeepfri - v1.1.8

Added

• 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

Fixed

• hetero atom bug introduced by Ruff (c044a158)
• MacOS CI/CD bug connected to Foldcomp binary

- Python
Published by github-actions[bot] almost 2 years ago

mdeepfri - v1.1.7

Fixed

• resolved old naming issues (closes #84)

- Python
Published by github-actions[bot] almost 2 years ago

mdeepfri - v1.1.6

Added

• MMSeqs2 API + tests
• rudimentary documentation website
• fixed bugs of v1.1.5

- Python
Published by github-actions[bot] almost 2 years ago

mdeepfri - 1.1.5

Added

• improved logging
• support for ESM databases (closes #80)

Changed

• retrieval of structures from PDB & FoldComp databases
• optimized contact map alignment via Cython - improved search in large databases (ESM)

- Python
Published by github-actions[bot] about 2 years ago

mdeepfri - v1.1.4

Added

• --skip-pdb flag in case of unexpected PDB bugs
• user parameter for allowed protein lengths --min-length and --max-length

Fixes

• 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%)

- Python
Published by github-actions[bot] about 2 years ago

mdeepfri - v1.1.3

Fixes

• bug where MMseqs2 returned empty results search #73

- Python
Published by github-actions[bot] about 2 years ago

mdeepfri - v1.1.2

Added

• chunked loading of MMSeqs2 preselected targets - improves runtime

Fixed

• C++17 lowered to C++14 for compatibility
• pyopal API v0.5 integrated
• removed scipy distance calculation with function
• replaced biopython with biotite for structure manipulation - better runtime and easier deploy
• tests fixed & added to CI/CD

- Python
Published by valentynbez over 2 years ago

mdeepfri - v1.1.1

Added

• Automatic setup of the PDB database during the first run
• Automatic parsing of both mmCIF and PDB files
• Removed torch dependency - significant improvement in startup times
• added models of v1.1 - available for the download via get-models subcommand
• CI/CD

- Python
Published by github-actions[bot] over 2 years ago

mdeepfri - v2.0.0-alpha

• optimised way to interact with protein structure databases through FoldComp
• improved CPU and GPU utilisation with ONNX
• Cython for targeting future bottleneck
• Alignment step biopython -> pyopal
• Automatic CPU/GPU switch
• better memory management

- Python
Published by valentynbez almost 3 years ago

mdeepfri -

- Python
Published by SoliareofAstora over 4 years ago