@kent-tokyo/chematic 0.2.0 → 0.2.10

package/chematic_wasm.js

@@ -1,9 +1,4792 @@
 /* @ts-self-types="./chematic_wasm.d.ts" */
-import * as wasm from "./chematic_wasm_bg.wasm";
-import { __wbg_set_wasm } from "./chematic_wasm_bg.js";
-
-__wbg_set_wasm(wasm);
-wasm.__wbindgen_start();
-export {
-    ConformerHandle, DepictOptions, MhfpLshHandle, MolHandle, add_hydrogens, atom_pair_bitvec, autocorr_2d_json, autocorr_3d_json, balance_check_json, brics_fragment_count, brics_fragments_json, butina_cluster_ecfp4_json, canonical_tautomer, cdxml_to_smiles_json, cip_assignments_json, compare_molecules_batch_json, compare_molecules_json, coulomb_energy_json, cpk_color, depict_data_json, depict_data_with_coords_json, depict_reaction_svg, depict_svg_grid, depict_svg_grid_highlighted, detect_functional_groups, dice_ecfp4, dice_ecfp6, dice_maccs, ecfp4_bitvec, ecfp4_bitvec_with_chirality, ecfp6_bitvec, ecfp6_bitvec_with_chirality, ecfp_bitvec_custom, enumerate_library_2way, enumerate_stereo_isomers_json, enumerate_tautomers_json, estate_indices_json, fcfp4_bitvec, fcfp6_bitvec, find_reaction_center_json, gasteiger_charges_json, generate_3d_etkdg_minimized_pdb, generate_3d_etkdg_pdb, generate_3d_from_smiles, generate_3d_minimized_pdb, generate_3d_optimized_pdb, generate_3d_pdb, generic_murcko_scaffold, get_atom_info, get_bond_between, get_bond_info, get_bond_length_json, get_descriptors_json, get_dihedral_json, getaway_descriptors_json, identify_functional_groups, inchi_from_smiles, inchikey_from_smiles, invert_stereocenter_at, is_valid_smiles, labute_asa_per_atom_json, largest_fragment, logp_per_atom_json, maccs_bitvec, match_smarts_smiles, maxmin_picks_ecfp4_json, mcs_smiles_json, mhfp_hashes_json, minimize_dreiding_json, mmff94_charges_json, mmp_pairs_json, mol2_to_smiles, mol_block_coords_json, mol_block_from_smiles, mol_from_cdxml, mol_from_cml, mol_from_pdb, mol_from_sdf_block, mol_from_v3000_block, mol_from_xyz, mol_next_atom_idx, mol_with_atom_added, mol_with_atom_charge, mol_with_atom_element, mol_with_atom_removed, mol_with_bond_added, mol_with_bond_removed, molecule_report_json, mqn_json, mr_per_atom_json, murcko_scaffold, nearest_neighbors_json, neutralize_charges, normalize_cxsmiles, normalize_reaction_smiles, pains_matches_json, parse_cxsmarts_json, parse_cxsmiles_json, parse_smiles, peoe_vsa_json, pharmacophore_features_json, pharmacophore_fp_2d_summary, pharmacophore_fp_3d_summary, random_smiles_json, remove_hydrogens, rgroup_decompose_json, ring_families_json, run_md_json, run_reactants, sa_score, screen_smiles_json, sdf_from_records_json, sdf_to_records_json, sdf_to_smiles_json, set_dihedral_json, shape_descriptors_json, slogp_vsa_json, smarts_match_atoms, smarts_match_atoms_with_chirality, smiles_array_to_sdf, smiles_to_mol2, smiles_to_svg_highlighted, smr_vsa_json, sssr_rings_json, standardize_smiles, standardize_smiles_report_json, start, tanimoto_atom_pair, tanimoto_ecfp4, tanimoto_ecfp6, tanimoto_fcfp4, tanimoto_fcfp6, tanimoto_maccs, tanimoto_mhfp_smiles, tanimoto_smiles, tanimoto_topo_path, tanimoto_torsion, to_cml, to_mol_block, to_mol_v3000_block, to_xyz, torsion_bitvec, whim_descriptors_json, whim_getaway_combined_json, write_smiles
-} from "./chematic_wasm_bg.js";
+
+/**
+ * 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 {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        ConformerHandleFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_conformerhandle_free(ptr, 0);
+    }
+    /**
+     * Generate a new 3D conformer using distance-geometry and add it to the ensemble.
+     *
+     * Returns the index of the newly added conformer.
+     * @returns {number}
+     */
+    add_generated_conformer() {
+        const ret = wasm.conformerhandle_add_generated_conformer(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Generate a new 3D conformer, run force-field minimization, and add it.
+     *
+     * Returns the index of the newly added conformer.
+     * @returns {number}
+     */
+    add_minimized_conformer() {
+        const ret = wasm.conformerhandle_add_minimized_conformer(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Cluster conformers by Kabsch-aligned RMSD and return a JSON object
+     * describing which conformers to keep.
+     *
+     * Uses greedy leader-linkage: conformers are visited in index order; each
+     * is compared against existing cluster representatives. If the RMSD to any
+     * representative is < `rms_threshold`, the conformer is discarded; otherwise
+     * it starts a new cluster and is kept.
+     *
+     * Returns `{"kept_indices":[0,3,7,...],"removed_count":5}` on success.
+     * @param {number} rms_threshold
+     * @returns {string}
+     */
+    cluster_conformers_json(rms_threshold) {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.conformerhandle_cluster_conformers_json(this.__wbg_ptr, rms_threshold);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Number of conformers currently stored.
+     * @returns {number}
+     */
+    conformer_count() {
+        const ret = wasm.conformerhandle_conformer_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Kabsch-aligned RMSD (Å) between conformers `a` and `b`.
+     *
+     * Returns `NaN` if either index is out of range.
+     * @param {number} a
+     * @param {number} b
+     * @returns {number}
+     */
+    conformer_rmsd(a, b) {
+        const ret = wasm.conformerhandle_conformer_rmsd(this.__wbg_ptr, a, b);
+        return ret;
+    }
+    /**
+     * Un-aligned (translation + rotation NOT removed) RMSD (Å) between conformers `a` and `b`.
+     *
+     * Returns `NaN` if either index is out of range.
+     * @param {number} a
+     * @param {number} b
+     * @returns {number}
+     */
+    conformer_rmsd_no_align(a, b) {
+        const ret = wasm.conformerhandle_conformer_rmsd_no_align(this.__wbg_ptr, a, b);
+        return ret;
+    }
+    /**
+     * Return conformer `idx` as a PDB string, or `null` if `idx` is out of range.
+     * @param {number} idx
+     * @returns {string | undefined}
+     */
+    get_conformer_pdb(idx) {
+        const ret = wasm.conformerhandle_get_conformer_pdb(this.__wbg_ptr, idx);
+        let v1;
+        if (ret[0] !== 0) {
+            v1 = getStringFromWasm0(ret[0], ret[1]).slice();
+            wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+        }
+        return v1;
+    }
+    /**
+     * The ensemble's molecule as a `MolHandle`.
+     * @returns {MolHandle}
+     */
+    mol() {
+        const ret = wasm.conformerhandle_mol(this.__wbg_ptr);
+        return MolHandle.__wrap(ret);
+    }
+    /**
+     * Create a new empty ensemble for the molecule given by `smiles`.
+     *
+     * Returns a JS error on SMILES parse failure.
+     * @param {string} smiles
+     */
+    constructor(smiles) {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.conformerhandle_new(ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0];
+        ConformerHandleFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Remove conformer `idx` and return `true`, or `false` if `idx` is out of range.
+     * @param {number} idx
+     * @returns {boolean}
+     */
+    remove_conformer(idx) {
+        const ret = wasm.conformerhandle_remove_conformer(this.__wbg_ptr, idx);
+        return ret !== 0;
+    }
+}
+if (Symbol.dispose) ConformerHandle.prototype[Symbol.dispose] = ConformerHandle.prototype.free;
+
+/**
+ * Style options for [`MolHandle::depict_svg_opts`].
+ *
+ * Construct with `new DepictOptions()`, then call setters:
+ * ```js
+ * const opts = new DepictOptions();
+ * opts.set_background("transparent");
+ * opts.set_dark(true);
+ * opts.set_width(240);
+ * opts.set_height(240);
+ * ```
+ */
+export class DepictOptions {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        DepictOptionsFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_depictoptions_free(ptr, 0);
+    }
+    constructor() {
+        const ret = wasm.depictoptions_new();
+        this.__wbg_ptr = ret;
+        DepictOptionsFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Set a per-atom color override (CSS color string).  Calling multiple times
+     * for the same `idx` uses the last value.  The atom is highlighted even if
+     * not in `set_highlight_atoms`.
+     * @param {number} idx
+     * @param {string} color
+     */
+    set_atom_color(idx, color) {
+        const ptr0 = passStringToWasm0(color, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.depictoptions_set_atom_color(this.__wbg_ptr, idx, ptr0, len0);
+    }
+    /**
+     * @param {boolean} v
+     */
+    set_atom_ids(v) {
+        wasm.depictoptions_set_atom_ids(this.__wbg_ptr, v);
+    }
+    /**
+     * @param {string} bg
+     */
+    set_background(bg) {
+        const ptr0 = passStringToWasm0(bg, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.depictoptions_set_background(this.__wbg_ptr, ptr0, len0);
+    }
+    /**
+     * @param {boolean} dark
+     */
+    set_dark(dark) {
+        wasm.depictoptions_set_dark(this.__wbg_ptr, dark);
+    }
+    /**
+     * @param {number} h
+     */
+    set_height(h) {
+        wasm.depictoptions_set_height(this.__wbg_ptr, h);
+    }
+    /**
+     * @param {Uint32Array} atoms
+     */
+    set_highlight_atoms(atoms) {
+        const ptr0 = passArray32ToWasm0(atoms, wasm.__wbindgen_malloc);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.depictoptions_set_highlight_atoms(this.__wbg_ptr, ptr0, len0);
+    }
+    /**
+     * @param {Uint32Array} bonds
+     */
+    set_highlight_bonds(bonds) {
+        const ptr0 = passArray32ToWasm0(bonds, wasm.__wbindgen_malloc);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.depictoptions_set_highlight_bonds(this.__wbg_ptr, ptr0, len0);
+    }
+    /**
+     * @param {string} color
+     */
+    set_highlight_color(color) {
+        const ptr0 = passStringToWasm0(color, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.depictoptions_set_highlight_color(this.__wbg_ptr, ptr0, len0);
+    }
+    /**
+     * @param {boolean} v
+     */
+    set_kekulize(v) {
+        wasm.depictoptions_set_kekulize(this.__wbg_ptr, v);
+    }
+    /**
+     * @param {number} p
+     */
+    set_padding(p) {
+        wasm.depictoptions_set_padding(this.__wbg_ptr, p);
+    }
+    /**
+     * @param {boolean} v
+     */
+    set_show_atom_indices(v) {
+        wasm.depictoptions_set_show_atom_indices(this.__wbg_ptr, v);
+    }
+    /**
+     * @param {number} w
+     */
+    set_width(w) {
+        wasm.depictoptions_set_width(this.__wbg_ptr, w);
+    }
+}
+if (Symbol.dispose) DepictOptions.prototype[Symbol.dispose] = DepictOptions.prototype.free;
+
+/**
+ * MinHash LSH index: insert MHFP fingerprints and query by approximate similarity.
+ *
+ * ```js
+ * const idx = new MhfpLshHandle(128);
+ * const i0 = idx.add_smiles("c1ccccc1");    // benzene → index 0
+ * const i1 = idx.add_smiles("Cc1ccccc1");   // toluene → index 1
+ * const hits = JSON.parse(idx.query_json("c1ccccc1", 0.5));
+ * // hits: [{index:0,similarity:1.0}, {index:1,similarity:0.xxx}]
+ * ```
+ */
+export class MhfpLshHandle {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        MhfpLshHandleFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_mhfplshhandle_free(ptr, 0);
+    }
+    /**
+     * Add a molecule by SMILES; returns its 0-based index in the index.
+     * @param {string} smiles
+     * @returns {number}
+     */
+    add_smiles(smiles) {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mhfplshhandle_add_smiles(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * True if the index contains no molecules.
+     * @returns {boolean}
+     */
+    is_empty() {
+        const ret = wasm.mhfplshhandle_is_empty(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Number of molecules in the index.
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.mhfplshhandle_len(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Create a new LSH index for MHFP fingerprints with `num_hashes` hash lanes.
+     * Default band decomposition: 16 bands × (num_hashes / 16) rows.
+     * `num_hashes` must be a multiple of 16 (e.g. 128).
+     * @param {number} num_hashes
+     */
+    constructor(num_hashes) {
+        const ret = wasm.mhfplshhandle_new(num_hashes);
+        this.__wbg_ptr = ret;
+        MhfpLshHandleFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Query by SMILES for all entries with similarity ≥ threshold.
+     *
+     * Returns a JSON array `[{"index":N,"similarity":0.xxx},...]` sorted by
+     * descending similarity.  Empty array `[]` when nothing qualifies.
+     * @param {string} query_smiles
+     * @param {number} threshold
+     * @returns {string}
+     */
+    query_json(query_smiles, threshold) {
+        let deferred3_0;
+        let deferred3_1;
+        try {
+            const ptr0 = passStringToWasm0(query_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len0 = WASM_VECTOR_LEN;
+            const ret = wasm.mhfplshhandle_query_json(this.__wbg_ptr, ptr0, len0, threshold);
+            var ptr2 = ret[0];
+            var len2 = ret[1];
+            if (ret[3]) {
+                ptr2 = 0; len2 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred3_0 = ptr2;
+            deferred3_1 = len2;
+            return getStringFromWasm0(ptr2, len2);
+        } finally {
+            wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+        }
+    }
+}
+if (Symbol.dispose) MhfpLshHandle.prototype[Symbol.dispose] = MhfpLshHandle.prototype.free;
+
+/**
+ * A handle to a parsed molecule.  Owns the molecule behind an `Rc` so that
+ * it can be cheaply cloned on the JS side without copying atom/bond data.
+ */
+export class MolHandle {
+    static __wrap(ptr) {
+        const obj = Object.create(MolHandle.prototype);
+        obj.__wbg_ptr = ptr;
+        MolHandleFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        MolHandleFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_molhandle_free(ptr, 0);
+    }
+    /**
+     * Number of aromatic rings (all ring atoms aromatic).
+     * @returns {number}
+     */
+    aromatic_ring_count() {
+        const ret = wasm.molhandle_aromatic_ring_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Assign CIP (R/S/E/Z) stereocenters and return JSON.
+     *
+     * Format: `{"centers":[{"atom":0,"code":"R"},{"atom":3,"code":"E"}]}`
+     * @returns {string}
+     */
+    assign_cip_json() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_assign_cip_json(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Number of heavy atoms (explicit atoms in the graph; does not count implicit H).
+     * @returns {number}
+     */
+    atom_count() {
+        const ret = wasm.molhandle_atom_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Bertz complexity index (BertzCT).
+     * @returns {number}
+     */
+    bertz_ct() {
+        const ret = wasm.molhandle_bertz_ct(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Number of bonds.
+     * @returns {number}
+     */
+    bond_count() {
+        const ret = wasm.molhandle_bond_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Canonical SMILES string.
+     * @returns {string}
+     */
+    canonical_smiles() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_canonical_smiles(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Kier–Hall χ0 molecular connectivity index.
+     * @returns {number}
+     */
+    chi0() {
+        const ret = wasm.molhandle_chi0(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ0v valence-weighted connectivity index.
+     * @returns {number}
+     */
+    chi0v() {
+        const ret = wasm.molhandle_chi0v(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ1 molecular connectivity index.
+     * @returns {number}
+     */
+    chi1() {
+        const ret = wasm.molhandle_chi1(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ1v valence-weighted connectivity index.
+     * @returns {number}
+     */
+    chi1v() {
+        const ret = wasm.molhandle_chi1v(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ2 molecular connectivity index.
+     * @returns {number}
+     */
+    chi2() {
+        const ret = wasm.molhandle_chi2(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ2v valence-weighted connectivity index.
+     * @returns {number}
+     */
+    chi2v() {
+        const ret = wasm.molhandle_chi2v(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ3 molecular connectivity index.
+     * @returns {number}
+     */
+    chi3() {
+        const ret = wasm.molhandle_chi3(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ3v valence-weighted connectivity index.
+     * @returns {number}
+     */
+    chi3v() {
+        const ret = wasm.molhandle_chi3v(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ4 molecular connectivity index.
+     * @returns {number}
+     */
+    chi4() {
+        const ret = wasm.molhandle_chi4(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Kier–Hall χ4v valence-weighted connectivity index.
+     * @returns {number}
+     */
+    chi4v() {
+        const ret = wasm.molhandle_chi4v(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * 2D PNG depiction (rasterized from SVG).
+     * Returns PNG data as base64-encoded string for embedding in HTML/JS.
+     * @returns {Uint8Array}
+     */
+    depict_png() {
+        const ret = wasm.molhandle_depict_png(this.__wbg_ptr);
+        var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+        return v1;
+    }
+    /**
+     * 2D SVG depiction of the molecule (CPK coloring).
+     * @returns {string}
+     */
+    depict_svg() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_depict_svg(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * 2D SVG depiction with style options.
+     * @param {DepictOptions} opts
+     * @returns {string}
+     */
+    depict_svg_opts(opts) {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            _assertClass(opts, DepictOptions);
+            const ret = wasm.molhandle_depict_svg_opts(this.__wbg_ptr, opts.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Returns `true` if the molecule passes Egan's absorption criteria
+     * (TPSA ≤ 131.6 Ų and LogP ≤ 5.88).
+     * @returns {boolean}
+     */
+    egan_passes() {
+        const ret = wasm.molhandle_egan_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Monoisotopic (exact) mass.
+     * @returns {number}
+     */
+    exact_mass() {
+        const ret = wasm.molhandle_exact_mass(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Sum of formal charges.
+     * @returns {number}
+     */
+    formal_charge_sum() {
+        const ret = wasm.molhandle_formal_charge_sum(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Molecular formula string (Hill notation: C first, H second, then alphabetical).
+     * @returns {string}
+     */
+    formula() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_formula(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Fraction of sp3 carbons (Fsp3).
+     * @returns {number}
+     */
+    fsp3() {
+        const ret = wasm.molhandle_fsp3(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Returns `true` if the molecule passes Ghose's drug-likeness filter
+     * (MW 160–480, LogP −0.4–5.6, HeavyAtoms 20–70, MR 40–130).
+     * @returns {boolean}
+     */
+    ghose_passes() {
+        const ret = wasm.molhandle_ghose_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Number of hydrogen bond acceptors (Lipinski: all N and O atoms).
+     * @returns {number}
+     */
+    hba_count() {
+        const ret = wasm.molhandle_hba_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of hydrogen bond donors (N-H or O-H groups).
+     * @returns {number}
+     */
+    hbd_count() {
+        const ret = wasm.molhandle_hbd_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of non-hydrogen heavy atoms.
+     * @returns {number}
+     */
+    heavy_atom_count() {
+        const ret = wasm.molhandle_heavy_atom_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Isotope distribution as JSON.
+     *
+     * Returns `[{"mass":100.0,"abundance":0.9},...]` sorted by mass.
+     * `resolution`: m/z bin width in Da (e.g. `0.1` for nominal, `0.01` for high-res).
+     * @param {number} resolution
+     * @returns {string}
+     */
+    isotope_distribution_json(resolution) {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_isotope_distribution_json(this.__wbg_ptr, resolution);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Generate IUPAC systematic name for the molecule.
+     *
+     * Returns the name string on success, or an empty string when the
+     * structure is outside the supported naming scope (complex polycyclics,
+     * multi-functional groups, etc.).
+     * @returns {string}
+     */
+    iupac_name() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_iupac_name(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Hall–Kier κ1 shape index.
+     * @returns {number}
+     */
+    kappa1() {
+        const ret = wasm.molhandle_kappa1(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Hall–Kier κ2 shape index.
+     * @returns {number}
+     */
+    kappa2() {
+        const ret = wasm.molhandle_kappa2(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Hall–Kier κ3 shape index.
+     * @returns {number}
+     */
+    kappa3() {
+        const ret = wasm.molhandle_kappa3(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Labute approximate surface area (Ų).
+     * @returns {number}
+     */
+    labute_asa() {
+        const ret = wasm.molhandle_labute_asa(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Returns `true` if the molecule satisfies Lipinski's Rule of Five.
+     * @returns {boolean}
+     */
+    lipinski_passes() {
+        const ret = wasm.molhandle_lipinski_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * LogD (distribution coefficient) at a specific pH.
+     *
+     * Accounts for ionization state: neutral molecules return LogP unchanged,
+     * ionizable molecules are adjusted by log(neutral_fraction).
+     * @param {number} ph
+     * @returns {number}
+     */
+    logd_at_ph(ph) {
+        const ret = wasm.molhandle_logd_at_ph(this.__wbg_ptr, ph);
+        return ret;
+    }
+    /**
+     * LogD profile across a pH range as JSON.
+     *
+     * Returns `[{"ph":0.0,"logd":2.5}, ...]` with `steps` evenly-spaced pH points.
+     * @param {number} ph_start
+     * @param {number} ph_end
+     * @param {number} steps
+     * @returns {string}
+     */
+    logd_profile_json(ph_start, ph_end, steps) {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_logd_profile_json(this.__wbg_ptr, ph_start, ph_end, steps);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Crippen–Wildman octanol/water partition coefficient (LogP).
+     * @returns {number}
+     */
+    logp_crippen() {
+        const ret = wasm.molhandle_logp_crippen(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Maximum EState index across all heavy atoms.
+     * @returns {number}
+     */
+    max_estate() {
+        const ret = wasm.molhandle_max_estate(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Minimum EState index across all heavy atoms.
+     * @returns {number}
+     */
+    min_estate() {
+        const ret = wasm.molhandle_min_estate(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Wildman–Crippen molar refractivity (MR).
+     * @returns {number}
+     */
+    molar_refractivity() {
+        const ret = wasm.molhandle_molar_refractivity(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Average molecular weight (Da).
+     * @returns {number}
+     */
+    molecular_weight() {
+        const ret = wasm.molhandle_molecular_weight(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Morgan count fingerprint as a JSON object string (`{"<hash>": count, …}`).
+     *
+     * `radius` controls the ECFP radius (2 = ECFP4-equivalent).
+     * @param {number} radius
+     * @returns {string}
+     */
+    morgan_fp_counts_json(radius) {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_morgan_fp_counts_json(this.__wbg_ptr, radius);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Number of non-aromatic rings containing at least one heteroatom.
+     * @returns {number}
+     */
+    num_aliphatic_heterocycles() {
+        const ret = wasm.molhandle_num_aliphatic_heterocycles(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Count of aliphatic (non-aromatic) rings in the SSSR.
+     * @returns {number}
+     */
+    num_aliphatic_rings() {
+        const ret = wasm.molhandle_num_aliphatic_rings(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of aromatic rings containing at least one heteroatom (N, O, S, …).
+     * @returns {number}
+     */
+    num_aromatic_heterocycles() {
+        const ret = wasm.molhandle_num_aromatic_heterocycles(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of bridgehead atoms (shared by ≥2 rings with ≥3 ring bonds).
+     * @returns {number}
+     */
+    num_bridgehead_atoms() {
+        const ret = wasm.molhandle_num_bridgehead_atoms(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of heteroatoms (non-C, non-H heavy atoms).
+     * @returns {number}
+     */
+    num_heteroatoms() {
+        const ret = wasm.molhandle_num_heteroatoms(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of fully saturated rings containing at least one heteroatom.
+     * @returns {number}
+     */
+    num_saturated_heterocycles() {
+        const ret = wasm.molhandle_num_saturated_heterocycles(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Count of fully saturated rings in the SSSR.
+     * @returns {number}
+     */
+    num_saturated_rings() {
+        const ret = wasm.molhandle_num_saturated_rings(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of spiro atoms (sole shared atom between exactly 2 rings).
+     * @returns {number}
+     */
+    num_spiro_atoms() {
+        const ret = wasm.molhandle_num_spiro_atoms(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of assigned stereocenters (R/S).
+     * @returns {number}
+     */
+    num_stereocenters() {
+        const ret = wasm.molhandle_num_stereocenters(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Count of tetrahedral stereocenters with unspecified configuration.
+     * @returns {number}
+     */
+    num_unspecified_stereocenters() {
+        const ret = wasm.molhandle_num_unspecified_stereocenters(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Returns `true` if the molecule has no PAINS structural alerts.
+     * @returns {boolean}
+     */
+    pains_passes() {
+        const ret = wasm.molhandle_pains_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Quantitative Estimate of Drug-likeness (QED); range [0, 1].
+     * @returns {number}
+     */
+    qed() {
+        const ret = wasm.molhandle_qed(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Randić connectivity index (χ₀).
+     *
+     * χ₀ = Σ 1/√(d_i × d_j) over all bonds, where d is heavy-atom degree.
+     * @returns {number}
+     */
+    randic_index() {
+        const ret = wasm.molhandle_randic_index(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Returns `true` if the molecule passes the REOS (Rapid Elimination Of Swill) filter.
+     * @returns {boolean}
+     */
+    reos_passes() {
+        const ret = wasm.molhandle_reos_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Total number of rings (SSSR count).
+     * @returns {number}
+     */
+    ring_count() {
+        const ret = wasm.molhandle_ring_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of rotatable bonds.
+     * @returns {number}
+     */
+    rotatable_bond_count() {
+        const ret = wasm.molhandle_rotatable_bond_count(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Sum of EState indices over all heavy atoms.
+     * @returns {number}
+     */
+    sum_estate() {
+        const ret = wasm.molhandle_sum_estate(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * InChI string representation of the molecule.
+     * @returns {string}
+     */
+    to_inchi() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_to_inchi(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * InChIKey (27-character identifier) for the molecule.
+     * @returns {string}
+     */
+    to_inchikey() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_to_inchikey(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Topological polar surface area (Ų).
+     * @returns {number}
+     */
+    tpsa() {
+        const ret = wasm.molhandle_tpsa(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Returns `true` if the molecule passes Veber's oral bioavailability criteria
+     * (TPSA ≤ 140 Ų and rotatable bonds ≤ 10).
+     * @returns {boolean}
+     */
+    veber_passes() {
+        const ret = wasm.molhandle_veber_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Wiener topological index (sum of all pairwise shortest-path distances).
+     * @returns {number}
+     */
+    wiener_index() {
+        const ret = wasm.molhandle_wiener_index(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Zagreb index M1: Σ d_i² over all heavy atoms.
+     * @returns {number}
+     */
+    zagreb_index_m1() {
+        const ret = wasm.molhandle_zagreb_index_m1(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+}
+if (Symbol.dispose) MolHandle.prototype[Symbol.dispose] = MolHandle.prototype.free;
+
+/**
+ * Return a copy of the molecule with all implicit hydrogens converted to explicit H atoms.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function add_hydrogens(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.add_hydrogens(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * AtomPair fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function atom_pair_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.atom_pair_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * AutoCorr2D descriptor (7 values: topological distance lags 1-7).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function autocorr_2d_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.autocorr_2d_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * AutoCorr3D descriptor (8 values: Euclidean distance bins 1-8 Å).
+ * Requires 3D coordinates (generated automatically).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function autocorr_3d_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.autocorr_3d_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Check whether a reaction SMILES is atom-balanced.
+ *
+ * Returns JSON: `{ "balanced": true|false, "diff": ["C: 1 reactant vs 2 product", ...] }`
+ * Returns `"error:<msg>"` on parse failure.
+ * @param {string} reaction_smiles
+ * @returns {string}
+ */
+export function balance_check_json(reaction_smiles) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(reaction_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.balance_check_json(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Number of BRICS fragments produced by fragmenting the molecule.
+ *
+ * Returns 1 if no BRICS-breakable bonds exist (whole molecule is one fragment).
+ * @param {MolHandle} mol
+ * @returns {number}
+ */
+export function brics_fragment_count(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.brics_fragment_count(mol.__wbg_ptr);
+    return ret >>> 0;
+}
+
+/**
+ * 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`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function brics_fragments_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.brics_fragments_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} smiles_json
+ * @param {number} cutoff
+ * @returns {string}
+ */
+export function butina_cluster_ecfp4_json(smiles_json, cutoff) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.butina_cluster_ecfp4_json(ptr0, len0, cutoff);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Canonical tautomer of `mol`.
+ *
+ * Applies a rule-based tautomer normalisation and returns the canonical form
+ * as a new `MolHandle`.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function canonical_tautomer(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.canonical_tautomer(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * Compute the canonical tautomer with specific atoms blocked from H-transfer.
+ *
+ * `blocked_atom_indices_json`: JSON array of 0-based atom indices, e.g. `[0, 3]`.
+ * Any tautomer move whose donor, bridge, or acceptor is in the blocked set is suppressed.
+ *
+ * Returns canonical SMILES of the result, or `{"error":"..."}` on failure.
+ * Out-of-range indices are silently ignored (no effect).
+ * @param {MolHandle} mol
+ * @param {string} blocked_atom_indices_json
+ * @returns {string}
+ */
+export function canonical_tautomer_with_blocked_atoms_json(mol, blocked_atom_indices_json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(blocked_atom_indices_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.canonical_tautomer_with_blocked_atoms_json(mol.__wbg_ptr, ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} cdxml
+ * @returns {string}
+ */
+export function cdxml_to_smiles_json(cdxml) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(cdxml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.cdxml_to_smiles_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function cip_assignments_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.cip_assignments_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compare multiple SMILES strings (up to 256 by default).
+ * Accepts a delimiter-separated list (e.g., newline or comma).
+ *
+ * # Example (JS)
+ * ```javascript
+ * const smilesList = "c1ccccc1\nCc1ccccc1\nCCc1ccccc1";
+ * const json = module.compare_molecules_batch_json(smilesList, "\n");
+ * const comparison = JSON.parse(json);
+ * ```
+ * @param {string} smiles_batch
+ * @param {string} delimiter
+ * @returns {string}
+ */
+export function compare_molecules_batch_json(smiles_batch, delimiter) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_batch, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(delimiter, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.compare_molecules_batch_json(ptr0, len0, ptr1, len1);
+        var ptr3 = ret[0];
+        var len3 = ret[1];
+        if (ret[3]) {
+            ptr3 = 0; len3 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred4_0 = ptr3;
+        deferred4_1 = len3;
+        return getStringFromWasm0(ptr3, len3);
+    } finally {
+        wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+    }
+}
+
+/**
+ * Compare two or more SMILES strings (JSON string output).
+ * Returns the JSON representation of a `MoleculeComparison` struct.
+ *
+ * # Example (JS)
+ * ```javascript
+ * const json = module.compare_molecules_json("c1ccccc1", "Cc1ccccc1");
+ * const comparison = JSON.parse(json);
+ * console.log(comparison.pairwise[0].similarities.ecfp4_tanimoto);
+ * ```
+ * @param {string} smiles1
+ * @param {string} smiles2
+ * @returns {string}
+ */
+export function compare_molecules_json(smiles1, smiles2) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles1, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(smiles2, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.compare_molecules_json(ptr0, len0, ptr1, len1);
+        var ptr3 = ret[0];
+        var len3 = ret[1];
+        if (ret[3]) {
+            ptr3 = 0; len3 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred4_0 = ptr3;
+        deferred4_1 = len3;
+        return getStringFromWasm0(ptr3, len3);
+    } finally {
+        wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+    }
+}
+
+/**
+ * Compute direct Coulomb energy for a molecule with Gasteiger partial charges.
+ *
+ * Returns JSON object: `{ "coulomb_energy": E, "unit": "kcal/mol" }`
+ *
+ * # Arguments
+ * * `mol` - Molecule to evaluate
+ *
+ * # Example (JavaScript)
+ * ```js
+ * const mol = parse_smiles("CCO");
+ * const result = coulomb_energy_json(mol);
+ * // { "coulomb_energy": -12.34, "unit": "kcal/mol" }
+ * ```
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function coulomb_energy_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.coulomb_energy_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Return the CPK color (CSS hex string) for the given element symbol.
+ *
+ * Returns `"#000000"` (black) for carbon and unknown elements.
+ * @param {string} element_symbol
+ * @returns {string}
+ */
+export function cpk_color(element_symbol) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(element_symbol, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.cpk_color(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * 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"`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function depict_data_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.depict_data_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * 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`.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @returns {string}
+ */
+export function depict_data_with_coords_json(mol, coords_json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.depict_data_with_coords_json(mol.__wbg_ptr, ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Render a reaction SMILES string (e.g. `"CC(=O)O.CCO>>CC(=O)OCC.O"`) as a
+ * single SVG showing reactants → products with `+` separators.
+ *
+ * Returns a self-contained SVG string.  Returns a JS error on invalid input.
+ * @param {string} rxn_smiles
+ * @returns {string}
+ */
+export function depict_reaction_svg(rxn_smiles) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(rxn_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.depict_reaction_svg(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Render a grid SVG from newline-separated SMILES (one per line).
+ *
+ * Lines that fail to parse are silently skipped.
+ * `cols` controls the number of columns (each cell is 200×200 px).
+ * @param {string} smiles_block
+ * @param {number} cols
+ * @returns {string}
+ */
+export function depict_svg_grid(smiles_block, cols) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.depict_svg_grid(ptr0, len0, cols);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * 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).
+ * @param {string} smiles_block
+ * @param {number} cols
+ * @param {string} match_smarts
+ * @returns {string}
+ */
+export function depict_svg_grid_highlighted(smiles_block, cols, match_smarts) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(match_smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.depict_svg_grid_highlighted(ptr0, len0, cols, ptr1, len1);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Detect named functional groups in `mol`.
+ *
+ * Returns a JSON array of `{"name":"hydroxyl","atoms":[3]}` objects.
+ * Multiple matches of the same group (e.g. two hydroxyl groups) each appear
+ * as a separate entry.  Overlapping groups (carboxylic acid → "carboxyl" +
+ * "hydroxyl" + "carbonyl") are all returned.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function detect_functional_groups(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.detect_functional_groups(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Infer bond connectivity and bond orders from an XYZ-format string.
+ *
+ * Explicit hydrogen atoms must be present in the XYZ for reliable bond-order
+ * assignment (without H, carbonyl C=O cannot be distinguished from C-O).
+ *
+ * Returns JSON on success: `{"smiles":"CCO","atom_count":3,"bond_count":2}`.
+ * `atom_count` and `bond_count` refer to the heavy-atom skeleton (H removed).
+ *
+ * Returns JSON on error: `{"error":"molecule has 450 atoms; maximum is 300"}`.
+ *
+ * Safe: never freezes. All internal loops are O(n²). Capped at 300 atoms.
+ * @param {string} xyz_str
+ * @returns {string}
+ */
+export function determine_bonds_from_xyz_json(xyz_str) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(xyz_str, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.determine_bonds_from_xyz_json(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Dice similarity between `a` and `b` using ECFP4 fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function dice_ecfp4(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.dice_ecfp4(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Dice similarity between `a` and `b` using ECFP6 fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function dice_ecfp6(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.dice_ecfp6(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Dice similarity between `a` and `b` using MACCS 166-bit fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function dice_maccs(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.dice_maccs(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Compute the ECFP4 fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function ecfp4_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.ecfp4_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Like `ecfp4_bitvec` but with explicit chirality control.
+ *
+ * When `use_chirality=true`, tetrahedral stereochemistry is included in the
+ * initial atom hash, making enantiomers have different fingerprints.
+ * When `false` (default), chirality is ignored.
+ * @param {MolHandle} mol
+ * @param {boolean} use_chirality
+ * @returns {Uint8Array}
+ */
+export function ecfp4_bitvec_with_chirality(mol, use_chirality) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.ecfp4_bitvec_with_chirality(mol.__wbg_ptr, use_chirality);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * ECFP6 (radius-3) fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function ecfp6_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.ecfp6_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Like `ecfp6_bitvec` but with explicit chirality control.
+ *
+ * When `use_chirality=true`, tetrahedral stereochemistry is included in the
+ * initial atom hash, making enantiomers have different fingerprints.
+ * When `false` (default), chirality is ignored.
+ * @param {MolHandle} mol
+ * @param {boolean} use_chirality
+ * @returns {Uint8Array}
+ */
+export function ecfp6_bitvec_with_chirality(mol, use_chirality) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.ecfp6_bitvec_with_chirality(mol.__wbg_ptr, use_chirality);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * 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.
+ * Compute a custom ECFP (Extended Connectivity FingerPrint) with specified radius and bit count.
+ *
+ * When `use_chirality=true`, tetrahedral stereochemistry is included in the initial
+ * atom hash. When `false` (default), chirality is ignored.
+ * @param {MolHandle} mol
+ * @param {number} radius
+ * @param {number} nbits
+ * @param {boolean} use_chirality
+ * @returns {Uint8Array}
+ */
+export function ecfp_bitvec_custom(mol, radius, nbits, use_chirality) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.ecfp_bitvec_custom(mol.__wbg_ptr, radius, nbits, use_chirality);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Enumerate a combinatorial library from a SMIRKS template and two fragment sets.
+ *
+ * Generates all products by combining every scaffold with every building block.
+ * Input format: `scaffolds_smiles` and `building_blocks_smiles` are pipe-delimited
+ * SMILES strings (e.g., `"c1ccccc1|Cc1ccccc1"`).
+ *
+ * Returns JSON array of product SMILES strings.
+ * Example: `enumerate_library_2way("[C:1][Cl].[C:2][NH2]>>[C:1]N[C:2]", "c1ccccc1|Cc1ccccc1", "NCc1ccccc1|NCC")`
+ * @param {string} template
+ * @param {string} scaffolds_smiles
+ * @param {string} building_blocks_smiles
+ * @returns {string}
+ */
+export function enumerate_library_2way(template, scaffolds_smiles, building_blocks_smiles) {
+    let deferred5_0;
+    let deferred5_1;
+    try {
+        const ptr0 = passStringToWasm0(template, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(scaffolds_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passStringToWasm0(building_blocks_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len2 = WASM_VECTOR_LEN;
+        const ret = wasm.enumerate_library_2way(ptr0, len0, ptr1, len1, ptr2, len2);
+        var ptr4 = ret[0];
+        var len4 = ret[1];
+        if (ret[3]) {
+            ptr4 = 0; len4 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred5_0 = ptr4;
+        deferred5_1 = len4;
+        return getStringFromWasm0(ptr4, len4);
+    } finally {
+        wasm.__wbindgen_free(deferred5_0, deferred5_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function enumerate_stereo_isomers_json(mol) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.enumerate_stereo_isomers_json(mol.__wbg_ptr);
+        var ptr1 = ret[0];
+        var len1 = ret[1];
+        if (ret[3]) {
+            ptr1 = 0; len1 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred2_0 = ptr1;
+        deferred2_1 = len1;
+        return getStringFromWasm0(ptr1, len1);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * All enumerated tautomers of `mol` as a JSON array of canonical SMILES strings.
+ *
+ * Example return value: `["Oc1cccc2ccccc12","O=C1C=CC=Cc2ccccc21"]`
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function enumerate_tautomers_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.enumerate_tautomers_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute ERG-style 315-element float histogram fingerprint.
+ * Returns JSON: {"len":315,"values":[f64,...]} or {"error":"..."}.
+ * Format: 21 pharmacophore-feature-pair × 15 distance bins with Gaussian fuzzing.
+ * See `chematic_fp::erg_vec` for details.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function erg_vec_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.erg_vec_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Per-atom EState values as a JSON array of f64.
+ *
+ * Indices match `mol.atoms()` order.  Hydrogen atoms get 0.0.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function estate_indices_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.estate_indices_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * FCFP4 (pharmacophore, radius-2) fingerprint as a bit-packed byte vector (256 bytes).
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function fcfp4_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.fcfp4_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * FCFP6 (pharmacophore, radius-3) fingerprint as a bit-packed byte vector (256 bytes).
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function fcfp6_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.fcfp6_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Analyze a reaction SMILES and return the reaction center as JSON.
+ *
+ * JSON schema: `{ broken: [[a1,a2],...], formed: [[a1,a2],...], changed: [a,...] }`
+ * where atom indices are 0-based within the first reactant molecule.
+ * Returns an error string prefixed with `"error:"` on failure.
+ * @param {string} reaction_smiles
+ * @returns {string}
+ */
+export function find_reaction_center_json(reaction_smiles) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(reaction_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.find_reaction_center_json(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Gasteiger-Marsili PEOE partial charges as a JSON array of f64.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function gasteiger_charges_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.gasteiger_charges_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Generate 3D coordinates using ETKDG and minimize with DREIDING force field.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function generate_3d_etkdg_minimized_pdb(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.generate_3d_etkdg_minimized_pdb(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Generate 3D coordinates using ETKDG (torsion angle preferences) and return PDB block.
+ * ETKDG produces higher-quality conformations than rule-based DG by applying
+ * experimental torsion angle preferences to common structural patterns.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function generate_3d_etkdg_pdb(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.generate_3d_etkdg_pdb(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Generate 3D coordinates from SMILES (raw distance geometry, no minimization).
+ * Returns PDB format string with atoms positioned in 3D space.
+ *
+ * # Example (JS)
+ * ```javascript
+ * const pdbStr = module.generate_3d_from_smiles("c1ccccc1");
+ * console.log(pdbStr);  // PDB file content
+ * ```
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function generate_3d_from_smiles(smiles) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.generate_3d_from_smiles(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function generate_3d_minimized_pdb(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.generate_3d_minimized_pdb(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Generate 3D coordinates and minimize from SMILES string.
+ * Pipeline: distance geometry → DREIDING minimization.
+ * Better geometry quality than raw DG; suitable for graphics.
+ *
+ * # Example (JS)
+ * ```javascript
+ * const pdbStr = module.generate_3d_optimized_pdb("c1ccccc1");
+ * console.log(pdbStr);  // PDB file with optimized geometry
+ * ```
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function generate_3d_optimized_pdb(smiles) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.generate_3d_optimized_pdb(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Generate 3D coordinates for the molecule and return a PDB string.
+ *
+ * Coordinates are generated using distance-geometry placement with ring templates.
+ * Returns heavy-atom PDB (HETATM records, no explicit H).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function generate_3d_pdb(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.generate_3d_pdb(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function generic_murcko_scaffold(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.generic_murcko_scaffold(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * Return information about a single atom as a JSON object.
+ *
+ * `idx` is the 0-based atom index (matching `atoms()` order).
+ * Returns `"null"` if `idx` is out of range.
+ *
+ * Fields: `element` (symbol), `hybridization` ("sp"/"sp2"/"sp3"),
+ * `charge` (formal charge integer), `isAromatic` (bool),
+ * `totalHydrogens` (explicit + implicit H count, integer).
+ * sp3d/sp3d2 (hypervalent P/S) are not distinguished from sp3/sp2.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @returns {string}
+ */
+export function get_atom_info(mol, idx) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.get_atom_info(mol.__wbg_ptr, idx);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Return bond information as a JSON object, looked up by the two bonded atom indices.
+ *
+ * Useful when you know the atom indices from SMARTS matching or `data-atom-idx` SVG
+ * attributes but not the bond index.  Returns `"null"` if no bond exists between them.
+ *
+ * Fields: same as `get_bond_info` plus `bondIdx` (u32).
+ * @param {MolHandle} mol
+ * @param {number} atom1
+ * @param {number} atom2
+ * @returns {string}
+ */
+export function get_bond_between(mol, atom1, atom2) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.get_bond_between(mol.__wbg_ptr, atom1, atom2);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Return bond information as a JSON object, looked up by bond index.
+ *
+ * `idx` is the 0-based bond index (order matches `mol.bonds()` iteration).
+ * Returns `"null"` if `idx` is out of range.
+ *
+ * Fields: `bondOrder` (1.0/1.5/2.0/3.0), `isAromatic` (bool),
+ * `isInRing` (bool), `atomFrom` (u32), `atomTo` (u32).
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @returns {string}
+ */
+export function get_bond_info(mol, idx) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.get_bond_info(mol.__wbg_ptr, idx);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Get bond length in Ångströms between two atoms from a SMILES string.
+ * Returns -1.0 if parsing fails or atom indices are out of range.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`: first atom index
+ * - `b`: second atom index
+ *
+ * # Example
+ * ```javascript
+ * const len = get_bond_length_json("CC", 0, 1);  // C-C single bond ≈ 1.54 Å
+ * ```
+ * @param {string} smiles
+ * @param {number} a
+ * @param {number} b
+ * @returns {number}
+ */
+export function get_bond_length_json(smiles, a, b) {
+    const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_bond_length_json(ptr0, len0, a, b);
+    return ret;
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function get_descriptors_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.get_descriptors_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Get dihedral angle A—B—C—D in degrees from a SMILES string.
+ * Returns null (JSON null) if any atom index is out of range or atoms are collinear.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`, `b`, `c`, `d`: atom indices
+ *
+ * # Example
+ * ```javascript
+ * const dihedral = get_dihedral_json("CCCC", 0, 1, 2, 3);  // A-B-C-D
+ * ```
+ * @param {string} smiles
+ * @param {number} a
+ * @param {number} b
+ * @param {number} c
+ * @param {number} d
+ * @returns {any}
+ */
+export function get_dihedral_json(smiles, a, b, c, d) {
+    const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_dihedral_json(ptr0, len0, a, b, c, d);
+    return ret;
+}
+
+/**
+ * Compute GETAWAY descriptors (GEometric, Topologic And wAveleT descriptors) from 3D coordinates.
+ * Returns JSON array of 9 values: [G1, G2, G3, D1, D2, D3, T, V, A]
+ * where G* = geometric autocorrelations (lag-1,2,3), D* = topologic distances,
+ * T = total pairwise distance, V = bounding-box volume, A = anisotropy ratio.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function getaway_descriptors_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.getaway_descriptors_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Identify functional groups. Returns a JSON array of objects:
+ * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function identify_functional_groups(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.identify_functional_groups(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Generate InChI string from SMILES.
+ *
+ * Returns `"error:<msg>"` on parse failure.
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function inchi_from_smiles(smiles) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.inchi_from_smiles(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Generate InChIKey from SMILES (27-character identifier).
+ *
+ * Returns `"error:<msg>"` on parse failure.
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function inchikey_from_smiles(smiles) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.inchikey_from_smiles(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Invert the stereochemistry of a tetrahedral stereocenter (U/D wedge bonds).
+ *
+ * If the atom has no wedge/dash bonds, returns an unchanged copy.
+ * Returns error if atom_idx is invalid.
+ * @param {MolHandle} mol
+ * @param {number} atom_idx
+ * @returns {MolHandle}
+ */
+export function invert_stereocenter_at(mol, atom_idx) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.invert_stereocenter_at(mol.__wbg_ptr, atom_idx);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Returns `true` if the SMILES string can be parsed without error.
+ * @param {string} s
+ * @returns {boolean}
+ */
+export function is_valid_smiles(s) {
+    const ptr0 = passStringToWasm0(s, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.is_valid_smiles(ptr0, len0);
+    return ret !== 0;
+}
+
+/**
+ * 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`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function labute_asa_per_atom_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.labute_asa_per_atom_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Return the largest fragment of `mol` (salt/solvent stripping).
+ *
+ * For single-component molecules returns a copy of the same molecule.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function largest_fragment(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.largest_fragment(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * Per-atom Crippen LogP contributions as a JSON array of f64.
+ *
+ * Index `i` corresponds to atom `i` in `mol.atoms()` order.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function logp_per_atom_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.logp_per_atom_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * MACCS 166-bit structural keys fingerprint as a byte array (21 bytes, LSB-first).
+ *
+ * Bit `i` (0-indexed) corresponds to MACCS key `i+1`.
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function maccs_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.maccs_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Find all SMARTS matches in a molecule given only SMILES strings.
+ *
+ * Convenience wrapper around `smarts_match_atoms` that accepts raw SMILES
+ * instead of a `MolHandle`.  Returns the same JSON format: `[[0,1],[3,4]]`.
+ * Returns a JS error on SMILES or SMARTS parse failure.
+ * @param {string} smiles
+ * @param {string} smarts
+ * @returns {string}
+ */
+export function match_smarts_smiles(smiles, smarts) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.match_smarts_smiles(ptr0, len0, ptr1, len1);
+        var ptr3 = ret[0];
+        var len3 = ret[1];
+        if (ret[3]) {
+            ptr3 = 0; len3 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred4_0 = ptr3;
+        deferred4_1 = len3;
+        return getStringFromWasm0(ptr3, len3);
+    } finally {
+        wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+    }
+}
+
+/**
+ * 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).
+ * @param {string} smiles_json
+ * @param {number} n
+ * @returns {string}
+ */
+export function maxmin_picks_ecfp4_json(smiles_json, n) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.maxmin_picks_ecfp4_json(ptr0, len0, n);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} smiles_json
+ * @returns {string}
+ */
+export function mcs_smiles_json(smiles_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mcs_smiles_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * MinHash fingerprint (128 hashes) as JSON.
+ *
+ * Returns `{"num_hashes":128,"hashes":[u64,...]}`.
+ * Use `tanimoto_mhfp_smiles` for direct SMILES-to-SMILES similarity.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mhfp_hashes_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mhfp_hashes_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Optimize molecular geometry using DREIDING force field.
+ *
+ * Performs geometry minimization with DREIDING force field parameters.
+ * Returns minimized coordinate PDB.
+ *
+ * # Arguments
+ * * `mol` - Molecule to optimize
+ *
+ * # Returns
+ * PDB format string with optimized coordinates
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function minimize_dreiding_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.minimize_dreiding_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Minimize geometry using MMFF94 steepest descent (Halgren 1996 full parameters).
+ * Generates 3D coords internally if needed.
+ * Returns JSON: {"energy":E,"rmsd":R,"converged":true,"iterations":N} or {"error":"..."}.
+ * @param {MolHandle} mol
+ * @param {number} max_iter
+ * @returns {string}
+ */
+export function minimize_mmff94_json(mol, max_iter) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.minimize_mmff94_json(mol.__wbg_ptr, max_iter);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Minimize geometry using MMFF94 L-BFGS (faster convergence than steepest descent).
+ * Returns JSON: {"energy":E,"rmsd":R,"converged":true,"iterations":N} or {"error":"..."}.
+ * @param {MolHandle} mol
+ * @param {number} max_iter
+ * @returns {string}
+ */
+export function minimize_mmff94_lbfgs_json(mol, max_iter) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.minimize_mmff94_lbfgs_json(mol.__wbg_ptr, max_iter);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * MMFF94 partial charges (BCI table, ±0.1e accuracy) as a JSON array of f64.
+ *
+ * Uses Bond Charge Increment (BCI) model (Halgren 1996) for 25 common bond types.
+ * Returns `[q0, q1, ..., qN]` — one value per heavy atom.
+ * Total charge equals the sum of formal charges (charge conserved).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mmff94_charges_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mmff94_charges_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute MMFF94-style atom-typed partial charges (improved over element-pair BCI).
+ * Returns JSON: {"charges":[f64,...]} or {"error":"..."}.
+ * Uses atom-type classification (Csp3/Ccarbonyl/Ohydroxyl/Oester/Nar/NarH etc.)
+ * for better accuracy (~±0.02e) vs element-pair BCI (~±0.05e).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mmff94_charges_typed_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mmff94_charges_typed_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute MMFF94 energy breakdown for current rule-based 3D geometry.
+ * Returns JSON: {"bond":B,"angle":A,"torsion":T,"vdw":V,"elec":E,"total":X} or {"error":"..."}.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mmff94_energy_breakdown_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mmff94_energy_breakdown_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute MMFF94 partial charges using numeric atom types (Halgren 1996 eq. 15).
+ * Returns JSON: {"charges":[-0.28,0.15,...]} or {"error":"..."}.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mmff94_partial_charges_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mmff94_partial_charges_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} smiles_json
+ * @returns {string}
+ */
+export function mmp_pairs_json(smiles_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mmp_pairs_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Parse a Tripos MOL2 string and return SMILES.
+ *
+ * Returns `"error:<msg>"` on failure.
+ * @param {string} mol2_str
+ * @returns {string}
+ */
+export function mol2_to_smiles(mol2_str) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(mol2_str, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mol2_to_smiles(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} mol_block
+ * @returns {string}
+ */
+export function mol_block_coords_json(mol_block) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(mol_block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mol_block_coords_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Serialize a SMILES string directly to a MOL V2000 block with 2D coordinates.
+ *
+ * Returns a JS error on SMILES parse failure.
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function mol_block_from_smiles(smiles) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mol_block_from_smiles(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} cdxml
+ * @returns {MolHandle}
+ */
+export function mol_from_cdxml(cdxml) {
+    const ptr0 = passStringToWasm0(cdxml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_cdxml(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Parse a CML string into a `MolHandle`.
+ *
+ * Returns a JS error if the CML is invalid (unknown element, bad bond, etc.).
+ * @param {string} cml
+ * @returns {MolHandle}
+ */
+export function mol_from_cml(cml) {
+    const ptr0 = passStringToWasm0(cml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_cml(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * 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).
+ * @param {string} pdb
+ * @returns {MolHandle}
+ */
+export function mol_from_pdb(pdb) {
+    const ptr0 = passStringToWasm0(pdb, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_pdb(ptr0, len0);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * Parse a MOL V2000 block and return a `MolHandle`.
+ *
+ * Returns a JS error string on parse failure.
+ * @param {string} block
+ * @returns {MolHandle}
+ */
+export function mol_from_sdf_block(block) {
+    const ptr0 = passStringToWasm0(block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_sdf_block(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Parse a MOL V3000 block and return a `MolHandle`.
+ *
+ * Returns a JS error string on parse failure.
+ * @param {string} block
+ * @returns {MolHandle}
+ */
+export function mol_from_v3000_block(block) {
+    const ptr0 = passStringToWasm0(block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_v3000_block(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Parse an XYZ file and return a `MolHandle` (topology only; coordinates are discarded).
+ *
+ * Returns a JS error on parse failure.
+ * @param {string} xyz
+ * @returns {MolHandle}
+ */
+export function mol_from_xyz(xyz) {
+    const ptr0 = passStringToWasm0(xyz, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_xyz(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Return the index that would be assigned to an atom appended to `mol`.
+ * @param {MolHandle} mol
+ * @returns {number}
+ */
+export function mol_next_atom_idx(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.mol_next_atom_idx(mol.__wbg_ptr);
+    return ret >>> 0;
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @param {string} element_symbol
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_added(mol, element_symbol) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(element_symbol, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_with_atom_added(mol.__wbg_ptr, ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Return a new `MolHandle` with the formal charge of atom `idx` changed.
+ *
+ * Returns a JS error if `idx` is out of range.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @param {number} charge
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_charge(mol, idx, charge) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.mol_with_atom_charge(mol.__wbg_ptr, idx, charge);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @param {string} element_symbol
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_element(mol, idx, element_symbol) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(element_symbol, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_with_atom_element(mol.__wbg_ptr, idx, ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_removed(mol, idx) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.mol_with_atom_removed(mol.__wbg_ptr, idx);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * 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`.
+ * @param {MolHandle} mol
+ * @param {number} a
+ * @param {number} b
+ * @param {number} order
+ * @returns {MolHandle}
+ */
+export function mol_with_bond_added(mol, a, b, order) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.mol_with_bond_added(mol.__wbg_ptr, a, b, order);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @returns {MolHandle}
+ */
+export function mol_with_bond_removed(mol, idx) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.mol_with_bond_removed(mol.__wbg_ptr, idx);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Generate a complete molecular report (JSON string) from a SMILES.
+ * Returns the JSON representation of a `MoleculeReport` struct.
+ *
+ * # Example (JS)
+ * ```javascript
+ * const json = module.molecule_report_json("CC(=O)Oc1ccccc1C(=O)O");
+ * const report = JSON.parse(json);
+ * console.log(report.canonical_smiles, report.descriptors.tpsa);
+ * ```
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function molecule_report_json(smiles) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.molecule_report_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * MQN descriptor (42 integer values: Molecular Quantum Numbers).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mqn_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mqn_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Per-atom molar refractivity contributions as a JSON array of f64.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mr_per_atom_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mr_per_atom_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Murcko scaffold of `mol` — the ring system plus linkers, side-chains removed.
+ *
+ * Returns a new `MolHandle`.  For acyclic molecules returns an empty molecule.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function murcko_scaffold(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.murcko_scaffold(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * Find the k nearest neighbours of a query SMILES in a list of db SMILES.
+ *
+ * `db_smiles_json`: JSON array of SMILES strings, e.g. `["CC","c1ccccc1"]`.
+ * Returns JSON: `[{"index":0,"tanimoto":0.95},...]` sorted by descending Tanimoto.
+ * Returns `"error:<msg>"` on parse failure.
+ * @param {string} query_smiles
+ * @param {string} db_smiles_json
+ * @param {number} k
+ * @returns {string}
+ */
+export function nearest_neighbors_json(query_smiles, db_smiles_json, k) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(query_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(db_smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.nearest_neighbors_json(ptr0, len0, ptr1, len1, k);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Neutralize formal charges on `mol` by proton addition/removal.
+ *
+ * Returns a new `MolHandle` with all formal charges set to zero where possible.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function neutralize_charges(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.neutralize_charges(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * Parse and re-serialize CXSMILES, preserving supported CX metadata.
+ * Returns error if atom count exceeds 10,000.
+ * @param {string} s
+ * @returns {string}
+ */
+export function normalize_cxsmiles(s) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(s, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.normalize_cxsmiles(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} rxn_smiles
+ * @returns {string}
+ */
+export function normalize_reaction_smiles(rxn_smiles) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(rxn_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.normalize_reaction_smiles(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function pains_matches_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.pains_matches_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Parse CXSMARTS and return preserved metadata as JSON.
+ * Returns error if atom count exceeds 10,000.
+ * @param {string} s
+ * @returns {string}
+ */
+export function parse_cxsmarts_json(s) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(s, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.parse_cxsmarts_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Parse CXSMILES and return preserved metadata as JSON.
+ *
+ * Supported CX fields: atom labels (`$...$`), `atomProp`, atom radicals (`^n:`),
+ * and zero-order bonds (`Z:`). The `cxsmiles` field is a re-serialized
+ * round-trip form using the supported fields.
+ * Returns error if atom count exceeds 10,000.
+ * @param {string} s
+ * @returns {string}
+ */
+export function parse_cxsmiles_json(s) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(s, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.parse_cxsmiles_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Parse a SMILES string into a `MolHandle`.
+ *
+ * Returns a JS error string on parse failure or if atom count exceeds 10,000.
+ * @param {string} s
+ * @returns {MolHandle}
+ */
+export function parse_smiles(s) {
+    const ptr0 = passStringToWasm0(s, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.parse_smiles(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * PEOE_VSA descriptors (14 bins) as a JSON array.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function peoe_vsa_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.peoe_vsa_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Detect pharmacophore features for virtual screening and lead optimization.
+ * Returns JSON array of features: [{type, atom_idx, neighbor_count}, ...]
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function pharmacophore_features_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.pharmacophore_features_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute 2D pharmacophore fingerprint (2048 bits) as a JSON feature count summary.
+ * Returns simplified JSON with feature type counts: {Donor, Acceptor, Aromatic, Hydrophobic, Positive, Negative}
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function pharmacophore_fp_2d_summary(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.pharmacophore_fp_2d_summary(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute 3D pharmacophore fingerprint from generated 3D coordinates.
+ * Returns simplified JSON with feature type counts (3D-aware version).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function pharmacophore_fp_3d_summary(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.pharmacophore_fp_3d_summary(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Generate `count` random SMILES from a SMILES string using the given seed.
+ * Atoms are permuted based on xorshift64 RNG. Each variant should parse back
+ * to the same molecule. Returns a JSON array of SMILES strings.
+ *
+ * # Arguments
+ * - `smiles`: input SMILES string
+ * - `count`: number of variants to generate (capped at 100)
+ * - `seed`: xorshift64 seed
+ *
+ * # Example
+ * ```javascript
+ * const variants = random_smiles_json("CC(C)O", 5, 42);
+ * // variants: ["CC(C)O", "C(C)(O)C", ...]
+ * ```
+ * @param {string} smiles
+ * @param {number} count
+ * @param {bigint} seed
+ * @returns {string}
+ */
+export function random_smiles_json(smiles, count, seed) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.random_smiles_json(ptr0, len0, count, seed);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Return a copy of the molecule with all explicit hydrogen atoms removed.
+ * @param {MolHandle} mol
+ * @returns {MolHandle}
+ */
+export function remove_hydrogens(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.remove_hydrogens(mol.__wbg_ptr);
+    return MolHandle.__wrap(ret);
+}
+
+/**
+ * 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.
+ * @param {string} smiles_json
+ * @param {string} core_smarts
+ * @returns {string}
+ */
+export function rgroup_decompose_json(smiles_json, core_smarts) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(core_smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.rgroup_decompose_json(ptr0, len0, ptr1, len1);
+        var ptr3 = ret[0];
+        var len3 = ret[1];
+        if (ret[3]) {
+            ptr3 = 0; len3 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred4_0 = ptr3;
+        deferred4_1 = len3;
+        return getStringFromWasm0(ptr3, len3);
+    } finally {
+        wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+    }
+}
+
+/**
+ * Ring family classification and detection as JSON.
+ * Returns an array of ring families with their atoms, ring indices, and topology kind.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function ring_families_json(mol) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.ring_families_json(mol.__wbg_ptr);
+        var ptr1 = ret[0];
+        var len1 = ret[1];
+        if (ret[3]) {
+            ptr1 = 0; len1 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred2_0 = ptr1;
+        deferred2_1 = len1;
+        return getStringFromWasm0(ptr1, len1);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Run molecular dynamics simulation and return trajectory as JSON.
+ *
+ * Returns JSON object with trajectory frames: `{ "frames": [{ "step": N, "potential": E, "kinetic": K, "temp": T }, …] }`
+ * Uses NVT ensemble (Berendsen thermostat) at 300 K by default.
+ * Note: Limited to molecules with ~50 atoms or fewer for practical WASM performance.
+ * @param {MolHandle} mol
+ * @param {number} steps
+ * @param {number} temp_k
+ * @returns {string}
+ */
+export function run_md_json(mol, steps, temp_k) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.run_md_json(mol.__wbg_ptr, steps, temp_k);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
+ *
+ * `reactants_smiles`: pipe-separated SMILES, one per reactant slot in the SMIRKS.
+ * Returns a JSON array of arrays: `[["product_smi", …], …]`.
+ * Returns a JS error on parse failure or arity mismatch.
+ * @param {string} smirks
+ * @param {string} reactants_smiles
+ * @returns {string}
+ */
+export function run_reactants(smirks, reactants_smiles) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(smirks, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(reactants_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.run_reactants(ptr0, len0, ptr1, len1);
+        var ptr3 = ret[0];
+        var len3 = ret[1];
+        if (ret[3]) {
+            ptr3 = 0; len3 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred4_0 = ptr3;
+        deferred4_1 = len3;
+        return getStringFromWasm0(ptr3, len3);
+    } finally {
+        wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+    }
+}
+
+/**
+ * Synthetic Accessibility Score (1 = easy, 10 = hard).
+ * @param {MolHandle} mol
+ * @returns {number}
+ */
+export function sa_score(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.sa_score(mol.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Screen a batch of SMILES strings (JSON string output).
+ * Returns per-record results including pass/fail with error details.
+ * Includes MaxMin diversity picking and Butina clustering by default.
+ *
+ * # Example (JS)
+ * ```javascript
+ * const smilesList = "c1ccccc1\nCC\nCCC";
+ * const json = module.screen_smiles_json(smilesList, "\n");
+ * const report = JSON.parse(json);
+ * console.log(report.records); // Array of ScreeningRecord
+ * console.log(report.maxmin_picks); // Diversity-selected indices
+ * console.log(report.butina_clusters); // Clustering result
+ * ```
+ * @param {string} smiles_batch
+ * @param {string} delimiter
+ * @returns {string}
+ */
+export function screen_smiles_json(smiles_batch, delimiter) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_batch, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(delimiter, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.screen_smiles_json(ptr0, len0, ptr1, len1);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} smiles_json
+ * @param {string} names_json
+ * @param {string} props_json
+ * @returns {string}
+ */
+export function sdf_from_records_json(smiles_json, names_json, props_json) {
+    let deferred5_0;
+    let deferred5_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(names_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passStringToWasm0(props_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len2 = WASM_VECTOR_LEN;
+        const ret = wasm.sdf_from_records_json(ptr0, len0, ptr1, len1, ptr2, len2);
+        var ptr4 = ret[0];
+        var len4 = ret[1];
+        if (ret[3]) {
+            ptr4 = 0; len4 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred5_0 = ptr4;
+        deferred5_1 = len4;
+        return getStringFromWasm0(ptr4, len4);
+    } finally {
+        wasm.__wbindgen_free(deferred5_0, deferred5_1, 1);
+    }
+}
+
+/**
+ * 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`.
+ * @param {string} sdf
+ * @returns {string}
+ */
+export function sdf_to_records_json(sdf) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(sdf, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.sdf_to_records_json(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Parse an SDF string and return a JSON array of canonical SMILES strings.
+ *
+ * Invalid records are represented as `null` in the array.
+ * @param {string} sdf
+ * @returns {string}
+ */
+export function sdf_to_smiles_json(sdf) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(sdf, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.sdf_to_smiles_json(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
+ * Rotates the D-side subtree around the B—C bond.
+ * Returns a JS error if parsing fails or atom indices are invalid.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`, `b`, `c`, `d`: atom indices
+ * - `angle_deg`: target dihedral angle in degrees
+ *
+ * # Example
+ * ```javascript
+ * const pdbBlock = set_dihedral_json("CCCC", 0, 1, 2, 3, 120.0);
+ * ```
+ * @param {string} smiles
+ * @param {number} a
+ * @param {number} b
+ * @param {number} c
+ * @param {number} d
+ * @param {number} angle_deg
+ * @returns {string}
+ */
+export function set_dihedral_json(smiles, a, b, c, d, angle_deg) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.set_dihedral_json(ptr0, len0, a, b, c, d, angle_deg);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function shape_descriptors_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.shape_descriptors_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * SlogP_VSA descriptors (12 bins) as a JSON array.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function slogp_vsa_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.slogp_vsa_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Find all substructure matches of a SMARTS pattern in `mol`.
+ *
+ * Returns JSON array of arrays of atom indices (sorted, 0-based).
+ * Example: `[[0,1,2],[3,4,5]]` — two matches.
+ * Returns `"[]"` if no match. Returns a JS error on invalid SMARTS.
+ * @param {string} smarts
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function smarts_match_atoms(smarts, mol) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        _assertClass(mol, MolHandle);
+        const ret = wasm.smarts_match_atoms(ptr0, len0, mol.__wbg_ptr);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Like `smarts_match_atoms` but with explicit chirality matching control.
+ *
+ * When `use_chirality=true`, SMARTS chirality primitives `[@]` and `[@@]` are
+ * matched against the target molecule's stereochemistry. When `false`, chirality
+ * is ignored (RDKit default).
+ * @param {string} smarts
+ * @param {MolHandle} mol
+ * @param {boolean} use_chirality
+ * @returns {string}
+ */
+export function smarts_match_atoms_with_chirality(smarts, mol, use_chirality) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        _assertClass(mol, MolHandle);
+        const ret = wasm.smarts_match_atoms_with_chirality(ptr0, len0, mol.__wbg_ptr, use_chirality);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {string} smiles_json
+ * @returns {string}
+ */
+export function smiles_array_to_sdf(smiles_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.smiles_array_to_sdf(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Convert a SMILES to a minimal Tripos MOL2 string (no 3D coordinates).
+ *
+ * Returns `"error:<msg>"` on parse failure.
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function smiles_to_mol2(smiles) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.smiles_to_mol2(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Render a highlighted SVG from a SMILES string in one call.
+ *
+ * `atoms` — 0-based atom indices to highlight (Uint32Array in JS).
+ * `bonds` — 0-based bond indices to highlight (Uint32Array in JS).
+ * `color` — CSS color for highlights (e.g. `"#ef4444"`); empty string uses default yellow.
+ *
+ * Returns a JS error on SMILES parse failure.
+ * @param {string} smiles
+ * @param {Uint32Array} atoms
+ * @param {Uint32Array} bonds
+ * @param {string} color
+ * @returns {string}
+ */
+export function smiles_to_svg_highlighted(smiles, atoms, bonds, color) {
+    let deferred6_0;
+    let deferred6_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(atoms, wasm.__wbindgen_malloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(bonds, wasm.__wbindgen_malloc);
+        const len2 = WASM_VECTOR_LEN;
+        const ptr3 = passStringToWasm0(color, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len3 = WASM_VECTOR_LEN;
+        const ret = wasm.smiles_to_svg_highlighted(ptr0, len0, ptr1, len1, ptr2, len2, ptr3, len3);
+        var ptr5 = ret[0];
+        var len5 = ret[1];
+        if (ret[3]) {
+            ptr5 = 0; len5 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred6_0 = ptr5;
+        deferred6_1 = len5;
+        return getStringFromWasm0(ptr5, len5);
+    } finally {
+        wasm.__wbindgen_free(deferred6_0, deferred6_1, 1);
+    }
+}
+
+/**
+ * SMR_VSA descriptors (10 bins) as a JSON array.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function smr_vsa_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.smr_vsa_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * 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]]`
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function sssr_rings_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.sssr_rings_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Standardize a SMILES string and return the canonical SMILES of the result.
+ *
+ * Applies: largest fragment extraction → charge neutralization.
+ * Returns `"error:<msg>"` on parse failure.
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function standardize_smiles(smiles) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.standardize_smiles(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * Standardize a SMILES string and return result SMILES plus an audit report as JSON.
+ *
+ * Boolean flags map directly to `StandardizeOptions`.
+ * Returns `"error:<msg>"` on parse or serialization failure.
+ * @param {string} smiles
+ * @param {boolean} largest_fragment_only
+ * @param {boolean} neutralize_charges
+ * @param {boolean} remove_explicit_h
+ * @param {boolean} canonical_tautomer
+ * @returns {string}
+ */
+export function standardize_smiles_report_json(smiles, largest_fragment_only, neutralize_charges, remove_explicit_h, canonical_tautomer) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.standardize_smiles_report_json(ptr0, len0, largest_fragment_only, neutralize_charges, remove_explicit_h, canonical_tautomer);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+export function start() {
+    wasm.start();
+}
+
+/**
+ * Tanimoto similarity between two molecules using AtomPair fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_atom_pair(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_atom_pair(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto similarity between two molecules using ECFP4 fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_ecfp4(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_ecfp4(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto similarity between `a` and `b` using ECFP6 fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_ecfp6(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_ecfp6(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto similarity between two molecules using FCFP4 fingerprints (pharmacophore-based).
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_fcfp4(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_fcfp4(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto similarity between `a` and `b` using FCFP6 (radius-3 pharmacophore) fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_fcfp6(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_fcfp6(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto similarity between `a` and `b` using MACCS 166-bit fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_maccs(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_maccs(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto-like similarity between two SMILES via MHFP (MinHash Jaccard approximation).
+ * @param {string} smi1
+ * @param {string} smi2
+ * @returns {number}
+ */
+export function tanimoto_mhfp_smiles(smi1, smi2) {
+    const ptr0 = passStringToWasm0(smi1, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ptr1 = passStringToWasm0(smi2, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len1 = WASM_VECTOR_LEN;
+    const ret = wasm.tanimoto_mhfp_smiles(ptr0, len0, ptr1, len1);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0];
+}
+
+/**
+ * Compute ECFP4 Tanimoto similarity from one query SMILES to all db SMILES (dense output).
+ *
+ * `db_smiles_json`: JSON array of SMILES strings (max 1024 via WASM_MAX_BATCH_ITEMS).
+ *
+ * Returns a flat JSON array of f32 scores, one per db entry, e.g. `[0.12,0.0,0.85]`.
+ * No zero-filtering: the length always equals the number of db entries.
+ * Returns `"error:<msg>"` on parse failure or oversized input.
+ * @param {string} query_smi
+ * @param {string} db_smiles_json
+ * @returns {string}
+ */
+export function tanimoto_row_json(query_smi, db_smiles_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(query_smi, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(db_smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.tanimoto_row_json(ptr0, len0, ptr1, len1);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Tanimoto similarity between two molecules given only SMILES strings (ECFP4).
+ *
+ * Returns a JS error on parse failure.
+ * @param {string} smiles1
+ * @param {string} smiles2
+ * @returns {number}
+ */
+export function tanimoto_smiles(smiles1, smiles2) {
+    const ptr0 = passStringToWasm0(smiles1, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ptr1 = passStringToWasm0(smiles2, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len1 = WASM_VECTOR_LEN;
+    const ret = wasm.tanimoto_smiles(ptr0, len0, ptr1, len1);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0];
+}
+
+/**
+ * Tanimoto similarity between two molecules using topological path fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_topo_path(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_topo_path(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Tanimoto similarity between two molecules using Topological Torsion fingerprints.
+ * @param {MolHandle} a
+ * @param {MolHandle} b
+ * @returns {number}
+ */
+export function tanimoto_torsion(a, b) {
+    _assertClass(a, MolHandle);
+    _assertClass(b, MolHandle);
+    const ret = wasm.tanimoto_torsion(a.__wbg_ptr, b.__wbg_ptr);
+    return ret;
+}
+
+/**
+ * Serialise a `MolHandle` to a CML string with 2D coordinates.
+ *
+ * Coordinates are generated using the same 2D layout engine as `to_mol_block`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function to_cml(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.to_cml(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Serialize a molecule to a MOL V2000 block with 2D coordinates.
+ *
+ * Atom positions are computed via the same layout engine used for SVG depiction
+ * and converted to Ångström units (`1.5 Å` per bond).
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function to_mol_block(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.to_mol_block(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Serialise a `MolHandle` to MOL V3000 format with 2D coordinates.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function to_mol_v3000_block(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.to_mol_v3000_block(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Serialize a molecule to XYZ format.
+ *
+ * 3D coordinates are generated via distance-geometry placement.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function to_xyz(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.to_xyz(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Torsion fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function torsion_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.torsion_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Scan a torsion dihedral i-j-k-l from 0° to 360° in `steps` increments.
+ * Returns JSON array: [{"angle":0.0,"energy":E},...] or {"error":"..."}.
+ * @param {MolHandle} mol
+ * @param {number} i
+ * @param {number} j
+ * @param {number} k
+ * @param {number} l
+ * @param {number} steps
+ * @returns {string}
+ */
+export function torsion_scan_json(mol, i, j, k, l, steps) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.torsion_scan_json(mol.__wbg_ptr, i, j, k, l, steps);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Virtual screen a query SMILES against a database of SMILES using ECFP4 Tanimoto.
+ *
+ * `db_smiles_json`: JSON array of SMILES strings (max 1024 via WASM_MAX_BATCH_ITEMS).
+ * `k`: number of top hits to return; clamped to db size if larger.
+ *
+ * Returns JSON: `{"results":[{"rank":1,"score":0.85,"smiles":"CCO","idx":42},...]}`.
+ * Returns `"error:<msg>"` on any parse failure or oversized input.
+ * @param {string} query_smi
+ * @param {string} db_smiles_json
+ * @param {number} k
+ * @returns {string}
+ */
+export function virtual_screen_ecfp4_json(query_smi, db_smiles_json, k) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(query_smi, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(db_smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.virtual_screen_ecfp4_json(ptr0, len0, ptr1, len1, k);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Compute WHIM descriptors (Weighted Holistic Invariant Molecular) from 3D coordinates.
+ * Returns JSON array of 10 values: [L1, L2, L3, P1, P2, P3, ALPHA, BETA, GAMMA, DELTA]
+ * where L* = inertia tensor eigenvalues, P* = principal moments, ALPHA = sum of moments,
+ * BETA = average pairwise interaction, GAMMA = geometric mean, DELTA = anisotropy.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function whim_descriptors_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.whim_descriptors_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Compute combined WHIM + GETAWAY descriptors (19 values total) as JSON array.
+ * Useful for ML pipelines requiring both shape and topologic features.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function whim_getaway_combined_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.whim_getaway_combined_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * 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.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function write_smiles(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.write_smiles(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+function __wbg_get_imports() {
+    const import0 = {
+        __proto__: null,
+        __wbg___wbindgen_string_get_72bdf95d3ae505b1: function(arg0, arg1) {
+            const obj = arg1;
+            const ret = typeof(obj) === 'string' ? obj : undefined;
+            var ptr1 = isLikeNone(ret) ? 0 : passStringToWasm0(ret, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            var len1 = WASM_VECTOR_LEN;
+            getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
+            getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
+        },
+        __wbg___wbindgen_throw_1506f2235d1bdba0: function(arg0, arg1) {
+            throw new Error(getStringFromWasm0(arg0, arg1));
+        },
+        __wbg_error_a6fa202b58aa1cd3: function(arg0, arg1) {
+            let deferred0_0;
+            let deferred0_1;
+            try {
+                deferred0_0 = arg0;
+                deferred0_1 = arg1;
+                console.error(getStringFromWasm0(arg0, arg1));
+            } finally {
+                wasm.__wbindgen_free(deferred0_0, deferred0_1, 1);
+            }
+        },
+        __wbg_getRandomValues_3f44b700395062e5: function() { return handleError(function (arg0, arg1) {
+            globalThis.crypto.getRandomValues(getArrayU8FromWasm0(arg0, arg1));
+        }, arguments); },
+        __wbg_new_227d7c05414eb861: function() {
+            const ret = new Error();
+            return ret;
+        },
+        __wbg_stack_3b0d974bbf31e44f: function(arg0, arg1) {
+            const ret = arg1.stack;
+            const ptr1 = passStringToWasm0(ret, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len1 = WASM_VECTOR_LEN;
+            getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
+            getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
+        },
+        __wbindgen_cast_0000000000000001: function(arg0) {
+            // Cast intrinsic for `F64 -> Externref`.
+            const ret = arg0;
+            return ret;
+        },
+        __wbindgen_cast_0000000000000002: function(arg0, arg1) {
+            // Cast intrinsic for `Ref(String) -> Externref`.
+            const ret = getStringFromWasm0(arg0, arg1);
+            return ret;
+        },
+        __wbindgen_init_externref_table: function() {
+            const table = wasm.__wbindgen_externrefs;
+            const offset = table.grow(4);
+            table.set(0, undefined);
+            table.set(offset + 0, undefined);
+            table.set(offset + 1, null);
+            table.set(offset + 2, true);
+            table.set(offset + 3, false);
+        },
+    };
+    return {
+        __proto__: null,
+        "./chematic_wasm_bg.js": import0,
+    };
+}
+
+const ConformerHandleFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_conformerhandle_free(ptr, 1));
+const DepictOptionsFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_depictoptions_free(ptr, 1));
+const MhfpLshHandleFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_mhfplshhandle_free(ptr, 1));
+const MolHandleFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_molhandle_free(ptr, 1));
+
+function addToExternrefTable0(obj) {
+    const idx = wasm.__externref_table_alloc();
+    wasm.__wbindgen_externrefs.set(idx, obj);
+    return idx;
+}
+
+function _assertClass(instance, klass) {
+    if (!(instance instanceof klass)) {
+        throw new Error(`expected instance of ${klass.name}`);
+    }
+}
+
+function getArrayU8FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
+}
+
+let cachedDataViewMemory0 = null;
+function getDataViewMemory0() {
+    if (cachedDataViewMemory0 === null || cachedDataViewMemory0.buffer.detached === true || (cachedDataViewMemory0.buffer.detached === undefined && cachedDataViewMemory0.buffer !== wasm.memory.buffer)) {
+        cachedDataViewMemory0 = new DataView(wasm.memory.buffer);
+    }
+    return cachedDataViewMemory0;
+}
+
+function getStringFromWasm0(ptr, len) {
+    return decodeText(ptr >>> 0, len);
+}
+
+let cachedUint32ArrayMemory0 = null;
+function getUint32ArrayMemory0() {
+    if (cachedUint32ArrayMemory0 === null || cachedUint32ArrayMemory0.byteLength === 0) {
+        cachedUint32ArrayMemory0 = new Uint32Array(wasm.memory.buffer);
+    }
+    return cachedUint32ArrayMemory0;
+}
+
+let cachedUint8ArrayMemory0 = null;
+function getUint8ArrayMemory0() {
+    if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
+        cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
+    }
+    return cachedUint8ArrayMemory0;
+}
+
+function handleError(f, args) {
+    try {
+        return f.apply(this, args);
+    } catch (e) {
+        const idx = addToExternrefTable0(e);
+        wasm.__wbindgen_exn_store(idx);
+    }
+}
+
+function isLikeNone(x) {
+    return x === undefined || x === null;
+}
+
+function passArray32ToWasm0(arg, malloc) {
+    const ptr = malloc(arg.length * 4, 4) >>> 0;
+    getUint32ArrayMemory0().set(arg, ptr / 4);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+
+function passStringToWasm0(arg, malloc, realloc) {
+    if (realloc === undefined) {
+        const buf = cachedTextEncoder.encode(arg);
+        const ptr = malloc(buf.length, 1) >>> 0;
+        getUint8ArrayMemory0().subarray(ptr, ptr + buf.length).set(buf);
+        WASM_VECTOR_LEN = buf.length;
+        return ptr;
+    }
+
+    let len = arg.length;
+    let ptr = malloc(len, 1) >>> 0;
+
+    const mem = getUint8ArrayMemory0();
+
+    let offset = 0;
+
+    for (; offset < len; offset++) {
+        const code = arg.charCodeAt(offset);
+        if (code > 0x7F) break;
+        mem[ptr + offset] = code;
+    }
+    if (offset !== len) {
+        if (offset !== 0) {
+            arg = arg.slice(offset);
+        }
+        ptr = realloc(ptr, len, len = offset + arg.length * 3, 1) >>> 0;
+        const view = getUint8ArrayMemory0().subarray(ptr + offset, ptr + len);
+        const ret = cachedTextEncoder.encodeInto(arg, view);
+
+        offset += ret.written;
+        ptr = realloc(ptr, len, offset, 1) >>> 0;
+    }
+
+    WASM_VECTOR_LEN = offset;
+    return ptr;
+}
+
+function takeFromExternrefTable0(idx) {
+    const value = wasm.__wbindgen_externrefs.get(idx);
+    wasm.__externref_table_dealloc(idx);
+    return value;
+}
+
+let cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+cachedTextDecoder.decode();
+const MAX_SAFARI_DECODE_BYTES = 2146435072;
+let numBytesDecoded = 0;
+function decodeText(ptr, len) {
+    numBytesDecoded += len;
+    if (numBytesDecoded >= MAX_SAFARI_DECODE_BYTES) {
+        cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+        cachedTextDecoder.decode();
+        numBytesDecoded = len;
+    }
+    return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
+}
+
+const cachedTextEncoder = new TextEncoder();
+
+if (!('encodeInto' in cachedTextEncoder)) {
+    cachedTextEncoder.encodeInto = function (arg, view) {
+        const buf = cachedTextEncoder.encode(arg);
+        view.set(buf);
+        return {
+            read: arg.length,
+            written: buf.length
+        };
+    };
+}
+
+let WASM_VECTOR_LEN = 0;
+
+let wasmModule, wasmInstance, wasm;
+function __wbg_finalize_init(instance, module) {
+    wasmInstance = instance;
+    wasm = instance.exports;
+    wasmModule = module;
+    cachedDataViewMemory0 = null;
+    cachedUint32ArrayMemory0 = null;
+    cachedUint8ArrayMemory0 = null;
+    wasm.__wbindgen_start();
+    return wasm;
+}
+
+async function __wbg_load(module, imports) {
+    if (typeof Response === 'function' && module instanceof Response) {
+        if (typeof WebAssembly.instantiateStreaming === 'function') {
+            try {
+                return await WebAssembly.instantiateStreaming(module, imports);
+            } catch (e) {
+                const validResponse = module.ok && expectedResponseType(module.type);
+
+                if (validResponse && module.headers.get('Content-Type') !== 'application/wasm') {
+                    console.warn("`WebAssembly.instantiateStreaming` failed because your server does not serve Wasm with `application/wasm` MIME type. Falling back to `WebAssembly.instantiate` which is slower. Original error:\n", e);
+
+                } else { throw e; }
+            }
+        }
+
+        const bytes = await module.arrayBuffer();
+        return await WebAssembly.instantiate(bytes, imports);
+    } else {
+        const instance = await WebAssembly.instantiate(module, imports);
+
+        if (instance instanceof WebAssembly.Instance) {
+            return { instance, module };
+        } else {
+            return instance;
+        }
+    }
+
+    function expectedResponseType(type) {
+        switch (type) {
+            case 'basic': case 'cors': case 'default': return true;
+        }
+        return false;
+    }
+}
+
+function initSync(module) {
+    if (wasm !== undefined) return wasm;
+
+
+    if (module !== undefined) {
+        if (Object.getPrototypeOf(module) === Object.prototype) {
+            ({module} = module)
+        } else {
+            console.warn('using deprecated parameters for `initSync()`; pass a single object instead')
+        }
+    }
+
+    const imports = __wbg_get_imports();
+    if (!(module instanceof WebAssembly.Module)) {
+        module = new WebAssembly.Module(module);
+    }
+    const instance = new WebAssembly.Instance(module, imports);
+    return __wbg_finalize_init(instance, module);
+}
+
+async function __wbg_init(module_or_path) {
+    if (wasm !== undefined) return wasm;
+
+
+    if (module_or_path !== undefined) {
+        if (Object.getPrototypeOf(module_or_path) === Object.prototype) {
+            ({module_or_path} = module_or_path)
+        } else {
+            console.warn('using deprecated parameters for the initialization function; pass a single object instead')
+        }
+    }
+
+    if (module_or_path === undefined) {
+        module_or_path = new URL('chematic_wasm_bg.wasm', import.meta.url);
+    }
+    const imports = __wbg_get_imports();
+
+    if (typeof module_or_path === 'string' || (typeof Request === 'function' && module_or_path instanceof Request) || (typeof URL === 'function' && module_or_path instanceof URL)) {
+        module_or_path = fetch(module_or_path);
+    }
+
+    const { instance, module } = await __wbg_load(await module_or_path, imports);
+
+    return __wbg_finalize_init(instance, module);
+}
+
+export { initSync, __wbg_init as default };