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bb6d2aa | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | # Data
**The processed training and validation data are not included in this release.**
They will be handled separately. This directory is a placeholder; nothing here
downloads, reconstructs, or redistributes a dataset.
## Where to place files
Training reads exactly two files, resolved from the config
(`configs/staplebridge_main.yaml`):
```yaml
data:
root: data/real # relative paths resolve against the release root
train_file: train.jsonl
valid_file: valid.jsonl
max_lead_length: 25
```
giving the default layout:
```
data/real/
├── train.jsonl
└── valid.jsonl
```
Any location works — set `data.root` to an absolute path if you prefer.
## Expected input schema
JSON Lines: one object per line, loaded into
`staplebridge.data.schemas.LeadExample` by
`staplebridge.data.dataset.load_leads`.
| Field | Type | Required | Meaning |
| --- | --- | --- | --- |
| `example_id` | str | yes | Unique lead identifier; also the property-cache key. |
| `linear_sequence` | str | yes | Linear lead peptide, one letter per residue. |
| `protected_positions` | list[int] | yes (may be `[]`) | 0-based positions edits must not touch; enforced as a hard constraint. |
| `target_context` | object | yes in practice | Must contain `peptide_ca` (below). |
| `target_id` | str \| null | no | Binding-partner identifier. |
| `preferred_property_direction` | object | no | Not used by the main objective. |
| `thresholds` | object | no | Not used by the main objective. |
| `known_active_motif_positions` | list[int] \| null | no | Optional motif annotation. |
`target_context.peptide_ca` must be a list of `[x, y, z]` Cα coordinates, one
per residue of `linear_sequence`, in order. Staple-geometry feasibility (the
`ca_window` span check gating every candidate plan) is computed from these; a
lead without them cannot yield a feasible plan support. Other keys in
`target_context` are ignored.
Leads longer than `max_lead_length` are filtered out before use.
|