@kent-tokyo/chematic 0.2.11 → 0.4.28

package/README.md

@@ -116,6 +116,12 @@ console.log(ifg); // [{"atoms":[1,2,3],"types":"OC=O"}, ...]
 - True MHFP (structural fragment hashing)
 - True ERG (Ertl 2017 functional group detection)
 
+## Bundle Size
+
+~500 KB gzip / ~1.3 MB raw (reduced from ~819 KB gzip in v0.4.17, -38.5%).
+
+PNG rasterization (`tiny_skia`) is excluded from the WASM build — use SVG output instead. All SVG depiction APIs remain fully available.
+
 ## Building from source
 
 ```sh

package/chematic_wasm.d.ts

@@ -106,17 +106,6 @@ export class DepictOptions {
     set_width(w: number): void;
 }
 
-/**
- * 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 {
     free(): void;
     [Symbol.dispose](): void;
@@ -169,6 +158,15 @@ export class MolHandle {
      * Number of heavy atoms (explicit atoms in the graph; does not count implicit H).
      */
     atom_count(): number;
+    /**
+     * Returns true when TPSA < 90 Ų, MW < 400, HBD ≤ 3.
+     */
+    bbb_passes(): boolean;
+    /**
+     * Clark (2000) blood-brain barrier logBB score.
+     * logBB > −1.0 = likely CNS penetrant.
+     */
+    bbb_score(): number;
     /**
      * Bertz complexity index (BertzCT).
      */
@@ -177,6 +175,11 @@ export class MolHandle {
      * Number of bonds.
      */
     bond_count(): number;
+    /**
+     * Palm (1997) Caco-2 intestinal permeability (logPCaco2).
+     * > −5.5 = high permeability.
+     */
+    caco2_permeability(): number;
     /**
      * Canonical SMILES string.
      */
@@ -222,8 +225,12 @@ export class MolHandle {
      */
     chi4v(): number;
     /**
-     * 2D PNG depiction (rasterized from SVG).
-     * Returns PNG data as base64-encoded string for embedding in HTML/JS.
+     * CYP3A4 metabolic inhibition risk score (0.0–1.0).
+     */
+    cyp3a4_inhibition_risk(): number;
+    /**
+     * 2D PNG depiction — not available in the WASM build (PNG stack disabled to reduce bundle size).
+     * Use `depict_svg()` in browser contexts; rasterize client-side if needed.
      */
     depict_png(): Uint8Array;
     /**
@@ -272,6 +279,10 @@ export class MolHandle {
      * Number of non-hydrogen heavy atoms.
      */
     heavy_atom_count(): number;
+    /**
+     * hERG cardiac toxicity risk score (0.0–1.0).
+     */
+    herg_risk_score(): number;
     /**
      * Isotope distribution as JSON.
      *
@@ -390,6 +401,14 @@ export class MolHandle {
      * Returns `true` if the molecule has no PAINS structural alerts.
      */
     pains_passes(): boolean;
+    /**
+     * Most acidic pKa in the molecule, or NaN if no acidic site.
+     */
+    pka_acid_value(): number;
+    /**
+     * Most basic pKa in the molecule, or NaN if no basic site.
+     */
+    pka_base_value(): number;
     /**
      * Quantitative Estimate of Drug-likeness (QED); range [0, 1].
      */
@@ -448,6 +467,18 @@ export class MolHandle {
  */
 export function add_hydrogens(mol: MolHandle): MolHandle;
 
+/**
+ * Compute a full ADMET property profile for a molecule.
+ *
+ * Returns a JSON object with fields:
+ * `bbb_score`, `bbb_passes`, `caco2`, `herg_risk`, `cyp3a4_risk`,
+ * `pka_acid` (null if absent), `pka_base` (null if absent),
+ * `esol`, `logd74`, `mw`, `logp`, `tpsa`, `hbd`, `hba`, `rotatable_bonds`
+ *
+ * Returns `{"error":"..."}` on parse failure.
+ */
+export function admet_profile_json(smiles: string): string;
+
 /**
  * AtomPair fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  */
@@ -472,6 +503,37 @@ export function autocorr_3d_json(mol: MolHandle): string;
  */
 export function balance_check_json(reaction_smiles: string): string;
 
+/**
+ * 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}]
+ * ```
+ * Generate a self-contained HTML report for a newline-separated list of SMILES.
+ *
+ * Empty lines and invalid SMILES are silently skipped.
+ * Returns the same card-grid HTML as Python's `chematic.report()`.
+ *
+ * ```js
+ * const html = mod.batch_report_html("CCO\nc1ccccc1\nCC(=O)O");
+ * const blob = new Blob([html], {type:'text/html'});
+ * const url  = URL.createObjectURL(blob);
+ * ```
+ */
+export function batch_report_html(smiles_lines: string): string;
+
+/**
+ * Predict GI absorption and BBB penetration using the BOILED-Egg method
+ * (Daina & Zoete 2016).
+ *
+ * Returns JSON: `{"gi_absorbed":bool,"bbb_penetrant":bool,"logp":f64,"tpsa":f64}`
+ */
+export function boiled_egg_json(smiles: string): string;
+
 /**
  * Number of BRICS fragments produced by fragmenting the molecule.
  *
@@ -566,21 +628,10 @@ export function compare_molecules_batch_json(smiles_batch: string, delimiter: st
 export function compare_molecules_json(smiles1: string, smiles2: string): string;
 
 /**
- * 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" }
- * ```
+ * Generate multiple conformers with RMSD-based pruning.
+ * Returns JSON: `{"conformers": [[[x,y,z],...], ...], "count": int}`.
  */
-export function coulomb_energy_json(mol: MolHandle): string;
+export function conformer_ensemble_json(mol: MolHandle, n: number, rmsd_threshold: number): string;
 
 /**
  * Return the CPK color (CSS hex string) for the given element symbol.
@@ -660,21 +711,6 @@ export function depict_svg_grid_highlighted(smiles_block: string, cols: number,
  */
 export function detect_functional_groups(mol: MolHandle): string;
 
-/**
- * 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.
- */
-export function determine_bonds_from_xyz_json(xyz_str: string): string;
-
 /**
  * Dice similarity between `a` and `b` using ECFP4 fingerprints.
  */
@@ -805,6 +841,19 @@ export function find_reaction_center_json(reaction_smiles: string): string;
  */
 export function gasteiger_charges_json(mol: MolHandle): string;
 
+/**
+ * Generate 3D coordinates as raw JSON array [[x,y,z], ...].
+ *
+ * Unlike `generate_3d_pdb`, this returns coordinates that can be passed
+ * to descriptor functions like `whim_descriptors_json` or `shape_descriptors_json`.
+ */
+export function generate_3d_coords_json(mol: MolHandle): string;
+
+/**
+ * Generate 3D coordinates using ETKDG as raw JSON array [[x,y,z], ...].
+ */
+export function generate_3d_etkdg_coords_json(mol: MolHandle): string;
+
 /**
  * Generate 3D coordinates using ETKDG and minimize with DREIDING force field.
  */
@@ -941,13 +990,33 @@ export function get_descriptors_json(mol: MolHandle): string;
 export function get_dihedral_json(smiles: string, a: number, b: number, c: number, d: number): any;
 
 /**
- * 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.
+ * Compute GETAWAY descriptors (GEometry, Topology and Atom-Weights AssemblY) from 3D coords.
+ *
+ * Returns a JSON array of **19** values:
+ * - `[0..7]`  H[1..8]  — leverage autocorrelation at topological lags 1–8
+ * - `[8..15]` R[1..8]  — H[k] normalised by pair count W_k
+ * - `[16]` Hmax, `[17]` Hmean, `[18]` Htot — per-atom leverage statistics
+ *
+ * Note: requires 3D coordinates (non-planar); for flat/2D structures the hat matrix
+ * is degenerate and descriptors reflect squared centroid distances, not true leverage.
  */
 export function getaway_descriptors_json(mol: MolHandle): string;
 
+/**
+ * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
+ *
+ * Compute an HDF fingerprint and return it as a JSON array of float32 values.
+ *
+ * Returns a unit-norm vector of length `dim` as a JSON number array.
+ * Use cosine dot product for similarity: `a · b = sum(a[i]*b[i])`.
+ *
+ * ```js
+ * const fp = JSON.parse(hdf_json(mol));        // float[] of length 1024
+ * const sim = fp.reduce((s, v, i) => s + v * fp2[i], 0);  // cosine similarity
+ * ```
+ */
+export function hdf_json(mol: MolHandle, dim: number, radius: number, seed: bigint): string;
+
 /**
  * Identify functional groups. Returns a JSON array of objects:
  * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
@@ -1036,6 +1105,16 @@ export function maxmin_picks_ecfp4_json(smiles_json: string, n: number): string;
  */
 export function mcs_smiles_json(smiles_json: string): string;
 
+/**
+ * MCS with ring-awareness constraints.
+ *
+ * `smiles_json` — JSON array of at least 2 SMILES strings.
+ * `ring_matches_ring_only` — ring atoms may only match ring atoms.
+ * `complete_rings_only` — partial ring inclusion is removed from the result.
+ * Returns the MCS SMILES, or `"null"` when no common substructure was found.
+ */
+export function mcs_smiles_json_with_ring_config(smiles_json: string, ring_matches_ring_only: boolean, complete_rings_only: boolean): string;
+
 /**
  * MinHash fingerprint (128 hashes) as JSON.
  *
@@ -1071,6 +1150,17 @@ export function minimize_mmff94_json(mol: MolHandle, max_iter: number): string;
  */
 export function minimize_mmff94_lbfgs_json(mol: MolHandle, max_iter: number): string;
 
+/**
+ * Minimise a molecule's geometry using the Universal Force Field (UFF).
+ *
+ * `coords_json` — JSON array of `[x,y,z]` arrays (Å), one per atom.
+ * `max_iter` — maximum iterations (0 = default 500).
+ *
+ * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool}`
+ * or `{"error":"<msg>"}` on failure.
+ */
+export function minimize_uff_json(smiles: string, coords_json: string, max_iter: number): string;
+
 /**
  * MMFF94 partial charges (BCI table, ±0.1e accuracy) as a JSON array of f64.
  *
@@ -1148,8 +1238,6 @@ export function mol_block_coords_json(mol_block: string): string;
 export function mol_block_from_smiles(smiles: string): string;
 
 /**
- * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
- *
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
  */
@@ -1162,6 +1250,14 @@ export function mol_from_cdxml(cdxml: string): MolHandle;
  */
 export function mol_from_cml(cml: string): MolHandle;
 
+/**
+ * Parse a MolJSON string into a `MolHandle`.
+ *
+ * MolJSON is a JSON-based molecular representation designed for LLM
+ * (large language model) compatibility.  Returns a JS error on invalid input.
+ */
+export function mol_from_moljson(json: string): MolHandle;
+
 /**
  * Parse a PDB file and return a `MolHandle` (topology only; coordinates are discarded).
  *
@@ -1357,6 +1453,15 @@ export function pharmacophore_fp_2d_summary(mol: MolHandle): string;
  */
 export function pharmacophore_fp_3d_summary(mol: MolHandle): string;
 
+/**
+ * Predict pKa for all ionizable sites in a molecule.
+ *
+ * Returns a JSON array: `[{"atom_idx":8,"pka":4.0,"type":"acid","group":"carboxylic_acid"},...]`
+ *
+ * Returns `[]` if no ionizable sites are found, or `{"error":"..."}` on parse failure.
+ */
+export function predict_pka_json(smiles: string): string;
+
 /**
  * Generate `count` random SMILES from a SMILES string using the given seed.
  * Atoms are permuted based on xorshift64 RNG. Each variant should parse back
@@ -1409,15 +1514,6 @@ export function rgroup_decompose_json(smiles_json: string, core_smarts: string):
  */
 export function ring_families_json(mol: MolHandle): string;
 
-/**
- * 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.
- */
-export function run_md_json(mol: MolHandle, steps: number, temp_k: number): string;
-
 /**
  * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
  *
@@ -1551,6 +1647,17 @@ export function smiles_array_to_sdf(smiles_json: string): string;
  */
 export function smiles_to_mol2(smiles: string): string;
 
+/**
+ * Write a molecule to AutoDock PDBQT format.
+ *
+ * `coords_json` — JSON array of `[x,y,z]` arrays (Å). Pass `"[]"` for zero coords.
+ * `charges_json` — JSON array of partial charges. Pass `"[]"` to write zeros.
+ * `name` — ligand name for the REMARK header.
+ *
+ * Returns the PDBQT string, or `"error:<msg>"` on failure.
+ */
+export function smiles_to_pdbqt(smiles: string, coords_json: string, charges_json: string, name: string): string;
+
 /**
  * Render a highlighted SVG from a SMILES string in one call.
  *
@@ -1676,6 +1783,14 @@ export function to_mol_block(mol: MolHandle): string;
  */
 export function to_mol_v3000_block(mol: MolHandle): string;
 
+/**
+ * Serialise a `MolHandle` to a MolJSON string (pretty-printed).
+ *
+ * Atom IDs are assigned as `"a1"`, `"a2"`, … in molecule atom order.
+ * The `hydrogens` field reflects computed implicit H count.
+ */
+export function to_moljson(mol: MolHandle): string;
+
 /**
  * Serialize a molecule to XYZ format.
  *
@@ -1688,12 +1803,6 @@ export function to_xyz(mol: MolHandle): string;
  */
 export function torsion_bitvec(mol: MolHandle): Uint8Array;
 
-/**
- * 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":"..."}.
- */
-export function torsion_scan_json(mol: MolHandle, i: number, j: number, k: number, l: number, steps: number): string;
-
 /**
  * Virtual screen a query SMILES against a database of SMILES using ECFP4 Tanimoto.
  *
@@ -1707,14 +1816,15 @@ export function virtual_screen_ecfp4_json(query_smi: string, db_smiles_json: str
 
 /**
  * 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.
+ * Returns JSON array of 22 values: 11 unit-weight descriptors followed by 11 mass-weight
+ * descriptors. Each 11-element block is [λ₁, λ₂, λ₃, ν₁, ν₂, ν₃, T, A, V, K, D].
  */
 export function whim_descriptors_json(mol: MolHandle): string;
 
 /**
- * Compute combined WHIM + GETAWAY descriptors (19 values total) as JSON array.
+ * Compute combined WHIM + GETAWAY descriptors (**41** values total) as JSON array.
+ *
+ * Returns WHIM[0..21] (22 values) followed by GETAWAY[0..18] (19 values) = 41 total.
  * Useful for ML pipelines requiring both shape and topologic features.
  */
 export function whim_getaway_combined_json(mol: MolHandle): string;
@@ -1728,6 +1838,18 @@ export function whim_getaway_combined_json(mol: MolHandle): string;
  */
 export function write_smiles(mol: MolHandle): string;
 
+/**
+ * XLogP3 partition coefficient (alternative to Crippen LogP).
+ * Returns JSON: `{"xlogp3": float}`.
+ */
+export function xlogp3_json(mol: MolHandle): string;
+
+/**
+ * Per-atom XLogP3 contributions.
+ * Returns JSON array of floats (one per heavy atom).
+ */
+export function xlogp3_per_atom_json(mol: MolHandle): string;
+
 export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembly.Module;
 
 export interface InitOutput {
@@ -1737,10 +1859,13 @@ export interface InitOutput {
     readonly __wbg_mhfplshhandle_free: (a: number, b: number) => void;
     readonly __wbg_molhandle_free: (a: number, b: number) => void;
     readonly add_hydrogens: (a: number) => number;
+    readonly admet_profile_json: (a: number, b: number) => [number, number];
     readonly atom_pair_bitvec: (a: number) => [number, number];
     readonly autocorr_2d_json: (a: number) => [number, number];
     readonly autocorr_3d_json: (a: number) => [number, number];
     readonly balance_check_json: (a: number, b: number) => [number, number];
+    readonly batch_report_html: (a: number, b: number) => [number, number];
+    readonly boiled_egg_json: (a: number, b: number) => [number, number];
     readonly brics_fragment_count: (a: number) => number;
     readonly brics_fragments_json: (a: number) => [number, number];
     readonly butina_cluster_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
@@ -1748,6 +1873,9 @@ export interface InitOutput {
     readonly canonical_tautomer_with_blocked_atoms_json: (a: number, b: number, c: number) => [number, number];
     readonly cdxml_to_smiles_json: (a: number, b: number) => [number, number, number, number];
     readonly cip_assignments_json: (a: number) => [number, number];
+    readonly compare_molecules_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly compare_molecules_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly conformer_ensemble_json: (a: number, b: number, c: number) => [number, number];
     readonly conformerhandle_add_generated_conformer: (a: number) => number;
     readonly conformerhandle_add_minimized_conformer: (a: number) => number;
     readonly conformerhandle_cluster_conformers_json: (a: number, b: number) => [number, number];
@@ -1758,7 +1886,6 @@ export interface InitOutput {
     readonly conformerhandle_mol: (a: number) => number;
     readonly conformerhandle_new: (a: number, b: number) => [number, number, number];
     readonly conformerhandle_remove_conformer: (a: number, b: number) => number;
-    readonly coulomb_energy_json: (a: number) => [number, number];
     readonly cpk_color: (a: number, b: number) => [number, number];
     readonly depict_data_json: (a: number) => [number, number];
     readonly depict_data_with_coords_json: (a: number, b: number, c: number) => [number, number];
@@ -1779,7 +1906,6 @@ export interface InitOutput {
     readonly depictoptions_set_show_atom_indices: (a: number, b: number) => void;
     readonly depictoptions_set_width: (a: number, b: number) => void;
     readonly detect_functional_groups: (a: number) => [number, number];
-    readonly determine_bonds_from_xyz_json: (a: number, b: number) => [number, number];
     readonly dice_ecfp4: (a: number, b: number) => number;
     readonly dice_ecfp6: (a: number, b: number) => number;
     readonly dice_maccs: (a: number, b: number) => number;
@@ -1797,9 +1923,13 @@ export interface InitOutput {
     readonly fcfp6_bitvec: (a: number) => [number, number];
     readonly find_reaction_center_json: (a: number, b: number) => [number, number];
     readonly gasteiger_charges_json: (a: number) => [number, number];
+    readonly generate_3d_coords_json: (a: number) => [number, number];
+    readonly generate_3d_etkdg_coords_json: (a: number) => [number, number];
     readonly generate_3d_etkdg_minimized_pdb: (a: number) => [number, number];
     readonly generate_3d_etkdg_pdb: (a: number) => [number, number];
+    readonly generate_3d_from_smiles: (a: number, b: number) => [number, number, number, number];
     readonly generate_3d_minimized_pdb: (a: number) => [number, number];
+    readonly generate_3d_optimized_pdb: (a: number, b: number) => [number, number, number, number];
     readonly generate_3d_pdb: (a: number) => [number, number];
     readonly generic_murcko_scaffold: (a: number) => number;
     readonly get_atom_info: (a: number, b: number) => [number, number];
@@ -1809,6 +1939,7 @@ export interface InitOutput {
     readonly get_descriptors_json: (a: number) => [number, number];
     readonly get_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number) => any;
     readonly getaway_descriptors_json: (a: number) => [number, number];
+    readonly hdf_json: (a: number, b: number, c: number, d: bigint) => [number, number];
     readonly identify_functional_groups: (a: number) => [number, number];
     readonly inchi_from_smiles: (a: number, b: number) => [number, number];
     readonly inchikey_from_smiles: (a: number, b: number) => [number, number];
@@ -1821,6 +1952,7 @@ export interface InitOutput {
     readonly match_smarts_smiles: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly maxmin_picks_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly mcs_smiles_json: (a: number, b: number) => [number, number, number, number];
+    readonly mcs_smiles_json_with_ring_config: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly mhfp_hashes_json: (a: number) => [number, number];
     readonly mhfplshhandle_add_smiles: (a: number, b: number, c: number) => [number, number, number];
     readonly mhfplshhandle_is_empty: (a: number) => number;
@@ -1830,6 +1962,7 @@ export interface InitOutput {
     readonly minimize_dreiding_json: (a: number) => [number, number];
     readonly minimize_mmff94_json: (a: number, b: number) => [number, number];
     readonly minimize_mmff94_lbfgs_json: (a: number, b: number) => [number, number];
+    readonly minimize_uff_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly mmff94_charges_json: (a: number) => [number, number];
     readonly mmff94_charges_typed_json: (a: number) => [number, number];
     readonly mmff94_energy_breakdown_json: (a: number) => [number, number];
@@ -1840,6 +1973,7 @@ export interface InitOutput {
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
     readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
     readonly mol_from_cml: (a: number, b: number) => [number, number, number];
+    readonly mol_from_moljson: (a: number, b: number) => [number, number, number];
     readonly mol_from_pdb: (a: number, b: number) => number;
     readonly mol_from_sdf_block: (a: number, b: number) => [number, number, number];
     readonly mol_from_v3000_block: (a: number, b: number) => [number, number, number];
@@ -1851,10 +1985,14 @@ export interface InitOutput {
     readonly mol_with_atom_removed: (a: number, b: number) => [number, number, number];
     readonly mol_with_bond_added: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly mol_with_bond_removed: (a: number, b: number) => [number, number, number];
+    readonly molecule_report_json: (a: number, b: number) => [number, number, number, number];
     readonly molhandle_aromatic_ring_count: (a: number) => number;
     readonly molhandle_assign_cip_json: (a: number) => [number, number];
+    readonly molhandle_bbb_passes: (a: number) => number;
+    readonly molhandle_bbb_score: (a: number) => number;
     readonly molhandle_bertz_ct: (a: number) => number;
     readonly molhandle_bond_count: (a: number) => number;
+    readonly molhandle_caco2_permeability: (a: number) => number;
     readonly molhandle_canonical_smiles: (a: number) => [number, number];
     readonly molhandle_chi0: (a: number) => number;
     readonly molhandle_chi0v: (a: number) => number;
@@ -1866,6 +2004,7 @@ export interface InitOutput {
     readonly molhandle_chi3v: (a: number) => number;
     readonly molhandle_chi4: (a: number) => number;
     readonly molhandle_chi4v: (a: number) => number;
+    readonly molhandle_cyp3a4_inhibition_risk: (a: number) => number;
     readonly molhandle_depict_png: (a: number) => [number, number];
     readonly molhandle_depict_svg: (a: number) => [number, number];
     readonly molhandle_depict_svg_opts: (a: number, b: number) => [number, number];
@@ -1878,6 +2017,7 @@ export interface InitOutput {
     readonly molhandle_hba_count: (a: number) => number;
     readonly molhandle_hbd_count: (a: number) => number;
     readonly molhandle_heavy_atom_count: (a: number) => number;
+    readonly molhandle_herg_risk_score: (a: number) => number;
     readonly molhandle_isotope_distribution_json: (a: number, b: number) => [number, number];
     readonly molhandle_iupac_name: (a: number) => [number, number];
     readonly molhandle_kappa1: (a: number) => number;
@@ -1904,6 +2044,8 @@ export interface InitOutput {
     readonly molhandle_num_stereocenters: (a: number) => number;
     readonly molhandle_num_unspecified_stereocenters: (a: number) => number;
     readonly molhandle_pains_passes: (a: number) => number;
+    readonly molhandle_pka_acid_value: (a: number) => number;
+    readonly molhandle_pka_base_value: (a: number) => number;
     readonly molhandle_qed: (a: number) => number;
     readonly molhandle_randic_index: (a: number) => number;
     readonly molhandle_reos_passes: (a: number) => number;
@@ -1931,13 +2073,14 @@ export interface InitOutput {
     readonly pharmacophore_features_json: (a: number) => [number, number];
     readonly pharmacophore_fp_2d_summary: (a: number) => [number, number];
     readonly pharmacophore_fp_3d_summary: (a: number) => [number, number];
+    readonly predict_pka_json: (a: number, b: number) => [number, number];
     readonly random_smiles_json: (a: number, b: number, c: number, d: bigint) => [number, number, number, number];
     readonly remove_hydrogens: (a: number) => number;
     readonly rgroup_decompose_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly ring_families_json: (a: number) => [number, number, number, number];
-    readonly run_md_json: (a: number, b: number, c: number) => [number, number];
     readonly run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly sa_score: (a: number) => number;
+    readonly screen_smiles_json: (a: number, b: number, c: number, d: number) => [number, number];
     readonly sdf_from_records_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
     readonly sdf_to_records_json: (a: number, b: number) => [number, number];
     readonly sdf_to_smiles_json: (a: number, b: number) => [number, number];
@@ -1948,6 +2091,7 @@ export interface InitOutput {
     readonly smarts_match_atoms_with_chirality: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly smiles_array_to_sdf: (a: number, b: number) => [number, number, number, number];
     readonly smiles_to_mol2: (a: number, b: number) => [number, number];
+    readonly smiles_to_pdbqt: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number];
     readonly smiles_to_svg_highlighted: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
     readonly smr_vsa_json: (a: number) => [number, number];
     readonly sssr_rings_json: (a: number) => [number, number];
@@ -1967,27 +2111,21 @@ export interface InitOutput {
     readonly to_cml: (a: number) => [number, number];
     readonly to_mol_block: (a: number) => [number, number];
     readonly to_mol_v3000_block: (a: number) => [number, number];
+    readonly to_moljson: (a: number) => [number, number];
     readonly to_xyz: (a: number) => [number, number];
     readonly torsion_bitvec: (a: number) => [number, number];
-    readonly torsion_scan_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number];
     readonly virtual_screen_ecfp4_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly whim_descriptors_json: (a: number) => [number, number];
     readonly whim_getaway_combined_json: (a: number) => [number, number];
     readonly write_smiles: (a: number) => [number, number];
-    readonly start: () => void;
+    readonly xlogp3_json: (a: number) => [number, number];
+    readonly xlogp3_per_atom_json: (a: number) => [number, number];
     readonly molhandle_atom_count: (a: number) => number;
-    readonly compare_molecules_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
-    readonly compare_molecules_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
-    readonly generate_3d_from_smiles: (a: number, b: number) => [number, number, number, number];
-    readonly generate_3d_optimized_pdb: (a: number, b: number) => [number, number, number, number];
-    readonly molecule_report_json: (a: number, b: number) => [number, number, number, number];
-    readonly screen_smiles_json: (a: number, b: number, c: number, d: number) => [number, number];
+    readonly start: () => void;
     readonly __wbindgen_malloc: (a: number, b: number) => number;
     readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
-    readonly __wbindgen_free: (a: number, b: number, c: number) => void;
-    readonly __wbindgen_exn_store: (a: number) => void;
-    readonly __externref_table_alloc: () => number;
     readonly __wbindgen_externrefs: WebAssembly.Table;
+    readonly __wbindgen_free: (a: number, b: number, c: number) => void;
     readonly __externref_table_dealloc: (a: number) => void;
     readonly __wbindgen_start: () => void;
 }