@kent-tokyo/chematic 1.1.1 → 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 1.1.1. 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.
 
@@ -18,7 +18,7 @@ npm install @kent-tokyo/chematic
 
 - Parse SMILES strings into molecule handles
 - Molecular descriptors: MW, TPSA, LogP, Fsp3, QED, exact mass, rotatable bonds, HBD/HBA, aromatic ring count, Labute ASA
-- Drug-likeness filters: Lipinski, Veber, Egan, REOS, Ghose
+- Drug-likeness filters: Lipinski, Veber, Egan, REOS, Ghose, PAINS, and Brenk
 - EState indices (Hall & Kier 1991): per-atom values, sum/max/min
 - Gasteiger-Marsili PEOE partial charges: per-heavy-atom charges
 - VSA descriptors: SlogP_VSA (×12), SMR_VSA (×10), PEOE_VSA (×14)
@@ -91,6 +91,7 @@ import init, {
   smr_vsa_json,
   peoe_vsa_json,
   identify_functional_groups,
+  brenk_report_json,
 } from '@kent-tokyo/chematic';
 
 await init();
@@ -113,6 +114,10 @@ console.log(mol.aromatic_ring_count()); // 1
 console.log(mol.lipinski_passes());     // true
 console.log(mol.canonical_smiles());    // canonical SMILES string
 
+// Brenk alerts, fully local in the browser/Node runtime
+console.log(JSON.parse(brenk_report_json('Oc1ccccc1')));
+// { passes: false, alerts: ['phenol'] }
+
 // BRICS fragmentation
 console.log(brics_fragment_count(mol)); // ≥ 2
 

package/chematic_wasm.d.ts

@@ -182,6 +182,14 @@ export class MolHandle {
      * Number of bonds.
      */
     bond_count(): number;
+    /**
+     * Returns `true` if the molecule has no Brenk structural alerts.
+     *
+     * This uses the same conservative core contract as the Rust, Python, and
+     * MCP bindings: an alert-search budget exhaustion is not reported as a
+     * clean pass.
+     */
+    brenk_passes(): boolean;
     /**
      * Palm (1997) Caco-2 intestinal permeability (logPCaco2).
      * > −5.5 = high permeability.
@@ -253,6 +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.
      */
@@ -740,6 +755,24 @@ export function batch_report_html(smiles_lines: string): string;
  */
 export function boiled_egg_json(smiles: string): string;
 
+/**
+ * Brenk structural-alert identifiers matched by `mol` as a JSON array.
+ *
+ * Returns `[]` when no alerts fire. Identifiers and ordering are identical to
+ * the Rust, Python, and MCP bindings.
+ */
+export function brenk_matches_json(mol: MolHandle): string;
+
+/**
+ * Parse `smiles` and return a complete Brenk report as JSON.
+ *
+ * The stable result shape is `{"passes":boolean,"alerts":string[]}`.
+ * Invalid or oversized SMILES throw the same ordinary JavaScript input error
+ * as `parse_smiles`; this function never converts invalid input into a clean
+ * report.
+ */
+export function brenk_report_json(smiles: string): string;
+
 /**
  * Number of BRICS fragments produced by fragmenting the molecule.
  *
@@ -788,6 +821,11 @@ export function canonical_tautomer(mol: MolHandle): MolHandle;
  */
 export function canonical_tautomer_with_blocked_atoms_json(mol: MolHandle, blocked_atom_indices_json: string): string;
 
+/**
+ * Return caller coordinates centered and aligned to their principal axes.
+ */
+export function canonicalize_conformer_from_coords_json(mol: MolHandle, coords_json: string, center_json: string | null | undefined, normalize_covar: boolean, ignore_hs: boolean): string;
+
 /**
  * Canonicalize a bounded delimiter-separated SMILES batch.
  *
@@ -914,6 +952,14 @@ export function compare_molecules_batch_json(smiles_batch: string, delimiter: st
  */
 export function compare_molecules_json(smiles1: string, smiles2: string): string;
 
+/**
+ * Compute an RDKit-style principal-axis transform from caller coordinates.
+ *
+ * Returns a row-major 4x4 JSON matrix. `center_json`, when supplied, must be
+ * `[x,y,z]`; otherwise the selected-atom centroid is used.
+ */
+export function compute_canonical_transform_from_coords_json(mol: MolHandle, coords_json: string, center_json: string | null | undefined, normalize_covar: boolean, ignore_hs: boolean): string;
+
 /**
  * Generate multiple conformers with RMSD-based pruning.
  * Returns JSON: `{"conformers": [[[x,y,z],...], ...], "count": int}`.
@@ -1121,6 +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
@@ -1346,6 +1401,11 @@ export function generic_murcko_scaffold(mol: MolHandle): MolHandle;
  */
 export function get_atom_info(mol: MolHandle, idx: number): string;
 
+/**
+ * Measure angle i-j-k in degrees from caller-supplied coordinates.
+ */
+export function get_bond_angle_from_coords_json(mol: MolHandle, coords_json: string, i: number, j: number, k: number): number;
+
 /**
  * Return bond information as a JSON object, looked up by the two bonded atom indices.
  *
@@ -1367,6 +1427,15 @@ export function get_bond_between(mol: MolHandle, atom1: number, atom2: number):
  */
 export function get_bond_info(mol: MolHandle, idx: number): string;
 
+/**
+ * Measure a bond length from caller-supplied coordinates.
+ *
+ * `coords_json` is `[[x,y,z], ...]` in molecule atom order. Unlike the
+ * legacy SMILES convenience function, this does not generate a new
+ * conformer, so callers can measure an imported or previously edited one.
+ */
+export function get_bond_length_from_coords_json(mol: MolHandle, coords_json: string, i: number, j: number): number;
+
 /**
  * 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.
@@ -1391,6 +1460,11 @@ export function get_bond_length_json(smiles: string, a: number, b: number): numb
  */
 export function get_descriptors_json(mol: MolHandle): string;
 
+/**
+ * Measure dihedral i-j-k-l in degrees from caller-supplied coordinates.
+ */
+export function get_dihedral_from_coords_json(mol: MolHandle, coords_json: string, i: number, j: number, k: number, l: number): number;
+
 /**
  * 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.
@@ -2647,6 +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;
 
@@ -2780,6 +2856,29 @@ export function semantic_expand_json_with_limits(base_smiles: string, model_json
  */
 export function semantic_model_json(model_json: string): string;
 
+/**
+ * Set angle i-j-k in degrees and return updated coordinate JSON.
+ *
+ * Atoms i and j stay fixed; atom k and its side of the graph rotate
+ * together. If both angle bonds belong to a ring the operation is rejected.
+ */
+export function set_bond_angle_from_coords_json(mol: MolHandle, coords_json: string, i: number, j: number, k: number, angle_deg: number): string;
+
+/**
+ * Set bond length i-j in caller-supplied coordinates and return updated JSON.
+ *
+ * Atom i stays fixed; atom j and its side of the graph move together. Ring
+ * bonds are rejected, following RDKit's `SetBondLength` contract.
+ */
+export function set_bond_length_from_coords_json(mol: MolHandle, coords_json: string, i: number, j: number, length: number): string;
+
+/**
+ * Set dihedral i-j-k-l in degrees and return updated coordinate JSON.
+ *
+ * The central j-k bond must exist and must not belong to a ring.
+ */
+export function set_dihedral_from_coords_json(mol: MolHandle, coords_json: string, i: number, j: number, k: number, l: number, angle_deg: number): string;
+
 /**
  * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
  * Rotates the D-side subtree around the B—C bond.
@@ -3251,11 +3350,14 @@ export interface InitOutput {
     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 brenk_matches_json: (a: number) => [number, number];
+    readonly brenk_report_json: (a: number, b: number) => [number, 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];
     readonly canonical_tautomer: (a: number) => number;
     readonly canonical_tautomer_with_blocked_atoms_json: (a: number, b: number, c: number) => [number, number];
+    readonly canonicalize_conformer_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number, number];
     readonly canonicalize_smiles_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly cdxml_document_from_json_v1: (a: number, b: number) => [number, number, number, number];
     readonly cdxml_document_json: (a: number, b: number) => [number, number, number, number];
@@ -3269,6 +3371,7 @@ export interface InitOutput {
     readonly cip_unresolved_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 compute_canonical_transform_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: 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;
@@ -3316,6 +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];
@@ -3340,10 +3444,13 @@ export interface InitOutput {
     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];
+    readonly get_bond_angle_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number];
     readonly get_bond_between: (a: number, b: number, c: number) => [number, number];
     readonly get_bond_info: (a: number, b: number) => [number, number];
+    readonly get_bond_length_from_coords_json: (a: number, b: number, c: number, d: number, e: number) => [number, number, number];
     readonly get_bond_length_json: (a: number, b: number, c: number, d: number) => number;
     readonly get_descriptors_json: (a: number) => [number, number];
+    readonly get_dihedral_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number];
     readonly get_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number) => any;
     readonly get_rdkit_descriptors_json: (a: number) => [number, number];
     readonly getaway_descriptors_json: (a: number) => [number, number];
@@ -3423,11 +3530,13 @@ export interface InitOutput {
     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_atom_count: (a: number) => number;
     readonly molhandle_atom_pseudo_labels_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_brenk_passes: (a: number) => number;
     readonly molhandle_caco2_permeability: (a: number) => number;
     readonly molhandle_canonical_smiles: (a: number) => [number, number];
     readonly molhandle_chi0: (a: number) => number;
@@ -3445,6 +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];
@@ -3598,6 +3708,9 @@ export interface InitOutput {
     readonly semantic_expand_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly semantic_expand_json_with_limits: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
     readonly semantic_model_json: (a: number, b: number) => [number, number, number, number];
+    readonly set_bond_angle_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number, number];
+    readonly set_bond_length_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
+    readonly set_dihedral_from_coords_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
     readonly set_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number, number];
     readonly shape_descriptors_json: (a: number) => [number, number];
     readonly slogp_vsa_json: (a: number) => [number, number];
@@ -3616,6 +3729,7 @@ export interface InitOutput {
     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 start: () => void;
     readonly stereo_parent_json: (a: number) => [number, number];
     readonly stoichiometry_report_json: (a: number, b: number) => [number, number];
     readonly super_parent_json: (a: number, b: number, c: number, d: number, e: bigint) => [number, number];
@@ -3662,8 +3776,6 @@ export interface InitOutput {
     readonly xlogp3_json: (a: number) => [number, number];
     readonly xlogp3_per_atom_json: (a: number) => [number, number];
     readonly xyz_frames_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
-    readonly molhandle_atom_count: (a: 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 __externref_table_alloc: () => number;

package/chematic_wasm.js

@@ -104,7 +104,7 @@ export class ConformerHandle {
         const ret = wasm.conformerhandle_get_conformer_pdb(this.__wbg_ptr, idx);
         let v1;
         if (ret[0] !== 0) {
-            v1 = getStringFromWasm0(ret[0], ret[1]).slice();
+            v1 = getStringFromWasm0(ret[0], ret[1]);
             wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
         }
         return v1;
@@ -456,6 +456,18 @@ export class MolHandle {
         const ret = wasm.molhandle_bond_count(this.__wbg_ptr);
         return ret >>> 0;
     }
+    /**
+     * Returns `true` if the molecule has no Brenk structural alerts.
+     *
+     * This uses the same conservative core contract as the Rust, Python, and
+     * MCP bindings: an alert-search budget exhaustion is not reported as a
+     * clean pass.
+     * @returns {boolean}
+     */
+    brenk_passes() {
+        const ret = wasm.molhandle_brenk_passes(this.__wbg_ptr);
+        return ret !== 0;
+    }
     /**
      * Palm (1997) Caco-2 intestinal permeability (logPCaco2).
      * > −5.5 = high permeability.
@@ -623,6 +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}
@@ -2039,6 +2078,59 @@ export function boiled_egg_json(smiles) {
     }
 }
 
+/**
+ * Brenk structural-alert identifiers matched by `mol` as a JSON array.
+ *
+ * Returns `[]` when no alerts fire. Identifiers and ordering are identical to
+ * the Rust, Python, and MCP bindings.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function brenk_matches_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.brenk_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 `smiles` and return a complete Brenk report as JSON.
+ *
+ * The stable result shape is `{"passes":boolean,"alerts":string[]}`.
+ * Invalid or oversized SMILES throw the same ordinary JavaScript input error
+ * as `parse_smiles`; this function never converts invalid input into a clean
+ * report.
+ * @param {string} smiles
+ * @returns {string}
+ */
+export function brenk_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.brenk_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);
+    }
+}
+
 /**
  * Number of BRICS fragments produced by fragmenting the molecule.
  *
@@ -2152,6 +2244,39 @@ export function canonical_tautomer_with_blocked_atoms_json(mol, blocked_atom_ind
     }
 }
 
+/**
+ * Return caller coordinates centered and aligned to their principal axes.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {string | null | undefined} center_json
+ * @param {boolean} normalize_covar
+ * @param {boolean} ignore_hs
+ * @returns {string}
+ */
+export function canonicalize_conformer_from_coords_json(mol, coords_json, center_json, normalize_covar, ignore_hs) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        var ptr1 = isLikeNone(center_json) ? 0 : passStringToWasm0(center_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        var len1 = WASM_VECTOR_LEN;
+        const ret = wasm.canonicalize_conformer_from_coords_json(mol.__wbg_ptr, ptr0, len0, ptr1, len1, normalize_covar, ignore_hs);
+        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);
+    }
+}
+
 /**
  * Canonicalize a bounded delimiter-separated SMILES batch.
  *
@@ -2523,6 +2648,42 @@ export function compare_molecules_json(smiles1, smiles2) {
     }
 }
 
+/**
+ * Compute an RDKit-style principal-axis transform from caller coordinates.
+ *
+ * Returns a row-major 4x4 JSON matrix. `center_json`, when supplied, must be
+ * `[x,y,z]`; otherwise the selected-atom centroid is used.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {string | null | undefined} center_json
+ * @param {boolean} normalize_covar
+ * @param {boolean} ignore_hs
+ * @returns {string}
+ */
+export function compute_canonical_transform_from_coords_json(mol, coords_json, center_json, normalize_covar, ignore_hs) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        var ptr1 = isLikeNone(center_json) ? 0 : passStringToWasm0(center_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        var len1 = WASM_VECTOR_LEN;
+        const ret = wasm.compute_canonical_transform_from_coords_json(mol.__wbg_ptr, ptr0, len0, ptr1, len1, normalize_covar, ignore_hs);
+        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);
+    }
+}
+
 /**
  * Generate multiple conformers with RMSD-based pruning.
  * Returns JSON: `{"conformers": [[[x,y,z],...], ...], "count": int}`.
@@ -3101,6 +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
@@ -3699,6 +3886,26 @@ export function get_atom_info(mol, idx) {
     }
 }
 
+/**
+ * Measure angle i-j-k in degrees from caller-supplied coordinates.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {number} i
+ * @param {number} j
+ * @param {number} k
+ * @returns {number}
+ */
+export function get_bond_angle_from_coords_json(mol, coords_json, i, j, k) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_bond_angle_from_coords_json(mol.__wbg_ptr, ptr0, len0, i, j, k);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0];
+}
+
 /**
  * Return bond information as a JSON object, looked up by the two bonded atom indices.
  *
@@ -3751,6 +3958,29 @@ export function get_bond_info(mol, idx) {
     }
 }
 
+/**
+ * Measure a bond length from caller-supplied coordinates.
+ *
+ * `coords_json` is `[[x,y,z], ...]` in molecule atom order. Unlike the
+ * legacy SMILES convenience function, this does not generate a new
+ * conformer, so callers can measure an imported or previously edited one.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {number} i
+ * @param {number} j
+ * @returns {number}
+ */
+export function get_bond_length_from_coords_json(mol, coords_json, i, j) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_bond_length_from_coords_json(mol.__wbg_ptr, ptr0, len0, i, j);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0];
+}
+
 /**
  * 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.
@@ -3798,6 +4028,27 @@ export function get_descriptors_json(mol) {
     }
 }
 
+/**
+ * Measure dihedral i-j-k-l in degrees from caller-supplied coordinates.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {number} i
+ * @param {number} j
+ * @param {number} k
+ * @param {number} l
+ * @returns {number}
+ */
+export function get_dihedral_from_coords_json(mol, coords_json, i, j, k, l) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_dihedral_from_coords_json(mol.__wbg_ptr, ptr0, len0, i, j, k, l);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0];
+}
+
 /**
  * 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.
@@ -6255,7 +6506,7 @@ export function pqr_infer_element(group_pdb, res_name, atom_name) {
     const ret = wasm.pqr_infer_element(ptr0, len0, ptr1, len1, ptr2, len2);
     let v4;
     if (ret[0] !== 0) {
-        v4 = getStringFromWasm0(ret[0], ret[1]).slice();
+        v4 = getStringFromWasm0(ret[0], ret[1]);
         wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
     }
     return v4;
@@ -7118,6 +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}
@@ -7535,6 +7788,110 @@ export function semantic_model_json(model_json) {
     }
 }
 
+/**
+ * Set angle i-j-k in degrees and return updated coordinate JSON.
+ *
+ * Atoms i and j stay fixed; atom k and its side of the graph rotate
+ * together. If both angle bonds belong to a ring the operation is rejected.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {number} i
+ * @param {number} j
+ * @param {number} k
+ * @param {number} angle_deg
+ * @returns {string}
+ */
+export function set_bond_angle_from_coords_json(mol, coords_json, i, j, k, angle_deg) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.set_bond_angle_from_coords_json(mol.__wbg_ptr, ptr0, len0, i, j, k, 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);
+    }
+}
+
+/**
+ * Set bond length i-j in caller-supplied coordinates and return updated JSON.
+ *
+ * Atom i stays fixed; atom j and its side of the graph move together. Ring
+ * bonds are rejected, following RDKit's `SetBondLength` contract.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {number} i
+ * @param {number} j
+ * @param {number} length
+ * @returns {string}
+ */
+export function set_bond_length_from_coords_json(mol, coords_json, i, j, length) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.set_bond_length_from_coords_json(mol.__wbg_ptr, ptr0, len0, i, j, length);
+        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);
+    }
+}
+
+/**
+ * Set dihedral i-j-k-l in degrees and return updated coordinate JSON.
+ *
+ * The central j-k bond must exist and must not belong to a ring.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {number} i
+ * @param {number} j
+ * @param {number} k
+ * @param {number} l
+ * @param {number} angle_deg
+ * @returns {string}
+ */
+export function set_dihedral_from_coords_json(mol, coords_json, i, j, k, l, angle_deg) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.set_dihedral_from_coords_json(mol.__wbg_ptr, ptr0, len0, i, j, k, l, 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);
+    }
+}
+
 /**
  * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
  * Rotates the D-side subtree around the B—C bond.
@@ -8959,11 +9316,11 @@ export function xyz_frames_batch_json(text, offset, batch_size) {
 function __wbg_get_imports() {
     const import0 = {
         __proto__: null,
-        __wbg___wbindgen_is_undefined_35bb9f4c7fd651d5: function(arg0) {
+        __wbg___wbindgen_is_undefined_8865fb403f8fe9d8: function(arg0) {
             const ret = arg0 === undefined;
             return ret;
         },
-        __wbg___wbindgen_string_get_d109740c0d18f4d7: function(arg0, arg1) {
+        __wbg___wbindgen_string_get_0380ccaa2f57f0d9: 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);
@@ -8971,18 +9328,18 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_throw_9c31b086c2b26051: function(arg0, arg1) {
+        __wbg___wbindgen_throw_41e9ee4f547fc59a: function(arg0, arg1) {
             throw new Error(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_error_f085d7e62279b703: function(arg0) {
+        __wbg_error_c9cf3fc2064683a9: function(arg0) {
             console.error(arg0);
         },
-        __wbg_new_from_slice_02962bf7778cf945: function(arg0, arg1) {
-            const ret = new Float64Array(getArrayF64FromWasm0(arg0, arg1));
+        __wbg_new_from_slice_37a3c3a194266cb8: function(arg0, arg1) {
+            const ret = new Uint32Array(getArrayU32FromWasm0(arg0, arg1));
             return ret;
         },
-        __wbg_new_from_slice_f92bf65e9a895613: function(arg0, arg1) {
-            const ret = new Uint32Array(getArrayU32FromWasm0(arg0, arg1));
+        __wbg_new_from_slice_f545fd22ddc142b8: function(arg0, arg1) {
+            const ret = new Float64Array(getArrayF64FromWasm0(arg0, arg1));
             return ret;
         },
         __wbg_now_e7c6795a7f81e10f: function(arg0) {
@@ -8993,28 +9350,28 @@ function __wbg_get_imports() {
             const ret = arg0.performance;
             return ret;
         },
-        __wbg_static_accessor_GLOBAL_THIS_02344c9b09eb08a9: function() {
-            const ret = typeof globalThis === 'undefined' ? null : globalThis;
+        __wbg_static_accessor_GLOBAL_266715b9d96ba635: function() {
+            const ret = typeof global === 'undefined' ? null : global;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbg_static_accessor_GLOBAL_ac6d4ac874d5cd54: function() {
-            const ret = typeof global === 'undefined' ? null : global;
+        __wbg_static_accessor_GLOBAL_THIS_10fb7dc1ae063179: function() {
+            const ret = typeof globalThis === 'undefined' ? null : globalThis;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbg_static_accessor_SELF_9b2406c23aeb2023: function() {
+        __wbg_static_accessor_SELF_0b583911f537483a: function() {
             const ret = typeof self === 'undefined' ? null : self;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbg_static_accessor_WINDOW_b34d2126934e16ba: function() {
+        __wbg_static_accessor_WINDOW_d7f903d1508cbdc4: function() {
             const ret = typeof window === 'undefined' ? null : window;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbindgen_cast_0000000000000001: function(arg0) {
+        __wbindgen_generic_0000000000000001: function(arg0) {
             // Cast intrinsic for `F64 -> Externref`.
             const ret = arg0;
             return ret;
         },
-        __wbindgen_cast_0000000000000002: function(arg0, arg1) {
+        __wbindgen_generic_0000000000000002: function(arg0, arg1) {
             // Cast intrinsic for `Ref(String) -> Externref`.
             const ret = getStringFromWasm0(arg0, arg1);
             return ret;
@@ -9221,11 +9578,15 @@ function __wbg_finalize_init(instance, module) {
 
 async function __wbg_load(module, imports) {
     if (typeof Response === 'function' && module instanceof Response) {
+        if (!module.ok) {
+            throw new Error(`failed to fetch Wasm: ${module.status} ${module.statusText} fetching '${module.url}'`);
+        }
+
         if (typeof WebAssembly.instantiateStreaming === 'function') {
             try {
                 return await WebAssembly.instantiateStreaming(module, imports);
             } catch (e) {
-                const validResponse = module.ok && expectedResponseType(module.type);
+                const validResponse = 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);

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": "1.1.1",
+  "version": "1.1.3",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",