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):
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.