@kent-tokyo/chematic 0.1.19 → 0.1.21

package/chematic_wasm.d.ts

@@ -1,6 +1,64 @@
 /* tslint:disable */
 /* eslint-disable */
 
+/**
+ * A conformer ensemble: one molecule geometry with multiple 3D coordinate sets.
+ *
+ * Create with `new(smiles)`, then add conformers with `add_generated_conformer`
+ * or `add_minimized_conformer`.  Retrieve coordinates as PDB strings via
+ * `get_conformer_pdb(idx)`.  Compare conformers with `conformer_rmsd`.
+ */
+export class ConformerHandle {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Generate a new 3D conformer using distance-geometry and add it to the ensemble.
+     *
+     * Returns the index of the newly added conformer.
+     */
+    add_generated_conformer(): number;
+    /**
+     * Generate a new 3D conformer, run force-field minimization, and add it.
+     *
+     * Returns the index of the newly added conformer.
+     */
+    add_minimized_conformer(): number;
+    /**
+     * Number of conformers currently stored.
+     */
+    conformer_count(): number;
+    /**
+     * Kabsch-aligned RMSD (Å) between conformers `a` and `b`.
+     *
+     * Returns `NaN` if either index is out of range.
+     */
+    conformer_rmsd(a: number, b: number): number;
+    /**
+     * Un-aligned (translation + rotation NOT removed) RMSD (Å) between conformers `a` and `b`.
+     *
+     * Returns `NaN` if either index is out of range.
+     */
+    conformer_rmsd_no_align(a: number, b: number): number;
+    /**
+     * Return conformer `idx` as a PDB string, or `null` if `idx` is out of range.
+     */
+    get_conformer_pdb(idx: number): string | undefined;
+    /**
+     * The ensemble's molecule as a `MolHandle`.
+     */
+    mol(): MolHandle;
+    /**
+     * Create a new empty ensemble for the molecule given by `smiles`.
+     *
+     * Returns a JS error on SMILES parse failure.
+     */
+    constructor(smiles: string);
+    /**
+     * Remove conformer `idx` and return `true`, or `false` if `idx` is out of range.
+     */
+    remove_conformer(idx: number): boolean;
+}
+
 /**
  * Style options for [`MolHandle::depict_svg_opts`].
  *
@@ -200,6 +258,10 @@ export class MolHandle {
      * Number of non-aromatic rings containing at least one heteroatom.
      */
     num_aliphatic_heterocycles(): number;
+    /**
+     * Count of aliphatic (non-aromatic) rings in the SSSR.
+     */
+    num_aliphatic_rings(): number;
     /**
      * Number of aromatic rings containing at least one heteroatom (N, O, S, …).
      */
@@ -216,6 +278,10 @@ export class MolHandle {
      * Number of fully saturated rings containing at least one heteroatom.
      */
     num_saturated_heterocycles(): number;
+    /**
+     * Count of fully saturated rings in the SSSR.
+     */
+    num_saturated_rings(): number;
     /**
      * Number of spiro atoms (sole shared atom between exactly 2 rings).
      */
@@ -224,6 +290,10 @@ export class MolHandle {
      * Number of assigned stereocenters (R/S).
      */
     num_stereocenters(): number;
+    /**
+     * Count of tetrahedral stereocenters with unspecified configuration.
+     */
+    num_unspecified_stereocenters(): number;
     /**
      * Returns `true` if the molecule has no PAINS structural alerts.
      */
@@ -268,6 +338,11 @@ export class MolHandle {
  */
 export function add_hydrogens(mol: MolHandle): MolHandle;
 
+/**
+ * AtomPair fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ */
+export function atom_pair_bitvec(mol: MolHandle): Uint8Array;
+
 /**
  * Number of BRICS fragments produced by fragmenting the molecule.
  *
@@ -275,6 +350,94 @@ export function add_hydrogens(mol: MolHandle): MolHandle;
  */
 export function brics_fragment_count(mol: MolHandle): number;
 
+/**
+ * BRICS fragment SMILES as a JSON array.
+ *
+ * Applies the BRICS fragmentation rules and returns the canonical SMILES of
+ * every resulting fragment.  Returns `[]` for molecules with no BRICS-breakable
+ * bonds (e.g. benzene).
+ *
+ * The count of fragments equals `brics_fragment_count`.
+ */
+export function brics_fragments_json(mol: MolHandle): string;
+
+/**
+ * Cluster molecules by structural similarity (Butina algorithm, ECFP4 Tanimoto).
+ *
+ * `smiles_json` — a JSON array of SMILES strings.
+ * `cutoff` — Tanimoto similarity threshold (0.0–1.0); molecules within this
+ *   distance of a cluster centre are assigned to that cluster.
+ * Returns a JSON array of clusters, each cluster being an array of 0-based input indices.
+ * Returns a JS error if any SMILES fails to parse.
+ */
+export function butina_cluster_ecfp4_json(smiles_json: string, cutoff: number): string;
+
+/**
+ * Canonical tautomer of `mol`.
+ *
+ * Applies a rule-based tautomer normalisation and returns the canonical form
+ * as a new `MolHandle`.
+ */
+export function canonical_tautomer(mol: MolHandle): MolHandle;
+
+/**
+ * Parse all molecular fragments from a CDXML string.
+ *
+ * Returns a JSON array of SMILES strings, one per fragment:
+ * `["CC","c1ccccc1"]`
+ *
+ * Stereochemistry (wedge/dash bonds) is read from the `Display` attribute
+ * of bond elements.
+ */
+export function cdxml_to_smiles_json(cdxml: string): string;
+
+/**
+ * CIP stereo assignments as a JSON array of `{atomIdx, cipCode}` objects.
+ *
+ * `cipCode` is one of `"R"`, `"S"`, `"E"`, or `"Z"`.
+ * Returns `[]` for molecules with no specified stereocenters.
+ */
+export function cip_assignments_json(mol: MolHandle): string;
+
+/**
+ * Return the CPK color (CSS hex string) for the given element symbol.
+ *
+ * Returns `"#000000"` (black) for carbon and unknown elements.
+ */
+export function cpk_color(element_symbol: string): string;
+
+/**
+ * Compute structured depiction data for `mol` as a JSON object.
+ *
+ * Returns:
+ * ```json
+ * {
+ *   "atoms": [
+ *     {"idx": 0, "element": "C", "x": 1.5, "y": 0.0, "charge": 0,
+ *      "label": null, "color": "#000000"},
+ *     ...
+ *   ],
+ *   "bonds": [
+ *     {"idx": 0, "atom1": 0, "atom2": 1, "kind": "Single"},
+ *     ...
+ *   ]
+ * }
+ * ```
+ *
+ * `label` is `null` for carbon atoms in skeletal structures (label suppressed).
+ * `kind` is one of `"Single"`, `"Double"`, `"Triple"`, `"Aromatic"`, `"Up"`, `"Down"`.
+ */
+export function depict_data_json(mol: MolHandle): string;
+
+/**
+ * Compute structured depiction data using caller-supplied 2D coordinates.
+ *
+ * `coords_json` — JSON array of `[x, y]` pairs, one per atom in order.
+ *
+ * Returns the same JSON format as `depict_data_json`.
+ */
+export function depict_data_with_coords_json(mol: MolHandle, coords_json: string): string;
+
 /**
  * Render a reaction SMILES string (e.g. `"CC(=O)O.CCO>>CC(=O)OCC.O"`) as a
  * single SVG showing reactants → products with `+` separators.
@@ -291,6 +454,19 @@ export function depict_reaction_svg(rxn_smiles: string): string;
  */
 export function depict_svg_grid(smiles_block: string, cols: number): string;
 
+/**
+ * Render a molecule grid with SMARTS-based atom highlighting.
+ *
+ * `smiles_block` — newline-separated SMILES strings (same format as `depict_svg_grid`).
+ * `cols` — number of grid columns.
+ * `match_smarts` — SMARTS pattern; matched atoms in each molecule are highlighted.
+ *   Pass an empty string `""` to render without any highlighting.
+ *
+ * Invalid SMILES are rendered as empty cells; SMARTS parse failure returns an
+ * unhighlighted grid (the SMARTS is silently ignored).
+ */
+export function depict_svg_grid_highlighted(smiles_block: string, cols: number, match_smarts: string): string;
+
 /**
  * Detect named functional groups in `mol`.
  *
@@ -301,11 +477,63 @@ export function depict_svg_grid(smiles_block: string, cols: number): string;
  */
 export function detect_functional_groups(mol: MolHandle): string;
 
+/**
+ * Dice similarity between `a` and `b` using ECFP4 fingerprints.
+ */
+export function dice_ecfp4(a: MolHandle, b: MolHandle): number;
+
+/**
+ * Dice similarity between `a` and `b` using ECFP6 fingerprints.
+ */
+export function dice_ecfp6(a: MolHandle, b: MolHandle): number;
+
+/**
+ * Dice similarity between `a` and `b` using MACCS 166-bit fingerprints.
+ */
+export function dice_maccs(a: MolHandle, b: MolHandle): number;
+
 /**
  * Compute the ECFP4 fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  */
 export function ecfp4_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * ECFP6 (radius-3) fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ */
+export function ecfp6_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * Compute a fingerprint bit-vector with configurable ECFP radius and bit width.
+ *
+ * `radius` — Morgan radius (1 = ECFP2, 2 = ECFP4, 3 = ECFP6).
+ * `nbits` — bit width; must be one of 256, 512, 1024, or 2048.
+ *   Returns a `Uint8Array` of `nbits/8` bytes.
+ *
+ * The hash modulo is applied at fingerprint-generation time (`id % nbits`),
+ * so no post-processing fold is needed.
+ */
+export function ecfp_bitvec_custom(mol: MolHandle, radius: number, nbits: number): Uint8Array;
+
+/**
+ * Enumerate all stereoisomers arising from unspecified tetrahedral stereocenters.
+ *
+ * Only considers carbon stereocenters without explicit `@`/`@@` annotation.
+ * Already-specified centers and E/Z double-bond geometry are unchanged.
+ * Returns a JSON array of canonical SMILES strings.
+ *
+ * At most 2^6 = 64 combinations are enumerated; if more than 6 unspecified
+ * centers are present this function returns a JS error to avoid combinatorial
+ * explosion.
+ */
+export function enumerate_stereo_isomers_json(mol: MolHandle): string;
+
+/**
+ * All enumerated tautomers of `mol` as a JSON array of canonical SMILES strings.
+ *
+ * Example return value: `["Oc1cccc2ccccc12","O=C1C=CC=Cc2ccccc21"]`
+ */
+export function enumerate_tautomers_json(mol: MolHandle): string;
+
 /**
  * Per-atom EState values as a JSON array of f64.
  *
@@ -313,11 +541,30 @@ export function ecfp4_bitvec(mol: MolHandle): Uint8Array;
  */
 export function estate_indices_json(mol: MolHandle): string;
 
+/**
+ * FCFP4 (pharmacophore, radius-2) fingerprint as a bit-packed byte vector (256 bytes).
+ */
+export function fcfp4_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * FCFP6 (pharmacophore, radius-3) fingerprint as a bit-packed byte vector (256 bytes).
+ */
+export function fcfp6_bitvec(mol: MolHandle): Uint8Array;
+
 /**
  * Gasteiger-Marsili PEOE partial charges as a JSON array of f64.
  */
 export function gasteiger_charges_json(mol: MolHandle): string;
 
+/**
+ * Generate energy-minimized 3D coordinates and return a PDB string.
+ *
+ * Runs distance-geometry placement followed by gradient-descent force-field
+ * minimization.  Geometry quality is better than `generate_3d_pdb` for
+ * flexible molecules; the force field is approximate (not MMFF94/UFF).
+ */
+export function generate_3d_minimized_pdb(mol: MolHandle): string;
+
 /**
  * Generate 3D coordinates for the molecule and return a PDB string.
  *
@@ -326,6 +573,14 @@ export function gasteiger_charges_json(mol: MolHandle): string;
  */
 export function generate_3d_pdb(mol: MolHandle): string;
 
+/**
+ * Generic (atom-type-erased) Murcko scaffold of `mol`.
+ *
+ * All atoms become carbon and all bonds become single bonds, giving the pure
+ * graph topology of the scaffold.
+ */
+export function generic_murcko_scaffold(mol: MolHandle): MolHandle;
+
 /**
  * Return information about a single atom as a JSON object.
  *
@@ -360,6 +615,14 @@ export function get_bond_between(mol: MolHandle, atom1: number, atom2: number):
  */
 export function get_bond_info(mol: MolHandle, idx: number): string;
 
+/**
+ * All scalar molecular descriptors as a single JSON object.
+ *
+ * Keys use camelCase and match the individual `MolHandle` method names.
+ * Drug-likeness rule outcomes are included as boolean fields.
+ */
+export function get_descriptors_json(mol: MolHandle): string;
+
 /**
  * Identify functional groups. Returns a JSON array of objects:
  * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
@@ -371,6 +634,34 @@ export function identify_functional_groups(mol: MolHandle): string;
  */
 export function is_valid_smiles(s: string): boolean;
 
+/**
+ * Per-atom Labute approximate surface area contributions as a JSON array of f64.
+ *
+ * Non-finite values (single-atom molecules etc.) are emitted as JSON `null`.
+ */
+export function labute_asa_per_atom_json(mol: MolHandle): string;
+
+/**
+ * Return the largest fragment of `mol` (salt/solvent stripping).
+ *
+ * For single-component molecules returns a copy of the same molecule.
+ */
+export function largest_fragment(mol: MolHandle): MolHandle;
+
+/**
+ * Per-atom Crippen LogP contributions as a JSON array of f64.
+ *
+ * Index `i` corresponds to atom `i` in `mol.atoms()` order.
+ */
+export function logp_per_atom_json(mol: MolHandle): string;
+
+/**
+ * MACCS 166-bit structural keys fingerprint as a byte array (21 bytes, LSB-first).
+ *
+ * Bit `i` (0-indexed) corresponds to MACCS key `i+1`.
+ */
+export function maccs_bitvec(mol: MolHandle): Uint8Array;
+
 /**
  * Find all SMARTS matches in a molecule given only SMILES strings.
  *
@@ -381,13 +672,86 @@ export function is_valid_smiles(s: string): boolean;
 export function match_smarts_smiles(smiles: string, smarts: string): string;
 
 /**
- * Serialize a SMILES string directly to a MOL V2000 block.
+ * Select `n` maximally-diverse molecules (MaxMin algorithm, ECFP4 Tanimoto).
+ *
+ * `smiles_json` — a JSON array of SMILES strings, e.g. `["CC","c1ccccc1","CCO"]`.
+ * Returns a JSON array of 0-based indices into the input array.
+ * Returns a JS error if any SMILES fails to parse (indices would otherwise shift).
+ */
+export function maxmin_picks_ecfp4_json(smiles_json: string, n: number): string;
+
+/**
+ * Maximum Common Substructure of a set of molecules, returned as a canonical SMILES string.
+ *
+ * `smiles_json` — a JSON array of at least 2 SMILES strings.
+ * Returns the MCS SMILES, or `"null"` when no common substructure was found.
+ * Returns a JS error on SMILES parse failure.
+ */
+export function mcs_smiles_json(smiles_json: string): string;
+
+/**
+ * Find matched molecular pairs in a set of molecules as JSON.
+ *
+ * `smiles_json` — JSON array of SMILES strings to analyze.
+ *
+ * Returns a JSON array of matched pairs:
+ * ```json
+ * [
+ *   {
+ *     "mol_a": "CC(=O)Oc1ccccc1",
+ *     "mol_b": "CC(=O)Nc1ccccc1",
+ *     "core": "c1ccccc1[*]",
+ *     "fragment_a": "[*]OC(C)=O",
+ *     "fragment_b": "[*]NC(C)=O"
+ *   }
+ * ]
+ * ```
+ *
+ * Each pair represents molecules that share a common core scaffold but differ
+ * by exactly one structural fragment at a single BRICS-breakable bond cut.
+ *
+ * Returns a JS error if any SMILES fails to parse.
+ */
+export function mmp_pairs_json(smiles_json: string): string;
+
+/**
+ * Parse a MOL V2000 string and return 2D coordinates as a JSON array.
+ *
+ * Returns `[[x0,y0],[x1,y1],...]` in atom-insertion order.
+ * Coordinates are in Ångström as stored in the MOL file.
+ */
+export function mol_block_coords_json(mol_block: string): string;
+
+/**
+ * Serialize a SMILES string directly to a MOL V2000 block with 2D coordinates.
  *
- * Convenience wrapper; all atom coordinates are 0.0.
  * Returns a JS error on SMILES parse failure.
  */
 export function mol_block_from_smiles(smiles: string): string;
 
+/**
+ * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
+ *
+ * Only the first molecular fragment in the document is returned.
+ * Returns a JS error if the document cannot be parsed.
+ */
+export function mol_from_cdxml(cdxml: string): MolHandle;
+
+/**
+ * Parse a CML string into a `MolHandle`.
+ *
+ * Returns a JS error if the CML is invalid (unknown element, bad bond, etc.).
+ */
+export function mol_from_cml(cml: string): MolHandle;
+
+/**
+ * Parse a PDB file and return a `MolHandle` (topology only; coordinates are discarded).
+ *
+ * Uses CONECT records for connectivity if present; otherwise infers bonds from
+ * atom distances (the same heuristic as the internal `pdb_to_molecule` function).
+ */
+export function mol_from_pdb(pdb: string): MolHandle;
+
 /**
  * Parse a MOL V2000 block and return a `MolHandle`.
  *
@@ -395,6 +759,107 @@ export function mol_block_from_smiles(smiles: string): string;
  */
 export function mol_from_sdf_block(block: string): MolHandle;
 
+/**
+ * Parse a MOL V3000 block and return a `MolHandle`.
+ *
+ * Returns a JS error string on parse failure.
+ */
+export function mol_from_v3000_block(block: string): MolHandle;
+
+/**
+ * Parse an XYZ file and return a `MolHandle` (topology only; coordinates are discarded).
+ *
+ * Returns a JS error on parse failure.
+ */
+export function mol_from_xyz(xyz: string): MolHandle;
+
+/**
+ * Return the index that would be assigned to an atom appended to `mol`.
+ */
+export function mol_next_atom_idx(mol: MolHandle): number;
+
+/**
+ * Return a new `MolHandle` with one atom appended.
+ *
+ * The second return value is the new atom's index (as a JS number).
+ * Use `with_atom_added_idx` to retrieve the index.
+ */
+export function mol_with_atom_added(mol: MolHandle, element_symbol: string): MolHandle;
+
+/**
+ * Return a new `MolHandle` with the formal charge of atom `idx` changed.
+ *
+ * Returns a JS error if `idx` is out of range.
+ */
+export function mol_with_atom_charge(mol: MolHandle, idx: number, charge: number): MolHandle;
+
+/**
+ * Return a new `MolHandle` with the element of atom `idx` changed.
+ *
+ * `element_symbol` — periodic-table symbol, e.g. `"N"`, `"O"`, `"Cl"`.
+ * Returns a JS error if `idx` is out of range or the symbol is unknown.
+ */
+export function mol_with_atom_element(mol: MolHandle, idx: number, element_symbol: string): MolHandle;
+
+/**
+ * Return a new `MolHandle` with atom `idx` and all its bonds removed.
+ *
+ * Atom indices above `idx` shift down by 1.  Returns a JS error if `idx`
+ * is out of range.
+ */
+export function mol_with_atom_removed(mol: MolHandle, idx: number): MolHandle;
+
+/**
+ * Return a new `MolHandle` with one bond added between `a` and `b`.
+ *
+ * `order` — 1 = single, 2 = double, 3 = triple.
+ * Returns a JS error if the bond already exists or `a == b`.
+ */
+export function mol_with_bond_added(mol: MolHandle, a: number, b: number, order: number): MolHandle;
+
+/**
+ * Return a new `MolHandle` with bond `idx` removed.
+ *
+ * Atom indices are unchanged; bond indices above `idx` shift down.
+ * Returns a JS error if `idx` is out of range.
+ */
+export function mol_with_bond_removed(mol: MolHandle, idx: number): MolHandle;
+
+/**
+ * Per-atom molar refractivity contributions as a JSON array of f64.
+ */
+export function mr_per_atom_json(mol: MolHandle): string;
+
+/**
+ * Murcko scaffold of `mol` — the ring system plus linkers, side-chains removed.
+ *
+ * Returns a new `MolHandle`.  For acyclic molecules returns an empty molecule.
+ */
+export function murcko_scaffold(mol: MolHandle): MolHandle;
+
+/**
+ * Neutralize formal charges on `mol` by proton addition/removal.
+ *
+ * Returns a new `MolHandle` with all formal charges set to zero where possible.
+ */
+export function neutralize_charges(mol: MolHandle): MolHandle;
+
+/**
+ * Parse and re-serialise a reaction SMILES string, returning the normalised form.
+ *
+ * Useful for validating reaction SMILES and obtaining a canonical representation.
+ * Returns a JS error on parse failure.
+ */
+export function normalize_reaction_smiles(rxn_smiles: string): string;
+
+/**
+ * PAINS structural alert names matched by `mol` as a JSON array.
+ *
+ * Returns `[]` when no alerts fire, or e.g. `["ene_six_het_A(483)"]`.
+ * Use alongside `pains_passes()` to know *which* alerts triggered.
+ */
+export function pains_matches_json(mol: MolHandle): string;
+
 /**
  * Parse a SMILES string into a `MolHandle`.
  *
@@ -412,6 +877,29 @@ export function peoe_vsa_json(mol: MolHandle): string;
  */
 export function remove_hydrogens(mol: MolHandle): MolHandle;
 
+/**
+ * Decompose a set of molecules against a core SMARTS, returning R-group SMILES.
+ *
+ * `smiles_json` — JSON array of SMILES strings.
+ * `core_smarts` — SMARTS pattern with `*` (wildcard) atoms marking R-group
+ *   attachment points.  For example `c1ccc(*)cc1` for para-substituted benzene.
+ *
+ * Returns a JSON array with one entry per input molecule:
+ * ```json
+ * [
+ *   {"matched":true, "r1":"C"},
+ *   {"matched":true, "r1":"CC"},
+ *   {"matched":false}
+ * ]
+ * ```
+ * R-group keys are `"r1"`, `"r2"`, … in the order the `*` atoms appear in
+ * the SMARTS pattern.  A molecule that does not contain the core gets
+ * `"matched": false` and no R-group keys.
+ *
+ * Returns a JS error if the SMARTS fails to parse or any SMILES is invalid.
+ */
+export function rgroup_decompose_json(smiles_json: string, core_smarts: string): string;
+
 /**
  * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
  *
@@ -426,6 +914,37 @@ export function run_reactants(smirks: string, reactants_smiles: string): string;
  */
 export function sa_score(mol: MolHandle): number;
 
+/**
+ * Serialize multiple molecules with properties to an SDF string.
+ *
+ * # Arguments
+ * * `smiles_json` — JSON array of SMILES strings, e.g. `["CC(=O)O","c1ccccc1"]`
+ * * `names_json`  — JSON array of molecule names (same length as `smiles_json`)
+ * * `props_json`  — JSON array where each element encodes one molecule's SD data fields
+ *   as `"key1\tvalue1\nkey2\tvalue2"` (tab-separated key/value, `\n`-separated pairs;
+ *   pass `""` for a molecule with no properties)
+ *
+ * Returns the SDF string, or a JS error if any SMILES fails to parse or the
+ * arrays have mismatched lengths.
+ *
+ * The `\n` and `\t` sequences in `props_json` are JSON-escaped — they are
+ * decoded to the actual characters before SDF formatting.
+ */
+export function sdf_from_records_json(smiles_json: string, names_json: string, props_json: string): string;
+
+/**
+ * Parse an SDF string and return a JSON array of record objects.
+ *
+ * Each record has the shape:
+ * ```json
+ * {"smiles":"CC(=O)O","name":"aspirin","properties":{"MW":"180.2","Activity":"high"}}
+ * ```
+ *
+ * Invalid records are represented as `null`.  SD data fields are included in
+ * `properties`; multi-line values are joined with `\n`.
+ */
+export function sdf_to_records_json(sdf: string): string;
+
 /**
  * Parse an SDF string and return a JSON array of canonical SMILES strings.
  *
@@ -433,6 +952,15 @@ export function sa_score(mol: MolHandle): number;
  */
 export function sdf_to_smiles_json(sdf: string): string;
 
+/**
+ * 3D shape descriptors as a JSON object.
+ *
+ * Keys: `pmi1`, `pmi2`, `pmi3`, `npr1`, `npr2`, `asphericity`, `eccentricity`,
+ * `radiusOfGyration`, `planeOfBestFit`.  Non-finite values (e.g. single-atom
+ * molecules where pmi3 = 0) are serialised as JSON `null`.
+ */
+export function shape_descriptors_json(mol: MolHandle): string;
+
 /**
  * SlogP_VSA descriptors (12 bins) as a JSON array.
  */
@@ -447,6 +975,14 @@ export function slogp_vsa_json(mol: MolHandle): string;
  */
 export function smarts_match_atoms(smarts: string, mol: MolHandle): string;
 
+/**
+ * Serialise a JSON array of SMILES to an SDF string.
+ *
+ * Generates 2D coordinates for each molecule.  Property data can be
+ * included by using `sdf_from_records_json` instead.
+ */
+export function smiles_array_to_sdf(smiles_json: string): string;
+
 /**
  * Render a highlighted SVG from a SMILES string in one call.
  *
@@ -463,6 +999,14 @@ export function smiles_to_svg_highlighted(smiles: string, atoms: Uint32Array, bo
  */
 export function smr_vsa_json(mol: MolHandle): string;
 
+/**
+ * Smallest Set of Smallest Rings (SSSR) as a JSON array of atom-index arrays.
+ *
+ * Example return value for naphthalene:
+ * `[[0,1,2,3,4,5],[5,6,7,8,9,4]]`
+ */
+export function sssr_rings_json(mol: MolHandle): string;
+
 export function start(): void;
 
 /**
@@ -475,11 +1019,26 @@ export function tanimoto_atom_pair(a: MolHandle, b: MolHandle): number;
  */
 export function tanimoto_ecfp4(a: MolHandle, b: MolHandle): number;
 
+/**
+ * Tanimoto similarity between `a` and `b` using ECFP6 fingerprints.
+ */
+export function tanimoto_ecfp6(a: MolHandle, b: MolHandle): number;
+
 /**
  * Tanimoto similarity between two molecules using FCFP4 fingerprints (pharmacophore-based).
  */
 export function tanimoto_fcfp4(a: MolHandle, b: MolHandle): number;
 
+/**
+ * Tanimoto similarity between `a` and `b` using FCFP6 (radius-3 pharmacophore) fingerprints.
+ */
+export function tanimoto_fcfp6(a: MolHandle, b: MolHandle): number;
+
+/**
+ * Tanimoto similarity between `a` and `b` using MACCS 166-bit fingerprints.
+ */
+export function tanimoto_maccs(a: MolHandle, b: MolHandle): number;
+
 /**
  * Tanimoto similarity between two molecules given only SMILES strings (ECFP4).
  *
@@ -498,23 +1057,76 @@ export function tanimoto_topo_path(a: MolHandle, b: MolHandle): number;
 export function tanimoto_torsion(a: MolHandle, b: MolHandle): number;
 
 /**
- * Serialize a molecule to a MOL V2000 block.
+ * Serialise a `MolHandle` to a CML string with 2D coordinates.
+ *
+ * Coordinates are generated using the same 2D layout engine as `to_mol_block`.
+ */
+export function to_cml(mol: MolHandle): string;
+
+/**
+ * Serialize a molecule to a MOL V2000 block with 2D coordinates.
  *
- * All atom coordinates are written as 0.0 (the `Molecule` type has no 2D
- * coordinate storage; real coordinates would require a separate layout pass).
+ * Atom positions are computed via the same layout engine used for SVG depiction
+ * and converted to Ångström units (`1.5 Å` per bond).
  */
 export function to_mol_block(mol: MolHandle): string;
 
+/**
+ * Serialise a `MolHandle` to MOL V3000 format with 2D coordinates.
+ */
+export function to_mol_v3000_block(mol: MolHandle): string;
+
+/**
+ * Serialize a molecule to XYZ format.
+ *
+ * 3D coordinates are generated via distance-geometry placement.
+ */
+export function to_xyz(mol: MolHandle): string;
+
+/**
+ * Torsion fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ */
+export function torsion_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * Non-canonical SMILES for `mol`.
+ *
+ * Unlike `canonical_smiles`, the output depends on the internal atom ordering
+ * and is not normalised.  Useful when round-trip fidelity (preserving atom
+ * order) matters more than a canonical form.
+ */
+export function write_smiles(mol: MolHandle): string;
+
 export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembly.Module;
 
 export interface InitOutput {
     readonly memory: WebAssembly.Memory;
+    readonly __wbg_conformerhandle_free: (a: number, b: number) => void;
     readonly __wbg_depictoptions_free: (a: number, b: number) => void;
     readonly __wbg_molhandle_free: (a: number, b: number) => void;
     readonly add_hydrogens: (a: number) => number;
+    readonly atom_pair_bitvec: (a: number) => [number, number];
     readonly brics_fragment_count: (a: number) => number;
+    readonly brics_fragments_json: (a: number) => [number, number];
+    readonly butina_cluster_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly canonical_tautomer: (a: number) => number;
+    readonly cdxml_to_smiles_json: (a: number, b: number) => [number, number, number, number];
+    readonly cip_assignments_json: (a: number) => [number, number];
+    readonly conformerhandle_add_generated_conformer: (a: number) => number;
+    readonly conformerhandle_add_minimized_conformer: (a: number) => number;
+    readonly conformerhandle_conformer_count: (a: number) => number;
+    readonly conformerhandle_conformer_rmsd: (a: number, b: number, c: number) => number;
+    readonly conformerhandle_conformer_rmsd_no_align: (a: number, b: number, c: number) => number;
+    readonly conformerhandle_get_conformer_pdb: (a: number, b: number) => [number, number];
+    readonly conformerhandle_mol: (a: number) => number;
+    readonly conformerhandle_new: (a: number, b: number) => [number, number, number];
+    readonly conformerhandle_remove_conformer: (a: number, b: number) => number;
+    readonly cpk_color: (a: number, b: number) => [number, number];
+    readonly depict_data_json: (a: number) => [number, number];
+    readonly depict_data_with_coords_json: (a: number, b: number, c: number) => [number, number];
     readonly depict_reaction_svg: (a: number, b: number) => [number, number, number, number];
     readonly depict_svg_grid: (a: number, b: number, c: number) => [number, number];
+    readonly depict_svg_grid_highlighted: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly depictoptions_new: () => number;
     readonly depictoptions_set_atom_color: (a: number, b: number, c: number, d: number) => void;
     readonly depictoptions_set_atom_ids: (a: number, b: number) => void;
@@ -529,20 +1141,51 @@ export interface InitOutput {
     readonly depictoptions_set_show_atom_indices: (a: number, b: number) => void;
     readonly depictoptions_set_width: (a: number, b: number) => void;
     readonly detect_functional_groups: (a: number) => [number, number];
+    readonly dice_ecfp4: (a: number, b: number) => number;
+    readonly dice_ecfp6: (a: number, b: number) => number;
+    readonly dice_maccs: (a: number, b: number) => number;
     readonly ecfp4_bitvec: (a: number) => [number, number];
+    readonly ecfp6_bitvec: (a: number) => [number, number];
+    readonly ecfp_bitvec_custom: (a: number, b: number, c: number) => [number, number];
+    readonly enumerate_stereo_isomers_json: (a: number) => [number, number, number, number];
+    readonly enumerate_tautomers_json: (a: number) => [number, number];
     readonly estate_indices_json: (a: number) => [number, number];
+    readonly fcfp4_bitvec: (a: number) => [number, number];
+    readonly fcfp6_bitvec: (a: number) => [number, number];
     readonly gasteiger_charges_json: (a: number) => [number, number];
+    readonly generate_3d_minimized_pdb: (a: number) => [number, number];
     readonly generate_3d_pdb: (a: number) => [number, number];
+    readonly generic_murcko_scaffold: (a: number) => number;
     readonly get_atom_info: (a: number, b: number) => [number, number];
     readonly get_bond_between: (a: number, b: number, c: number) => [number, number];
     readonly get_bond_info: (a: number, b: number) => [number, number];
+    readonly get_descriptors_json: (a: number) => [number, number];
     readonly identify_functional_groups: (a: number) => [number, number];
     readonly is_valid_smiles: (a: number, b: number) => number;
+    readonly labute_asa_per_atom_json: (a: number) => [number, number];
+    readonly largest_fragment: (a: number) => number;
+    readonly logp_per_atom_json: (a: number) => [number, number];
+    readonly maccs_bitvec: (a: number) => [number, number];
     readonly match_smarts_smiles: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly maxmin_picks_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly mcs_smiles_json: (a: number, b: number) => [number, number, number, number];
+    readonly mmp_pairs_json: (a: number, b: number) => [number, number, number, number];
+    readonly mol_block_coords_json: (a: number, b: number) => [number, number, number, number];
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
+    readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
+    readonly mol_from_cml: (a: number, b: number) => [number, number, number];
+    readonly mol_from_pdb: (a: number, b: number) => number;
     readonly mol_from_sdf_block: (a: number, b: number) => [number, number, number];
+    readonly mol_from_v3000_block: (a: number, b: number) => [number, number, number];
+    readonly mol_from_xyz: (a: number, b: number) => [number, number, number];
+    readonly mol_next_atom_idx: (a: number) => number;
+    readonly mol_with_atom_added: (a: number, b: number, c: number) => [number, number, number];
+    readonly mol_with_atom_charge: (a: number, b: number, c: number) => [number, number, number];
+    readonly mol_with_atom_element: (a: number, b: number, c: number, d: number) => [number, number, number];
+    readonly mol_with_atom_removed: (a: number, b: number) => [number, number, number];
+    readonly mol_with_bond_added: (a: number, b: number, c: number, d: number) => [number, number, number];
+    readonly mol_with_bond_removed: (a: number, b: number) => [number, number, number];
     readonly molhandle_aromatic_ring_count: (a: number) => number;
-    readonly molhandle_atom_count: (a: number) => number;
     readonly molhandle_bertz_ct: (a: number) => number;
     readonly molhandle_bond_count: (a: number) => number;
     readonly molhandle_canonical_smiles: (a: number) => [number, number];
@@ -579,12 +1222,15 @@ export interface InitOutput {
     readonly molhandle_molecular_weight: (a: number) => number;
     readonly molhandle_morgan_fp_counts_json: (a: number, b: number) => [number, number];
     readonly molhandle_num_aliphatic_heterocycles: (a: number) => number;
+    readonly molhandle_num_aliphatic_rings: (a: number) => number;
     readonly molhandle_num_aromatic_heterocycles: (a: number) => number;
     readonly molhandle_num_bridgehead_atoms: (a: number) => number;
     readonly molhandle_num_heteroatoms: (a: number) => number;
     readonly molhandle_num_saturated_heterocycles: (a: number) => number;
+    readonly molhandle_num_saturated_rings: (a: number) => number;
     readonly molhandle_num_spiro_atoms: (a: number) => number;
     readonly molhandle_num_stereocenters: (a: number) => number;
+    readonly molhandle_num_unspecified_stereocenters: (a: number) => number;
     readonly molhandle_pains_passes: (a: number) => number;
     readonly molhandle_qed: (a: number) => number;
     readonly molhandle_reos_passes: (a: number) => number;
@@ -594,24 +1240,44 @@ export interface InitOutput {
     readonly molhandle_tpsa: (a: number) => number;
     readonly molhandle_veber_passes: (a: number) => number;
     readonly molhandle_wiener_index: (a: number) => number;
+    readonly mr_per_atom_json: (a: number) => [number, number];
+    readonly murcko_scaffold: (a: number) => number;
+    readonly neutralize_charges: (a: number) => number;
+    readonly normalize_reaction_smiles: (a: number, b: number) => [number, number, number, number];
+    readonly pains_matches_json: (a: number) => [number, number];
     readonly parse_smiles: (a: number, b: number) => [number, number, number];
     readonly peoe_vsa_json: (a: number) => [number, number];
     readonly remove_hydrogens: (a: number) => number;
+    readonly rgroup_decompose_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly sa_score: (a: number) => number;
+    readonly sdf_from_records_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
+    readonly sdf_to_records_json: (a: number, b: number) => [number, number];
     readonly sdf_to_smiles_json: (a: number, b: number) => [number, number];
+    readonly shape_descriptors_json: (a: number) => [number, number];
     readonly slogp_vsa_json: (a: number) => [number, number];
     readonly smarts_match_atoms: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly smiles_array_to_sdf: (a: number, b: number) => [number, number, number, number];
     readonly smiles_to_svg_highlighted: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
     readonly smr_vsa_json: (a: number) => [number, number];
+    readonly sssr_rings_json: (a: number) => [number, number];
     readonly tanimoto_atom_pair: (a: number, b: number) => number;
     readonly tanimoto_ecfp4: (a: number, b: number) => number;
+    readonly tanimoto_ecfp6: (a: number, b: number) => number;
     readonly tanimoto_fcfp4: (a: number, b: number) => number;
+    readonly tanimoto_fcfp6: (a: number, b: number) => number;
+    readonly tanimoto_maccs: (a: number, b: number) => number;
     readonly tanimoto_smiles: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly tanimoto_topo_path: (a: number, b: number) => number;
     readonly tanimoto_torsion: (a: number, b: number) => number;
+    readonly to_cml: (a: number) => [number, number];
     readonly to_mol_block: (a: number) => [number, number];
+    readonly to_mol_v3000_block: (a: number) => [number, number];
+    readonly to_xyz: (a: number) => [number, number];
+    readonly torsion_bitvec: (a: number) => [number, number];
+    readonly write_smiles: (a: number) => [number, number];
     readonly start: () => void;
+    readonly molhandle_atom_count: (a: number) => number;
     readonly __wbindgen_free: (a: number, b: number, c: number) => void;
     readonly __wbindgen_malloc: (a: number, b: number) => number;
     readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;