How lafluceth/af3io works
af3io is a small collection of AlphaFold 3 file utilities. The main workflow accepts input JSON and existing data-pipeline outputs, matches sequences, and copies MSA/template fields into completed inputs; missing sequences can be emitted for pipeline processing. Separate capabilities summarize and compare inputs, compress and inspect confidence JSON, and read prediction archives and their confidence summaries. The CLI-to-data-fill calls are in omitted CLI excerpts, so those links are shown as unverified; other links follow shown calls or documented capabilities.
Main entry points: cli.py Utility CLI · data.py Sequence data operations · predictions.py Archive reader · input.py Input handling
Components 14
Input JSON
- Utility CLI
src/af3io/cli.py - Input handling
src/af3io/input.py - File helpers
src/af3io/core.py - Input JSON files
Data pipeline fill
- Sequence data operations
src/af3io/data.py - Pipeline output files
Confidence utilities
- Confidence encoding
src/af3io/confidences.py - Confidence decoding
src/af3io/confidences_eval.py - Compressed confidence
Prediction archives
- Archive reader
src/af3io/predictions.py - Prediction ZIP
- Confidence summaries
Other components
- Researcher
- AlphaFold 3 pipeline
Connections 16
- Researcher → Utility CLI: runs commands
src/af3io/cli.py - Utility CLI → Input handling: reads and writes
src/af3io/cli.py - Input handling → File helpers: opens files
src/af3io/input.py - Utility CLI → Input JSON files: summarizes inputs
src/af3io/cli.py - Utility CLI → Sequence data operations: fills inputs
- Sequence data operations → Input handling: reads sequences
src/af3io/data.py - Sequence data operations → Pipeline output files: indexes and reads
src/af3io/data.py - AlphaFold 3 pipeline → Pipeline output files: produces outputs
README.md - Sequence data operations → Input JSON files: writes filled inputs
README.md - Utility CLI → Confidence encoding: encodes confidence
src/af3io/cli.py - Confidence encoding → Compressed confidence: compresses values
- Utility CLI → Confidence encoding: reads and formats
src/af3io/cli.py - Confidence decoding → Compressed confidence: decodes expressions
- Researcher → Archive reader: uses reader
src/af3io/predictions.py - Archive reader → Prediction ZIP: reads ZIP entries
src/af3io/predictions.py - Archive reader → Confidence summaries: extracts scores
src/af3io/predictions.py