{ "openapi": "3.1.0", "info": { "title": "Quantum Orbitals API", "version": "16.5.1", "summary": "Molecular geometry, localized orbital, peptide conversion, nomenclature and rendering API.", "description": "API for the Quantum Orbitals web application. RDKit builds the molecular graph and one deterministic conformer; the qo_chem orbital layer (Coulson σ hybrids from the real bond angles, σ/π lone-pair typing, Hückel π with p axes taken from the geometry, Slater orbitals in a Löwdin basis) adds charges, bond orders, molecular orbitals and pKa descriptors. /api/model returns the 3D model with that layer in `chemistry`; /api/pi-model returns the compact π payload the browser turns into density, interference, charge-shift, potential and orbital maps. Real-space fields are never computed on the server. The protected SVG renderer requires a bearer token. The IUPAC/systematic-name endpoint is an optional capability (py2opsin + Java). /api/site (16.4) takes a protein structure (PDB, mmCIF, BinaryCIF, or a GL1X MolNFT record), finds a PROSITE motif or a metal site, cuts out a capped, protonated fragment, and returns its orbital layer in the protein's own frame, including the ligands' donor pairs and zinc's empty 4s/4p acceptor orbitals.", "license": { "name": "Project-specific / see repository" } }, "servers": [ { "url": "/", "description": "Current host" } ], "tags": [ { "name": "Core", "description": "Core molecular model and rendering." }, { "name": "Peptides", "description": "Standard peptide sequence/SMILES conversion." }, { "name": "Nomenclature", "description": "Optional systematic-name parsing." }, { "name": "Health", "description": "Deployment and capability diagnostics." } ], "paths": { "/api/model": { "post": { "tags": [ "Core" ], "summary": "Build a 3D molecular/local-orbital model from SMILES", "description": "Parses SMILES with RDKit, adds hydrogens, generates one deterministic ETKDG conformer, optimizes with MMFF/UFF when available, and returns atoms, bonds and a compact local s/p orbital model.", "operationId": "buildMoleculeModel", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SmilesRequest" }, "example": { "smiles": "CCO" } } } }, "responses": { "200": { "description": "Molecular model", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/MoleculeModel" } } } }, "400": { "description": "Invalid input or model-generation failure", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/pi-model": { "post": { "tags": [ "Core" ], "summary": "π layer and acid/base pairs for any SMILES", "description": "Builds the same conformer as /api/model, runs the qo_chem orbital layer, finds ionisable sites and, for each, builds the acid and base form on the same geometry (only the proton moves). Returns compact π payloads (axes, Slater exponents, Löwdin matrix, Hückel coefficients) that pi-field-engine.js turns into maps, plus three pKa descriptors and a calibrated π forecast with its leave-one-out error. The `speciation` block titrates every site together (≤ 6 sites, all protonation microstates): site pKa (parent value + substituent term, others neutral), its held-out error on IUPAC data, the site–site charge terms W (pKa units) and the macroscopic deprotonation steps.", "operationId": "buildPiModel", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PiModelRequest" }, "example": { "smiles": "Oc1ccc(cc1)[N+](=O)[O-]", "ph": 7.4 } } } }, "responses": { "200": { "description": "π model", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PiModelResult" } } } }, "400": { "description": "Invalid input or model-generation failure", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/render-svg": { "post": { "tags": [ "Core" ], "summary": "Render a standalone molecular/orbital SVG", "description": "Bearer-protected page-independent SVG renderer. This endpoint currently uses the server-side schematic/local-orbital renderer; it is not identical to the browser's harmonic 3Dmol surface renderer.", "operationId": "renderMoleculeSvg", "security": [ { "BearerAuth": [] } ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/RenderSvgRequest" }, "example": { "smiles": "N[C@@H](CS)C(=O)O", "render": { "width": 1200, "height": 820 } } } } }, "responses": { "200": { "description": "Standalone SVG", "content": { "image/svg+xml": { "schema": { "type": "string" } } } }, "400": { "description": "Invalid request", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "401": { "description": "Missing or incorrect bearer token", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "503": { "description": "Bearer token not configured on server", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/sequence-to-smiles": { "post": { "tags": [ "Peptides" ], "summary": "Convert a standard one-letter peptide sequence to SMILES", "description": "Supports the 20 standard amino acids and RDKit's standard linear-peptide construction.", "operationId": "sequenceToSmiles", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SequenceRequest" }, "example": { "sequence": "ACDEFGHIK" } } } }, "responses": { "200": { "description": "Peptide structure", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SequenceToSmilesResult" } } } }, "400": { "description": "Unsupported or invalid sequence", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/smiles-to-sequence": { "post": { "tags": [ "Peptides" ], "summary": "Conservatively recover a standard linear peptide sequence from SMILES", "description": "Only returns a sequence when the graph can be segmented into one connected linear peptide composed of standard residues. Modified, cyclic, branched or ambiguous peptides are rejected.", "operationId": "smilesToSequence", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SmilesRequest" }, "example": { "smiles": "N[C@@H](CS)C(=O)O" } } } }, "responses": { "200": { "description": "Recognized sequence", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SmilesToSequenceResult" } } } }, "400": { "description": "Not safely convertible to a standard linear peptide sequence", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/iupac-to-smiles": { "post": { "tags": [ "Nomenclature" ], "summary": "Parse a systematic chemical name to SMILES with optional local OPSIN", "description": "Optional capability. The server calls py2opsin/OPSIN if installed and then validates/canonicalizes the result with RDKit. Local OPSIN requires a Java runtime. Absence of OPSIN must not affect the core molecular API.", "operationId": "iupacToSmiles", "x-optional-capability": "opsin-local", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/IupacRequest" }, "example": { "name": "2,4-dimethylbenzaldehyde" } } } }, "responses": { "200": { "description": "Parsed and RDKit-validated structure", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/IupacResult" } } } }, "400": { "description": "Parsing failure or optional OPSIN capability unavailable", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/health": { "get": { "tags": [ "Health" ], "summary": "Core service health", "operationId": "api_health", "responses": { "200": { "description": "Health/capability report", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Health" } } } } } } }, "/api/catalogue-health": { "get": { "tags": [ "Health" ], "summary": "Functional-group catalogue and RDKit.js asset health", "operationId": "api_catalogue_health", "responses": { "200": { "description": "Health/capability report", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Health" } } } } } } }, "/api/viewer-health": { "get": { "tags": [ "Health" ], "summary": "3Dmol viewer asset health", "operationId": "api_viewer_health", "responses": { "200": { "description": "Health/capability report", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Health" } } } } } } }, "/api/pi-density-health": { "get": { "tags": [ "Health" ], "summary": "π-density module asset/data health", "operationId": "api_pi_density_health", "responses": { "200": { "description": "Health/capability report", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Health" } } } } }, "description": "Static assets of /pka-density, the 20-case dataset, the qo_chem version, a benzene self-test and the pKa calibration in use." } }, "/api/site": { "post": { "tags": [ "Core" ], "summary": "Orbitals of a protein site (motif, metal or ligand), in the protein's frame", "description": "Reads the structure, lists every occurrence of the motif (never across a chain break) and every metal site, builds the selected site as a capped, protonated fragment with its metal (placed by least squares when the file has none), runs the orbital layer on it and returns an /api/model-shaped payload. At most 1500 atoms with hydrogens (server option --max-site-atoms) and two concurrent computations. Ligand mode (16.5): send `ligand`; the answer adds `ligand` and `free_molecule`. Extra error codes: ligand_not_found, ligand_not_molecular.", "operationId": "buildSite", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SiteRequest" }, "example": { "example": "5a7u", "motif": "C-x(2,4)-C-x(12)-H-x(3,5)-H" } } } }, "responses": { "200": { "description": "Site", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SiteResult" } } } }, "400": { "description": "Invalid input (code: no_occurrence, invalid_motif, motif_too_general, site_too_large, gl1x, busy, ligand_not_found, ligand_not_molecular, bad_request)", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } }, "500": { "description": "Unexpected failure while reading or building", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Error" } } } } } } }, "/api/site-health": { "get": { "tags": [ "Health" ], "summary": "Protein-site deployment check", "operationId": "siteHealth", "description": "Whether zinc's radial functions are installed, the fragment size limit, whether the server fetches structures from GL1X (gl1x_fetch) and ligand definitions from data.rcsb.org (ccd_fetch), whether OPSIN reads ligand names (name_to_smiles), the examples and the formats it reads.", "responses": { "200": { "description": "Status", "content": { "application/json": { "schema": { "type": "object" } } } } } } } }, "components": { "securitySchemes": { "BearerAuth": { "type": "http", "scheme": "bearer", "bearerFormat": "opaque token", "description": "Token configured server-side with QUANTUM_ORBITALS_API_TOKEN." } }, "schemas": { "Error": { "type": "object", "required": [ "error" ], "properties": { "error": { "type": "string" }, "hint": { "type": "string" } }, "additionalProperties": true }, "SmilesRequest": { "type": "object", "required": [ "smiles" ], "properties": { "smiles": { "type": "string", "examples": [ "CCO", "N[C@@H](CS)C(=O)O" ] } }, "additionalProperties": false }, "RadialModel": { "type": [ "object", "null" ], "description": "Valence radial functions of the element: free-atom Hartree–Fock ns/np fitted by 1–6 Slater terms (qo_chem/radial.py). The same functions are used for π overlaps, π densities and the 3D surfaces.", "properties": { "model": { "type": "string", "examples": [ "hartree_fock_fit", "slater_rules" ] }, "units": { "type": "string", "examples": [ "bohr" ] }, "n": { "type": "integer" }, "s": { "type": "array", "description": "Slater terms [N, zeta (1/bohr), c] of R(r) = sum c (2 zeta)^(N+1/2)/sqrt((2N)!) r^(N-1) exp(-zeta r)", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 } }, "p": { "type": "array", "description": "Slater terms [N, zeta (1/bohr), c] of R(r) = sum c (2 zeta)^(N+1/2)/sqrt((2N)!) r^(N-1) exp(-zeta r)", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 } }, "extent_angstrom": { "type": "number", "description": "radius enclosing 99 % of the valence radial probability" }, "overlap_with_hartree_fock": { "type": "object", "additionalProperties": { "type": "number" } }, "radial_phase_convention": { "type": "string", "examples": [ "outermost_lobe_positive" ] }, "z_eff": { "type": "number", "description": "Slater's Z_eff, kept for viewers older than 16.1" } }, "additionalProperties": true }, "Atom": { "type": "object", "required": [ "id", "element", "atomic_number", "position", "formal_charge" ], "properties": { "id": { "type": "integer" }, "element": { "type": "string", "examples": [ "C" ] }, "atomic_number": { "type": "integer" }, "position": { "type": "array", "minItems": 3, "maxItems": 3, "items": { "type": "number" }, "description": "3D Cartesian coordinates in Å." }, "formal_charge": { "type": "integer" }, "partial_charge": { "type": "number", "description": "Heuristic Gasteiger charge where available." }, "partial_charge_model": { "type": "string" }, "radial_charge_proxy": { "type": "number", "description": "Display-oriented charge proxy used by the optional radial extent heuristic." }, "radial_charge_proxy_model": { "type": "string" }, "hybridization": { "type": "string" }, "valence_electrons": { "type": "integer" }, "color": { "type": "string" }, "valence_shell": { "type": [ "integer", "null" ] }, "valence_basis": { "type": "array", "items": { "type": "string" } }, "radial_model": { "$ref": "#/components/schemas/RadialModel" } }, "additionalProperties": true }, "Bond": { "type": "object", "required": [ "a", "b", "order", "aromatic", "type" ], "properties": { "a": { "type": "integer" }, "b": { "type": "integer" }, "order": { "type": "number" }, "aromatic": { "type": "boolean" }, "type": { "type": "string" } } }, "LocalOrbital": { "type": "object", "required": [ "kind", "occupancy", "direction", "coefficients_s_px_py_pz", "atom" ], "properties": { "kind": { "type": "string", "description": "Examples include sigma_direction, lone_pair, residual_sigma_space, pi_basis, s_basis." }, "bond_to": { "type": [ "integer", "null" ] }, "occupancy": { "type": "number" }, "direction": { "type": "array", "minItems": 3, "maxItems": 3, "items": { "type": "number" } }, "coefficients_s_px_py_pz": { "type": "array", "minItems": 4, "maxItems": 4, "items": { "type": "number" } }, "s_character": { "type": "number" }, "p_character": { "type": "number" }, "atom": { "type": "integer" } }, "additionalProperties": true }, "PiOverlap": { "type": "object", "properties": { "a": { "type": "integer" }, "b": { "type": "integer" }, "components": { "type": "integer" }, "aromatic": { "type": "boolean" } }, "additionalProperties": true }, "MoleculeSummary": { "type": "object", "properties": { "atoms_with_hydrogen": { "type": "integer" }, "heavy_atoms": { "type": "integer" }, "bonds": { "type": "integer" }, "local_orbitals": { "type": "integer" }, "pi_connections": { "type": "integer" } } }, "MoleculeModel": { "type": "object", "required": [ "smiles", "canonical_smiles", "formula", "molblock", "atoms", "bonds", "orbitals", "summary" ], "properties": { "smiles": { "type": "string" }, "canonical_smiles": { "type": "string" }, "formula": { "type": "string" }, "molblock": { "type": "string", "description": "RDKit MolBlock of the conformer, in the same centred coordinates as atoms[].position." }, "atoms": { "type": "array", "items": { "$ref": "#/components/schemas/Atom" } }, "bonds": { "type": "array", "items": { "$ref": "#/components/schemas/Bond" } }, "orbitals": { "type": "array", "items": { "$ref": "#/components/schemas/LocalOrbital" } }, "pi_overlaps": { "type": "array", "items": { "$ref": "#/components/schemas/PiOverlap" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "summary": { "$ref": "#/components/schemas/MoleculeSummary" }, "model_notes": { "type": "array", "items": { "type": "string" } }, "chemistry": { "type": [ "object", "null" ], "additionalProperties": true, "description": "qo-chem/16.1 orbital layer: badges, normalization, atoms (role, σ/π lone pairs, pi_charge, description), hybrids (Coulson labels sp^n, deviation_deg, lone_pair_sets incl. rotation_pair), pi_components (x, C, occ, charges, bond_orders, HOMO/LUMO), acceptors (sn2, pi_star), hammett, ions, radial (Hartree–Fock fit summary per element), sanity_checks, pka (descriptors per ionisable site), warnings, provenance." }, "orbital_model": { "type": "string", "example": "qo-chem/16.1: Coulson hybrids + σ/π lone pairs + Hückel π + Hartree–Fock radial fits" }, "pi_field": { "description": "The molecule's π layer in the PiForm payload, same conformer and centred frame as atoms[].position; the 3D viewer draws π density, interference, orbitals and potential from it. Null when the orbital layer is unavailable.", "oneOf": [ { "$ref": "#/components/schemas/PiForm" }, { "type": "null" } ] } }, "additionalProperties": true }, "RenderSvgRequest": { "type": "object", "required": [ "smiles" ], "properties": { "smiles": { "type": "string", "examples": [ "N[C@@H](CS)C(=O)O" ] }, "render": { "type": "object", "properties": { "width": { "type": "integer", "minimum": 320, "maximum": 2400, "default": 1200 }, "height": { "type": "integer", "minimum": 240, "maximum": 1800, "default": 820 }, "orbital_scale": { "type": "number", "minimum": 0.2, "maximum": 3.0, "default": 1.2 }, "atom_scale": { "type": "number", "minimum": 0.35, "maximum": 2.0, "default": 0.95 }, "show_hydrogens": { "type": "boolean", "default": true }, "show_sigma": { "type": "boolean", "default": true }, "show_lone_pairs": { "type": "boolean", "default": true }, "show_pi": { "type": "boolean", "default": true }, "show_labels": { "type": "boolean", "default": true } }, "additionalProperties": false } }, "additionalProperties": false }, "SequenceRequest": { "type": "object", "required": [ "sequence" ], "properties": { "sequence": { "type": "string", "examples": [ "ACDEFGHIK" ] } }, "additionalProperties": false }, "SequenceToSmilesResult": { "type": "object", "properties": { "sequence": { "type": "string" }, "length": { "type": "integer" }, "three_letter": { "type": "string" }, "smiles": { "type": "string" }, "formula": { "type": "string" }, "molblock": { "type": "string" }, "interpretation": { "type": "string" }, "limitations": { "type": "array", "items": { "type": "string" } } }, "additionalProperties": true }, "SmilesToSequenceResult": { "type": "object", "properties": { "smiles": { "type": "string" }, "sequence": { "type": "string" }, "length": { "type": "integer" }, "three_letter": { "type": "string" }, "formula": { "type": "string" }, "residues": { "type": "array", "items": { "type": "object", "additionalProperties": true } }, "stereochemistry": { "type": "string" }, "warnings": { "type": "array", "items": { "type": "string" } }, "interpretation": { "type": "string" }, "limitations": { "type": "array", "items": { "type": "string" } } }, "additionalProperties": true }, "IupacRequest": { "type": "object", "required": [ "name" ], "properties": { "name": { "type": "string", "maxLength": 1200, "examples": [ "2,4-dimethylbenzaldehyde" ] } }, "additionalProperties": false }, "IupacResult": { "type": "object", "properties": { "name": { "type": "string" }, "smiles": { "type": "string" }, "opsin_smiles": { "type": "string" }, "formula": { "type": "string" }, "heavy_atoms": { "type": "integer" }, "warnings": { "type": "array", "items": { "type": "string" } }, "parser": { "type": "string" }, "depiction_backend": { "type": [ "string", "null" ] }, "svg": { "type": [ "string", "null" ] } }, "additionalProperties": true }, "Health": { "type": "object", "properties": { "ok": { "type": "boolean" } }, "additionalProperties": true }, "PiModelRequest": { "type": "object", "required": [ "smiles" ], "properties": { "smiles": { "type": "string", "example": "Oc1ccc(cc1)[N+](=O)[O-]" }, "ph": { "type": "number", "minimum": 0, "maximum": 14, "description": "Optional: adds per-site protonation states at this pH." } } }, "PiOrbital": { "type": "object", "properties": { "atom": { "type": "integer" }, "axis": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 }, "type": { "type": "string", "description": "Streitwieser type: C, O=, O:, N=, N:, N+, S:, Cl …" } } }, "PiComponent": { "type": "object", "description": "One conjugated π system. C[r][k]: coefficient of orbital r in MO k (Löwdin basis). E_k = α + x_k β.", "properties": { "atoms": { "type": "array", "items": { "type": "integer" } }, "orbitals": { "type": "array", "items": { "$ref": "#/components/schemas/PiOrbital" } }, "basis": { "type": "object", "properties": { "positions": { "type": "array", "items": { "type": "array", "items": { "type": "number" } } }, "M": { "type": "array", "description": "S^-1/2 (Löwdin)", "items": { "type": "array", "items": { "type": "number" } } }, "radial": { "type": "array", "description": "per π orbital: its Slater terms [N, zeta, c]", "items": { "type": "array", "description": "Slater terms [N, zeta (1/bohr), c] of R(r) = sum c (2 zeta)^(N+1/2)/sqrt((2N)!) r^(N-1) exp(-zeta r)", "items": { "type": "array", "items": { "type": "number" }, "minItems": 3, "maxItems": 3 } } } } }, "x": { "type": "array", "items": { "type": "number" } }, "C": { "type": "array", "items": { "type": "array", "items": { "type": "number" } } }, "occ": { "type": "array", "items": { "type": "number" } }, "homo": { "type": [ "integer", "null" ] }, "lumo": { "type": [ "integer", "null" ] }, "n_electrons": { "type": "number" }, "bond_orders": { "type": "array", "items": { "type": "object" } } } }, "PiForm": { "type": "object", "description": "Everything the browser needs to draw one form of the molecule.", "properties": { "atoms": { "type": "array", "items": { "type": "object", "properties": { "el": { "type": "string" }, "x": { "type": "number" }, "y": { "type": "number" }, "z": { "type": "number" }, "Q": { "type": "number", "description": "net charge (π + formal)" }, "formal": { "type": "integer" }, "pi": { "type": "boolean" }, "label": { "type": "string" } } } }, "bonds": { "type": "array", "items": { "type": "array", "items": { "type": "integer" } } }, "components": { "type": "array", "items": { "$ref": "#/components/schemas/PiComponent" } }, "site": { "type": [ "integer", "null" ] }, "probe": { "type": [ "array", "null" ], "items": { "type": "number" } }, "E_pi": { "type": "number" } } }, "PkaSite": { "type": "object", "properties": { "kind": { "type": "string", "example": "phenol" }, "type": { "type": "string", "enum": [ "acid", "base" ] }, "group_pka": { "oneOf": [ { "type": "number" }, { "type": "array", "items": { "type": "number" } } ] }, "family": { "type": [ "string", "null" ] }, "descriptors": { "type": "object", "properties": { "Q_site": { "type": "number" }, "V_probe": { "type": "number" }, "dE_deloc": { "type": "number" } } }, "pi_forecast": { "type": [ "object", "null" ], "properties": { "pka": { "type": "number" }, "plus_minus": { "type": "number" }, "descriptor": { "type": "string" }, "calibration": { "type": "string" } } }, "outside_pi_model": { "type": "boolean" }, "forms": { "type": "object", "properties": { "acid": { "$ref": "#/components/schemas/PiForm" }, "base": { "$ref": "#/components/schemas/PiForm" } } } } }, "PiModelResult": { "type": "object", "properties": { "smiles": { "type": "string" }, "canonical_smiles": { "type": "string" }, "inchikey": { "type": [ "string", "null" ] }, "formula": { "type": "string" }, "model": { "type": "string", "example": "qo-chem/16" }, "molecule": { "$ref": "#/components/schemas/PiForm" }, "sites": { "type": "array", "items": { "$ref": "#/components/schemas/PkaSite" } }, "calibration": { "type": "object" }, "protonation": { "type": [ "object", "null" ] }, "tautomers": { "type": "object" }, "badges": { "type": "object" }, "warnings": { "type": "array", "items": { "type": "string" } }, "provenance": { "type": [ "object", "null" ] }, "summary": { "type": "object" }, "speciation": { "oneOf": [ { "$ref": "#/components/schemas/Speciation" }, { "type": "null" } ] } } }, "Speciation": { "type": "object", "description": "Coupled titration of all ionisable sites (qo_chem.speciation). Same order as `sites`. Weights: log10 w(h) = Σ h_i (pKa_i − pH) − Σ_{i/ or a gl1x.com record link. Alone, the server fetches the file from gl1x.com; with structure(_b64) it only labels the source.", "example": "0xbf7491af3407816dfa88a5ea4c82e8a2b1d721ed/1" }, "example": { "type": "string", "enum": [ "5a7u", "7ddo", "1hvr", "1a28", "19hc" ] }, "name": { "type": "string" }, "motif": { "type": "string", "description": "PROSITE pattern: x, x(n), x(n,m), [ST], {P}, <, >; or a bare sequence.", "example": "C-x(2,4)-C-x(12)-H-x(3,5)-H" }, "chain": { "type": "string" }, "occurrence": { "type": "integer", "minimum": 0, "default": 0 }, "metal_site": { "type": "integer", "minimum": 0, "description": "Used when no motif is given." }, "scope": { "type": "string", "enum": [ "segment", "ligands" ], "default": "segment" }, "metal": { "type": "string", "enum": [ "auto", "refit", "zn", "none" ], "default": "auto" }, "ph": { "type": "number", "minimum": 0, "maximum": 14, "default": 7.4 }, "list_only": { "type": "boolean", "default": false }, "return_structure": { "type": "boolean", "default": false, "description": "Add the whole first model as PDB (or mmCIF) text under `display`." }, "ligand": { "oneOf": [ { "type": "string" }, { "type": "integer", "minimum": 0 } ], "description": "A ligand instead of a motif: 'HEM:A:301', 'HEM A 301', 'A:301', 'HEM' (the first) or an index into `ligands`.", "example": "XK2:A:263" }, "smiles": { "type": "string", "maxLength": 4000, "description": "Template SMILES for the ligand, matched onto its atoms; the page sends the CCD's." }, "smiles_source": { "type": "string", "enum": [ "ccd", "user", "name" ], "default": "ccd" }, "ccd_name": { "type": "string" }, "ccd_formula": { "type": "string" }, "ccd": { "type": "boolean", "default": true, "description": "Without `smiles`, let the server fetch the CCD entry from data.rcsb.org (unless started with --no-ccd-fetch). It waits at most 5 s and, after failing to reach the RCSB, does not try again for 10 minutes." }, "name_to_smiles": { "oneOf": [ { "type": "boolean" }, { "type": "string", "enum": [ "always" ] } ], "default": true, "description": "Read the component's name with OPSIN, when the server has it: by default only when no dictionary fits the atoms (each new name starts Java); 'always' reads it as a check; false never." }, "pocket": { "type": "boolean", "default": true, "description": "Ligand mode: add the side chains within 4.5 Å and a zinc the ligand binds." } } }, "SiteResult": { "type": "object", "required": [ "schema", "source", "structure", "occurrences", "metal_sites" ], "properties": { "schema": { "type": "string", "const": "qo-site/1" }, "source": { "type": "object", "description": "kind (upload, gl1x, example), sha256, bytes; for GL1X the record and structure-file URLs and the collection." }, "structure": { "type": "object", "description": "id, title, method, resolution, format, predicted_model, atoms, chains, metals." }, "motif": { "type": "object" }, "occurrences": { "type": "array", "items": { "type": "object" } }, "metal_sites": { "type": "array", "items": { "type": "object" } }, "selected": { "type": "object" }, "site": { "type": "object", "description": "Report: residues, protonation, confidence (B-factor or pLDDT), metal with ligands, distances against Harding's targets, angles, refit or placement fit, warnings, notes." }, "model": { "type": "object", "description": "Shaped like /api/model (atoms with radial_model, orbitals, bonds, pi_field, molblock, summary) plus metal_bonds: donor hybrids, angles to the metal, donor–acceptor overlaps, acceptor and open-site orbitals." }, "fragment_pdb": { "type": "string" }, "display": { "type": "object" }, "timing_ms": { "type": "object" }, "ligands": { "type": "array", "description": "Every non-polymer residue but water (first 400).", "items": { "type": "object", "properties": { "key": { "type": "string" }, "index": { "type": "integer" }, "comp": { "type": "string" }, "chain": { "type": "string" }, "resseq": { "type": "integer" }, "icode": { "type": "string" }, "class": { "type": "string", "enum": [ "ligand", "sugar", "additive", "ion", "metal", "modified residue" ] }, "heavy_atoms": { "type": "integer" }, "name": { "type": [ "string", "null" ] }, "formula_file": { "type": [ "string", "null" ] }, "dictionary": { "type": "boolean", "description": "the file carries this component's bond table" }, "center": { "type": "array", "items": { "type": "number" } } } } }, "ligands_total": { "type": "integer" }, "ligand": { "type": "object", "description": "Ligand mode: which molecule it is. `routes` (file, ccd, name, user, geometry) each with smiles, same_graph, same_molecule, differences, stereo and leaving_atoms; `chosen` (route, smiles, smiles_bound, smiles_free, formulas); links, metal_contacts, pocket, polar_contacts, notes, warnings." }, "free_molecule": { "type": "object", "properties": { "smiles": { "type": "string" }, "source": { "type": "string" }, "smiles_bound": { "type": "string" }, "pages": { "type": "object", "additionalProperties": { "type": "string" }, "description": "links to /molviewer, /molecule, /pka-density, /catalogue and /name-to-smiles" } } } } } } } }