SMARTFlexDB

Download the entire dataset as flat files, or pull it programmatically. The derived data are released under CC-BY-4.0; atomic coordinates are from the RCSB PDB.

GET /api/pairs → {"pairs": [ … ]}

List every apo–holo pair (filtered to the public dataset) with summary fields: PDB IDs, ligand, method, resolution, RNA type, global / host-chain / pocket RMSD, whole-structure geometry, H-bond / water-bridge counts, ligand MW/logP, thumbnail. This is the table to start from. See the columns reference below.

pairs = requests.get(f"{BASE}/api/pairs").json()["pairs"]
print(len(pairs))            # number of public pairs
print(pairs[0]["id"], pairs[0]["pocket_rmsd"], pairs[0]["tm_score"])

GET /api/pair/{id} → full pair object

Full record for one pair: 2D (sequence + dot-bracket + per-position seqids/coords), per-residue displacement, atom-level interactions, water bridges, ligand properties, the pocket_dyn / geom sub-objects, and metadata. It also carries DSSR base pairs for both holo and apo (dssr_pairs / apo_dssr_pairs) and DSSR structural motifs for the holo state (dssr_motifs; no apo equivalent). Returns 404 for an unknown id.

Path · id - a pair ID from /api/pairs.
Query · apo=<pdb> - return the pocket compared against one of its curated cross-PDB apo states (the keys of apo_alternatives; the pair page's "Apo state" dropdown). copy=<chain> - compare against another same-entity apo copy in the same apo crystal (the keys of apo_copies; the "Apo copy" chooser). Either one returns the record for that combination. The apo-side fields (apo_pdb/apo_chain, rmsd, host_chain_rmsd, displacement, apo_2d, aux_chains, geom, pocket_dyn, bp_rewire, seq_identity, global_identity, the superposed / morph filenames) are those of the selected apo. The JSON therefore matches the pair.html?id=…&apo=… / &copy=… page exactly. A value the record does not carry is a 400, never a silent fall back to the default apo. Not carried per apo state / copy and therefore null on those responses: qc, apo_dssr_pairs, apo_clean and apo_pocket_ligand - they are measured against the pocket's default apo only. Every holo-side field (dssr_pairs, dssr_motifs, interactions3d, lig_props, method/resolution/RNA type) is unchanged by design.

pair = requests.get(f"{BASE}/api/pair/{PAIR}").json()
print(pair["holo_2d"]["seq"])           # holo sequence
print(pair["pocket_dyn"]["pocket_rmsd"])# pocket C1′ RMSD
print(len(pair["interactions3d"]))      # atom-level contacts

# the same pocket against one of its alternative apo states (400 if this pair has no such state)
alt = requests.get(f"{BASE}/api/pair/{PAIR}", params={"apo": "7R6M"}).json()
print(alt["apo_pdb"], alt["rmsd"], alt["apo_dssr_pairs"])   # 7R6M … None (default-apo-only field)

Interaction fields & provenance. The served type values in interactions3d (and in the bundled contacts.csv) are stable and unchanged for backward compatibility — notably hbond and vdw. These are not a single unified RNA-ligand interaction standard; they come from different sources and are surfaced in the UI under clearer labels:

DSSR base pairs / motifs / base-pair rewiring (dssr_pairs, apo_dssr_pairs, dssr_motifs) are DSSR-derived (RNA-internal) and keep their own labels.

GET /api/pockets → {"pockets": [ … ]}

Groups of matched RNA pockets bound to multiple ligands — holo pockets that share an RNA binding site and accommodate ≥2 distinct ligands. Light summary per group (size, RNA type, ligand list, members); per-ligand 2D / properties come from /api/pocket/{gid}.

groups = requests.get(f"{BASE}/api/pockets").json()["pockets"]
print(groups[0]["gid"], groups[0]["n_ligands"], groups[0]["ligands"])

GET /api/pocket/{gid} → pocket group object

One pocket group expanded: each distinct ligand's 2D depiction (SVG), SMILES, formula and RDKit properties, plus the shared pocket residues. Returns {"error": "not found"} for an unknown gid.

Path · gid - integer group ID from /api/pockets.

gid = groups[0]["gid"]
grp = requests.get(f"{BASE}/api/pocket/{gid}").json()
for lig in grp["ligands"]:
    print(lig["ligand"], lig["smiles"], lig["mw"])

GET /api/entry/{pdb} → RCSB metadata

RCSB Data API metadata for a PDB entry (title, experimental method, resolution, release/revision dates, authors, molecular weight, entity counts). Proxied and cached.

Path · pdb - a 3–5 char PDB ID.

meta = requests.get(f"{BASE}/api/entry/1EI2").json()
print(meta["title"], meta["method"], meta["resolution"])

GET /api/classification → cluster + t-SNE JSON

RNA-only non-redundancy clustering plus 2D t-SNE coordinates for the served pairs (n_pairs, method, axes: [sequence, structure, pocket], and pairs: [{id, cluster ids, x, y}]). Single-linkage components (RMscore ≥0.75 / MMseqs2 0.7) define non-redundant groups for ML train/test splits.

cls = requests.get(f"{BASE}/api/classification").json()
print(cls["n_pairs"], cls["method"], cls["axes"])
print(cls["pairs"][0])          # {id, cluster IDs, x/y t-SNE coords}

GET /api/structure/{pdb} → mmCIF

mmCIF for a PDB ID (proxied and cached from RCSB). media_type chemical/x-cif.

cif = requests.get(f"{BASE}/api/structure/1EI2").text
open("1EI2.cif", "w").write(cif)

GET /api/structure_pdb/{pdb} → PDB

PDB format, model 1 only — auth numbering + atom names match the contacts in interactions3d. Used by the 3D interaction viewer.

pdb_text = requests.get(f"{BASE}/api/structure_pdb/1EI2").text

GET /api/sup/{name} → PDB / mmCIF

Superposed apo structures and morph trajectories. The transform is the lowest-RMSD of a US-align fit and a sequence-anchored Kabsch fit on the paired C1′ atoms. Kabsch is the analytic minimiser of that RMSD, so it is the transform published for every served record. The exact filename is on the pair object (e.g. pair["apo_sup"]); must end in .pdb or .cif.

name = pair["apo_sup"]                       # e.g. "1EI2_..._apo_sup.pdb"
sup = requests.get(f"{BASE}/api/sup/{name}").content

GET /api/thumb/{id} → PNG

Pre-rendered 3D cartoon thumbnail (holo + superposed apo, same transform as /api/sup) for the gallery cards. 404 if not yet rendered.

png = requests.get(f"{BASE}/api/thumb/{PAIR}").content
open(f"{PAIR}.png", "wb").write(png)

GET /api/bundle/{id} → application/zip

Download one pair as a ZIP: holo/apo CIFs, the superposed apo (pocket-trimmed, exactly the overlay the viewer draws), ligand SDF, contacts CSV, and the full pair JSON.

Query · apo=<pdb> / copy=<chain> - the same apo-state / apo-copy selection /api/pair/{id} accepts (same 400 on an unknown value). The ZIP then contains that combination's superposed apo and pair record, and its folder/filename carries a __alt_<pdb> / __copy_<chain> suffix so two downloads of one pocket are distinguishable.

z = requests.get(f"{BASE}/api/bundle/{PAIR}").content
open(f"{PAIR}.zip", "wb").write(z)

z = requests.get(f"{BASE}/api/bundle/{PAIR}", params={"apo": "7R6M"}).content   # → {PAIR}__alt_7R6M.zip

POST /api/query → {"job_id": …}

Multipart upload. apo and holo are the two mmCIF files; ligand is a HET code (e.g. CNY) or, for a multi-copy ligand, a pinned instance LIG:CHAIN:RESSEQ (e.g. CNY:C:41). On success returns {job_id, ligand, lig_auth_chain, lig_resseq, pocket_pos}; a validation failure returns 400 with the message in detail.

Form · apo, holo - mmCIF files (≤30 MB each) · ligand - HET code or LIG:CHAIN:RESSEQ.

files = {"apo": open("apo.cif", "rb"), "holo": open("holo.cif", "rb")}
r = requests.post(f"{BASE}/api/query", files=files, data={"ligand": "CNY:C:41"})
r.raise_for_status()
job_id = r.json()["job_id"]

GET /api/query/{job_id}/status → {"state": …}

Job status — poll until state is done (or error, with a message). While running it reports the current pipeline stage.

Path · job_id - from the POST /api/query reply.

import time
while True:
    s = requests.get(f"{BASE}/api/query/{job_id}/status").json()
    if s["state"] in ("done", "error"): break
    time.sleep(2)

GET /api/query/{job_id}/pair → full pair object

The finished pair — the same response schema as /api/pair/{id}. Returns 404 ("result not ready") until the job is done.

Path · job_id - from the POST /api/query reply.

pair = requests.get(f"{BASE}/api/query/{job_id}/pair").json()
print(pair["pocket_dyn"]["pocket_rmsd"])