@kent-tokyo/chematic 0.1.25 → 0.1.36

package/chematic_wasm.d.ts

@@ -318,6 +318,14 @@ export class MolHandle {
      * Sum of EState indices over all heavy atoms.
      */
     sum_estate(): number;
+    /**
+     * InChI string representation of the molecule.
+     */
+    to_inchi(): string;
+    /**
+     * InChIKey (27-character identifier) for the molecule.
+     */
+    to_inchikey(): string;
     /**
      * Topological polar surface area (Ų).
      */
@@ -343,6 +351,14 @@ export function add_hydrogens(mol: MolHandle): MolHandle;
  */
 export function atom_pair_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * 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.
+ */
+export function balance_check_json(reaction_smiles: string): string;
+
 /**
  * Number of BRICS fragments produced by fragmenting the molecule.
  *
@@ -399,6 +415,49 @@ export function cdxml_to_smiles_json(cdxml: string): string;
  */
 export function cip_assignments_json(mol: MolHandle): string;
 
+/**
+ * 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);
+ * ```
+ */
+export function compare_molecules_batch_json(smiles_batch: string, delimiter: string): string;
+
+/**
+ * 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);
+ * ```
+ */
+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" }
+ * ```
+ */
+export function coulomb_energy_json(mol: MolHandle): string;
+
 /**
  * Return the CPK color (CSS hex string) for the given element symbol.
  *
@@ -497,11 +556,29 @@ export function dice_maccs(a: MolHandle, b: MolHandle): number;
  */
 export function ecfp4_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * 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.
+ */
+export function ecfp4_bitvec_with_chirality(mol: MolHandle, use_chirality: boolean): Uint8Array;
+
 /**
  * ECFP6 (radius-3) fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  */
 export function ecfp6_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * 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.
+ */
+export function ecfp6_bitvec_with_chirality(mol: MolHandle, use_chirality: boolean): Uint8Array;
+
 /**
  * Compute a fingerprint bit-vector with configurable ECFP radius and bit width.
  *
@@ -511,8 +588,12 @@ export function ecfp6_bitvec(mol: MolHandle): Uint8Array;
  *
  * 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.
  */
-export function ecfp_bitvec_custom(mol: MolHandle, radius: number, nbits: number): Uint8Array;
+export function ecfp_bitvec_custom(mol: MolHandle, radius: number, nbits: number, use_chirality: boolean): Uint8Array;
 
 /**
  * Enumerate all stereoisomers arising from unspecified tetrahedral stereocenters.
@@ -551,11 +632,32 @@ export function fcfp4_bitvec(mol: MolHandle): Uint8Array;
  */
 export function fcfp6_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * 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.
+ */
+export function find_reaction_center_json(reaction_smiles: string): string;
+
 /**
  * Gasteiger-Marsili PEOE partial charges as a JSON array of f64.
  */
 export function gasteiger_charges_json(mol: MolHandle): string;
 
+/**
+ * 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
+ * ```
+ */
+export function generate_3d_from_smiles(smiles: string): string;
+
 /**
  * Generate energy-minimized 3D coordinates and return a PDB string.
  *
@@ -565,6 +667,19 @@ export function gasteiger_charges_json(mol: MolHandle): string;
  */
 export function generate_3d_minimized_pdb(mol: MolHandle): string;
 
+/**
+ * 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
+ * ```
+ */
+export function generate_3d_optimized_pdb(smiles: string): string;
+
 /**
  * Generate 3D coordinates for the molecule and return a PDB string.
  *
@@ -629,6 +744,28 @@ export function get_descriptors_json(mol: MolHandle): string;
  */
 export function identify_functional_groups(mol: MolHandle): string;
 
+/**
+ * Generate InChI string from SMILES.
+ *
+ * Returns `"error:<msg>"` on parse failure.
+ */
+export function inchi_from_smiles(smiles: string): string;
+
+/**
+ * Generate InChIKey from SMILES (27-character identifier).
+ *
+ * Returns `"error:<msg>"` on parse failure.
+ */
+export function inchikey_from_smiles(smiles: string): string;
+
+/**
+ * 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.
+ */
+export function invert_stereocenter_at(mol: MolHandle, atom_idx: number): MolHandle;
+
 /**
  * Returns `true` if the SMILES string can be parsed without error.
  */
@@ -689,6 +826,20 @@ export function maxmin_picks_ecfp4_json(smiles_json: string, n: number): string;
  */
 export function mcs_smiles_json(smiles_json: string): string;
 
+/**
+ * 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
+ */
+export function minimize_dreiding_json(mol: MolHandle): string;
+
 /**
  * Find matched molecular pairs in a set of molecules as JSON.
  *
@@ -714,6 +865,13 @@ export function mcs_smiles_json(smiles_json: string): string;
  */
 export function mmp_pairs_json(smiles_json: string): string;
 
+/**
+ * Parse a Tripos MOL2 string and return SMILES.
+ *
+ * Returns `"error:<msg>"` on failure.
+ */
+export function mol2_to_smiles(mol2_str: string): string;
+
 /**
  * Parse a MOL V2000 string and return 2D coordinates as a JSON array.
  *
@@ -825,6 +983,19 @@ export function mol_with_bond_added(mol: MolHandle, a: number, b: number, order:
  */
 export function mol_with_bond_removed(mol: MolHandle, idx: number): MolHandle;
 
+/**
+ * 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);
+ * ```
+ */
+export function molecule_report_json(smiles: string): string;
+
 /**
  * Per-atom molar refractivity contributions as a JSON array of f64.
  */
@@ -837,6 +1008,15 @@ export function mr_per_atom_json(mol: MolHandle): string;
  */
 export function murcko_scaffold(mol: MolHandle): MolHandle;
 
+/**
+ * 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.
+ */
+export function nearest_neighbors_json(query_smiles: string, db_smiles_json: string, k: number): string;
+
 /**
  * Neutralize formal charges on `mol` by proton addition/removal.
  *
@@ -844,6 +1024,12 @@ export function murcko_scaffold(mol: MolHandle): MolHandle;
  */
 export function neutralize_charges(mol: MolHandle): MolHandle;
 
+/**
+ * Parse and re-serialize CXSMILES, preserving supported CX metadata.
+ * Returns error if atom count exceeds 10,000.
+ */
+export function normalize_cxsmiles(s: string): string;
+
 /**
  * Parse and re-serialise a reaction SMILES string, returning the normalised form.
  *
@@ -860,10 +1046,26 @@ export function normalize_reaction_smiles(rxn_smiles: string): string;
  */
 export function pains_matches_json(mol: MolHandle): string;
 
+/**
+ * Parse CXSMARTS and return preserved metadata as JSON.
+ * Returns error if atom count exceeds 10,000.
+ */
+export function parse_cxsmarts_json(s: string): string;
+
+/**
+ * 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.
+ */
+export function parse_cxsmiles_json(s: string): string;
+
 /**
  * Parse a SMILES string into a `MolHandle`.
  *
- * Returns a JS error string on parse failure.
+ * Returns a JS error string on parse failure or if atom count exceeds 10,000.
  */
 export function parse_smiles(s: string): MolHandle;
 
@@ -900,6 +1102,15 @@ export function remove_hydrogens(mol: MolHandle): MolHandle;
  */
 export function rgroup_decompose_json(smiles_json: string, core_smarts: string): 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.
  *
@@ -914,6 +1125,23 @@ export function run_reactants(smirks: string, reactants_smiles: string): string;
  */
 export function sa_score(mol: MolHandle): number;
 
+/**
+ * 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
+ * ```
+ */
+export function screen_smiles_json(smiles_batch: string, delimiter: string): string;
+
 /**
  * Serialize multiple molecules with properties to an SDF string.
  *
@@ -975,6 +1203,15 @@ export function slogp_vsa_json(mol: MolHandle): string;
  */
 export function smarts_match_atoms(smarts: string, mol: MolHandle): string;
 
+/**
+ * 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).
+ */
+export function smarts_match_atoms_with_chirality(smarts: string, mol: MolHandle, use_chirality: boolean): string;
+
 /**
  * Serialise a JSON array of SMILES to an SDF string.
  *
@@ -983,6 +1220,13 @@ export function smarts_match_atoms(smarts: string, mol: MolHandle): string;
  */
 export function smiles_array_to_sdf(smiles_json: string): string;
 
+/**
+ * Convert a SMILES to a minimal Tripos MOL2 string (no 3D coordinates).
+ *
+ * Returns `"error:<msg>"` on parse failure.
+ */
+export function smiles_to_mol2(smiles: string): string;
+
 /**
  * Render a highlighted SVG from a SMILES string in one call.
  *
@@ -1007,6 +1251,22 @@ export function smr_vsa_json(mol: MolHandle): string;
  */
 export function sssr_rings_json(mol: MolHandle): string;
 
+/**
+ * Standardize a SMILES string and return the canonical SMILES of the result.
+ *
+ * Applies: largest fragment extraction → charge neutralization.
+ * Returns `"error:<msg>"` on parse failure.
+ */
+export function standardize_smiles(smiles: string): string;
+
+/**
+ * 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.
+ */
+export function standardize_smiles_report_json(smiles: string, largest_fragment_only: boolean, neutralize_charges: boolean, remove_explicit_h: boolean, canonical_tautomer: boolean): string;
+
 export function start(): void;
 
 /**
@@ -1106,6 +1366,7 @@ export interface InitOutput {
     readonly __wbg_molhandle_free: (a: number, b: number) => void;
     readonly add_hydrogens: (a: number) => number;
     readonly atom_pair_bitvec: (a: number) => [number, number];
+    readonly balance_check_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];
@@ -1121,6 +1382,7 @@ 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];
@@ -1145,13 +1407,16 @@ export interface InitOutput {
     readonly dice_ecfp6: (a: number, b: number) => number;
     readonly dice_maccs: (a: number, b: number) => number;
     readonly ecfp4_bitvec: (a: number) => [number, number];
+    readonly ecfp4_bitvec_with_chirality: (a: number, b: number) => [number, number];
     readonly ecfp6_bitvec: (a: number) => [number, number];
-    readonly ecfp_bitvec_custom: (a: number, b: number, c: number) => [number, number];
+    readonly ecfp6_bitvec_with_chirality: (a: number, b: number) => [number, number];
+    readonly ecfp_bitvec_custom: (a: number, b: number, c: number, d: number) => [number, number];
     readonly enumerate_stereo_isomers_json: (a: number) => [number, number, number, number];
     readonly enumerate_tautomers_json: (a: number) => [number, number];
     readonly estate_indices_json: (a: number) => [number, number];
     readonly fcfp4_bitvec: (a: number) => [number, number];
     readonly fcfp6_bitvec: (a: number) => [number, number];
+    readonly find_reaction_center_json: (a: number, b: number) => [number, number];
     readonly gasteiger_charges_json: (a: number) => [number, number];
     readonly generate_3d_minimized_pdb: (a: number) => [number, number];
     readonly generate_3d_pdb: (a: number) => [number, number];
@@ -1161,6 +1426,9 @@ export interface InitOutput {
     readonly get_bond_info: (a: number, b: number) => [number, number];
     readonly get_descriptors_json: (a: number) => [number, number];
     readonly identify_functional_groups: (a: number) => [number, number];
+    readonly inchi_from_smiles: (a: number, b: number) => [number, number];
+    readonly inchikey_from_smiles: (a: number, b: number) => [number, number];
+    readonly invert_stereocenter_at: (a: number, b: number) => [number, number, number];
     readonly is_valid_smiles: (a: number, b: number) => number;
     readonly labute_asa_per_atom_json: (a: number) => [number, number];
     readonly largest_fragment: (a: number) => number;
@@ -1169,7 +1437,9 @@ 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 minimize_dreiding_json: (a: number) => [number, number];
     readonly mmp_pairs_json: (a: number, b: number) => [number, number, number, number];
+    readonly mol2_to_smiles: (a: number, b: number) => [number, number];
     readonly mol_block_coords_json: (a: number, b: number) => [number, number, number, number];
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
     readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
@@ -1237,18 +1507,25 @@ export interface InitOutput {
     readonly molhandle_ring_count: (a: number) => number;
     readonly molhandle_rotatable_bond_count: (a: number) => number;
     readonly molhandle_sum_estate: (a: number) => number;
+    readonly molhandle_to_inchi: (a: number) => [number, number];
+    readonly molhandle_to_inchikey: (a: number) => [number, number];
     readonly molhandle_tpsa: (a: number) => number;
     readonly molhandle_veber_passes: (a: number) => number;
     readonly molhandle_wiener_index: (a: number) => number;
     readonly mr_per_atom_json: (a: number) => [number, number];
     readonly murcko_scaffold: (a: number) => number;
+    readonly nearest_neighbors_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly neutralize_charges: (a: number) => number;
+    readonly normalize_cxsmiles: (a: number, b: number) => [number, number, number, number];
     readonly normalize_reaction_smiles: (a: number, b: number) => [number, number, number, number];
     readonly pains_matches_json: (a: number) => [number, number];
+    readonly parse_cxsmarts_json: (a: number, b: number) => [number, number, number, number];
+    readonly parse_cxsmiles_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_smiles: (a: number, b: number) => [number, number, number];
     readonly peoe_vsa_json: (a: number) => [number, number];
     readonly remove_hydrogens: (a: number) => number;
     readonly rgroup_decompose_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly run_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 sdf_from_records_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
@@ -1257,10 +1534,14 @@ export interface InitOutput {
     readonly shape_descriptors_json: (a: number) => [number, number];
     readonly slogp_vsa_json: (a: number) => [number, number];
     readonly smarts_match_atoms: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly 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_svg_highlighted: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
     readonly smr_vsa_json: (a: number) => [number, number];
     readonly sssr_rings_json: (a: number) => [number, number];
+    readonly standardize_smiles: (a: number, b: number) => [number, number];
+    readonly standardize_smiles_report_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number];
     readonly tanimoto_atom_pair: (a: number, b: number) => number;
     readonly tanimoto_ecfp4: (a: number, b: number) => number;
     readonly tanimoto_ecfp6: (a: number, b: number) => number;
@@ -1278,9 +1559,17 @@ export interface InitOutput {
     readonly write_smiles: (a: number) => [number, number];
     readonly start: () => void;
     readonly molhandle_atom_count: (a: number) => number;
-    readonly __wbindgen_free: (a: number, b: number, c: number) => void;
+    readonly 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 __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 __externref_table_dealloc: (a: number) => void;
     readonly __wbindgen_start: () => void;