@kent-tokyo/chematic 1.1.2 → 1.1.3

package/README.md

@@ -4,7 +4,7 @@ WebAssembly bindings for [chematic](https://github.com/kent-tokyo/chematic), a p
 
 Published to npm as [`@kent-tokyo/chematic`](https://www.npmjs.com/package/@kent-tokyo/chematic).
 
-The current workspace line is 1.1.2. The binding keeps bounded parsing,
+The current workspace line is 1.1.3. The binding keeps bounded parsing,
 typed failures, and opt-in `embed_pipeline_v2_json`; 3D/MMFF94 behavior remains
 Experimental and is not a claim of full RDKit parity.
 

package/chematic_wasm.d.ts

@@ -261,6 +261,13 @@ export class MolHandle {
      * (TPSA ≤ 131.6 Ų and LogP ≤ 5.88).
      */
     egan_passes(): boolean;
+    /**
+     * Seeded ETKDGv3 coordinates using the exact sixth-order torsion
+     * gradient tracked by RDKit issue #8715. At most 512 atoms are accepted.
+     * The result may intentionally differ from `rdkit_embed_json` for
+     * molecules with a non-zero sixth-order experimental torsion term.
+     */
+    etkdg_embed_corrected_json(random_seed: number, max_iterations: number): string;
     /**
      * Monoisotopic (exact) mass.
      */
@@ -1160,6 +1167,15 @@ export function edit_cdxml_document_json_v1(document_json: string, edit_json: st
  */
 export function edit_reaction_document_json_v1(document_json: string, edit_json: string): string;
 
+/**
+ * EEM partial charges from caller-supplied 3D coordinates.
+ *
+ * Returns `{"charges":[...]}`. Unlike RDKit 2026.09.1 and earlier (issue
+ * #9688), ionic charges sum to the molecule's formal charge rather than its
+ * negation. Errors are returned as `{"error":"..."}`.
+ */
+export function eem_charges_json(mol: MolHandle, coords_json: string): string;
+
 /**
  * Run `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
  * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
@@ -2705,6 +2721,8 @@ export function roundtrip_mol_v3000_block(block: string): 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.
+ * Product-template E/Z is resolved after all reactants are assembled, so an
+ * unspecified product double bond does not depend on reactant order.
  */
 export function run_reactants(smirks: string, reactants_smiles: string): string;
 
@@ -3401,6 +3419,7 @@ export interface InitOutput {
     readonly edit_cdxml_document_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly edit_cdxml_document_json_v1: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly edit_reaction_document_json_v1: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly eem_charges_json: (a: number, b: number, c: 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];
@@ -3535,6 +3554,7 @@ export interface InitOutput {
     readonly molhandle_depict_svg: (a: number) => [number, number];
     readonly molhandle_depict_svg_opts: (a: number, b: number) => [number, number];
     readonly molhandle_egan_passes: (a: number) => number;
+    readonly molhandle_etkdg_embed_corrected_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly molhandle_exact_mass: (a: number) => number;
     readonly molhandle_formal_charge_sum: (a: number) => number;
     readonly molhandle_formula: (a: number) => [number, number];

package/chematic_wasm.js

@@ -635,6 +635,33 @@ export class MolHandle {
         const ret = wasm.molhandle_egan_passes(this.__wbg_ptr);
         return ret !== 0;
     }
+    /**
+     * Seeded ETKDGv3 coordinates using the exact sixth-order torsion
+     * gradient tracked by RDKit issue #8715. At most 512 atoms are accepted.
+     * The result may intentionally differ from `rdkit_embed_json` for
+     * molecules with a non-zero sixth-order experimental torsion term.
+     * @param {number} random_seed
+     * @param {number} max_iterations
+     * @returns {string}
+     */
+    etkdg_embed_corrected_json(random_seed, max_iterations) {
+        let deferred2_0;
+        let deferred2_1;
+        try {
+            const ret = wasm.molhandle_etkdg_embed_corrected_json(this.__wbg_ptr, random_seed, max_iterations);
+            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);
+        }
+    }
     /**
      * Monoisotopic (exact) mass.
      * @returns {number}
@@ -3235,6 +3262,32 @@ export function edit_reaction_document_json_v1(document_json, edit_json) {
     }
 }
 
+/**
+ * EEM partial charges from caller-supplied 3D coordinates.
+ *
+ * Returns `{"charges":[...]}`. Unlike RDKit 2026.09.1 and earlier (issue
+ * #9688), ionic charges sum to the molecule's formal charge rather than its
+ * negation. Errors are returned as `{"error":"..."}`.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @returns {string}
+ */
+export function eem_charges_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.eem_charges_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 `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
  * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
@@ -7316,6 +7369,8 @@ export function roundtrip_mol_v3000_block(block) {
  * `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.
+ * Product-template E/Z is resolved after all reactants are assembled, so an
+ * unspecified product double bond does not depend on reactant order.
  * @param {string} smirks
  * @param {string} reactants_smiles
  * @returns {string}

package/package.json

@@ -5,7 +5,7 @@
     "Kentaro Tanabe (kent-tokyo) <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "1.1.2",
+  "version": "1.1.3",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",