@kent-tokyo/chematic 0.21.0 → 0.23.0

package/chematic_wasm.d.ts

@@ -823,6 +823,20 @@ export function ecfp6_bitvec_with_chirality(mol: MolHandle, use_chirality: boole
  */
 export function ecfp_bitvec_custom(mol: MolHandle, radius: number, nbits: number, use_chirality: boolean): Uint8Array;
 
+/**
+ * Run `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
+ * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
+ * for the config JSON shape and the success/failure envelope shape.
+ *
+ * Never throws. Always returns a JSON string tagged `schemaVersion: 1` and
+ * `ok: true`/`false`. `ok: false` covers both a WASM-level rejection
+ * (oversized input, too many atoms, malformed/incomplete config JSON) and a
+ * config `embed_ensemble_v2` itself rejects (currently only an invalid
+ * `rmsdThreshold`) -- distinguished by `error.stage` /
+ * `error.cause.kind`, same as `embed_pipeline_v2_json`.
+ */
+export function embed_ensemble_v2_json(mol: MolHandle, config_json: string): string;
+
 /**
  * Run the opt-in v2 embedding pipeline, applied directly to `mol`'s own atom
  * order (never canonicalizes/reparses -- see the module doc).
@@ -1307,6 +1321,25 @@ export function maxmin_picks_ecfp4_json(smiles_json: string, n: number): string;
  */
 export function mcs_smiles_json(smiles_json: string): string;
 
+/**
+ * Full `McsConfig` + `McsOutcome`-aware MCS search.
+ *
+ * `smiles_json` — JSON array of at least 2 SMILES strings.
+ * `config_json` — a JSON object with any subset of `McsConfig`'s fields
+ * (camelCase keys, all optional, defaulting to `McsConfig::default()`):
+ * `matchBonds`, `minAtoms`, `timeoutMs`, `ringMatchesRingOnly`,
+ * `completeRingsOnly`, `atomCompare` (`"elements"` | `"any_heavy_atom"` |
+ * `"any"`), `bondCompare` (`"order_or_aromatic"` | `"any"`),
+ * `matchChiralTag`, `matchCharge`, `matchIsotope`, `maximizeBonds`.
+ *
+ * Returns a JSON object `{"smiles": string|null, "wasTimedOut": bool}` --
+ * `smiles` is `null` when there is no common substructure; `wasTimedOut` is
+ * `true` if `timeoutMs` was reached before the search finished exhaustively
+ * (the returned `smiles`, if any, is then the best result found so far, not
+ * proven optimal).
+ */
+export function mcs_smiles_json_with_config(smiles_json: string, config_json: string): string;
+
 /**
  * MCS with ring-awareness constraints.
  *
@@ -2566,6 +2599,7 @@ export interface InitOutput {
     readonly ecfp6_bitvec: (a: 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 embed_ensemble_v2_json: (a: number, b: number, c: number) => [number, number];
     readonly embed_pipeline_v2_json: (a: number, b: number, c: number) => [number, number];
     readonly enumerate_library_2way: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
     readonly enumerate_stereo_isomers_json: (a: number) => [number, number, number, number];
@@ -2612,6 +2646,7 @@ 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_config: (a: number, b: number, c: number, d: 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];

package/chematic_wasm.js

@@ -1972,6 +1972,37 @@ export function ecfp_bitvec_custom(mol, radius, nbits, use_chirality) {
     return v1;
 }
 
+/**
+ * Run `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
+ * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
+ * for the config JSON shape and the success/failure envelope shape.
+ *
+ * Never throws. Always returns a JSON string tagged `schemaVersion: 1` and
+ * `ok: true`/`false`. `ok: false` covers both a WASM-level rejection
+ * (oversized input, too many atoms, malformed/incomplete config JSON) and a
+ * config `embed_ensemble_v2` itself rejects (currently only an invalid
+ * `rmsdThreshold`) -- distinguished by `error.stage` /
+ * `error.cause.kind`, same as `embed_pipeline_v2_json`.
+ * @param {MolHandle} mol
+ * @param {string} config_json
+ * @returns {string}
+ */
+export function embed_ensemble_v2_json(mol, config_json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(config_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.embed_ensemble_v2_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);
+    }
+}
+
 /**
  * Run the opt-in v2 embedding pipeline, applied directly to `mol`'s own atom
  * order (never canonicalizes/reparses -- see the module doc).
@@ -3148,6 +3179,49 @@ export function mcs_smiles_json(smiles_json) {
     }
 }
 
+/**
+ * Full `McsConfig` + `McsOutcome`-aware MCS search.
+ *
+ * `smiles_json` — JSON array of at least 2 SMILES strings.
+ * `config_json` — a JSON object with any subset of `McsConfig`'s fields
+ * (camelCase keys, all optional, defaulting to `McsConfig::default()`):
+ * `matchBonds`, `minAtoms`, `timeoutMs`, `ringMatchesRingOnly`,
+ * `completeRingsOnly`, `atomCompare` (`"elements"` | `"any_heavy_atom"` |
+ * `"any"`), `bondCompare` (`"order_or_aromatic"` | `"any"`),
+ * `matchChiralTag`, `matchCharge`, `matchIsotope`, `maximizeBonds`.
+ *
+ * Returns a JSON object `{"smiles": string|null, "wasTimedOut": bool}` --
+ * `smiles` is `null` when there is no common substructure; `wasTimedOut` is
+ * `true` if `timeoutMs` was reached before the search finished exhaustively
+ * (the returned `smiles`, if any, is then the best result found so far, not
+ * proven optimal).
+ * @param {string} smiles_json
+ * @param {string} config_json
+ * @returns {string}
+ */
+export function mcs_smiles_json_with_config(smiles_json, config_json) {
+    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(config_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.mcs_smiles_json_with_config(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);
+    }
+}
+
 /**
  * MCS with ring-awareness constraints.
  *

package/package.json

@@ -5,7 +5,7 @@
     "kent-tokyo <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "0.21.0",
+  "version": "0.23.0",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",