AlphaFold3 Format¶

Expected input format for tsp-maker parse af3.

Directory Structure¶

af3_outputs/
├── P12345/          ← Folder name becomes protein ID
│   ├── P12345_summary_confidences.json
│   ├── P12345_confidences.json
│   ├── seed-1_sample-0/
│   │   ├── model.cif
│   │   ├── summary_confidences.json
│   │   └── confidences.json
│   ├── seed-1_sample-1/
│   │   └── ...
│   └── ...
├── Q67890/          ← Folder name becomes protein ID
│   └── ...
└── ...

Folder Names = Protein IDs

The folder name (e.g., P12345) becomes the protein ID in your dataset. Ensure folders are named with the identifiers you want. See Protein ID Rules.

Required Files¶

Per-Sample Files¶

Each seed-{X}_sample-{Y}/ directory must contain:

File	Description
`model.cif`	Structure in mmCIF format
`summary_confidences.json`	Summary metrics
`confidences.json`	Full confidence data

summary_confidences.json¶

{
  "ranking_score": 0.85,
  "ptm": 0.82,
  "iptm": 0.78,
  "fraction_disordered": 0.05,
  "has_clash": false
}

confidences.json¶

{
  "atom_plddts": [85.2, 87.1, ...],
  "pae": [[0.5, 2.1, ...], ...]
}

Ranking¶

Samples are ranked by ranking_score from summary_confidences.json:

All seed-*_sample-* directories are scanned
Sorted by ranking_score (descending)
Top N samples extracted

Extracted Metrics¶

Metric	Source
`plddt_mean`	Mean of atom_plddts
`plddt_min`	Minimum
`plddt_median`	Median
`ptm`	summary_confidences
`iptm`	summary_confidences (multimers)
`ranking_score`	summary_confidences
`fraction_disordered`	summary_confidences
`has_clash`	summary_confidences
`pae_mean/min/max`	From PAE matrix

Multimer Detection¶

Multimer predictions are detected by the presence of iptm in summary confidences.

Additional multimer metrics: - chain_ptm - chain_iptm - chain_pair_iptm

Example Command¶

tsp-maker parse af3 /data/af3_outputs /intermediate --top-n 5

Output Naming¶

Files are named with _AF3_ suffix:

P12345_AF3_1.cif
P12345_AF3.json
P12345_AF3_1.npy

AlphaFold Server Output¶

The parser handles outputs from both: - Local AlphaFold3 installation - AlphaFold Server downloads

Both produce the same directory structure.