@kent-tokyo/chematic 1.0.11 → 1.0.12

package/chematic_wasm.d.ts

@@ -2237,6 +2237,17 @@ export function rgroup_decompose_json(smiles_json: string, core_smarts: string):
  */
 export function ring_families_json(mol: MolHandle): string;
 
+/**
+ * Parse and serialize a V3000 block while preserving opaque V3000 metadata.
+ *
+ * Unlike the topology-only [`mol_from_v3000_block`] + [`to_mol_v3000_block`]
+ * pair, this explicit round-trip API retains `SGROUP` logical lines and
+ * `COLLECTION` stereo groups. SGROUP semantics remain opaque until the core
+ * molecule model grows a typed representation; the API therefore preserves
+ * bytes at the logical-line level without claiming polymer/query semantics.
+ */
+export function roundtrip_mol_v3000_block(block: string): string;
+
 /**
  * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
  *
@@ -2345,6 +2356,11 @@ export function semantic_apply_json_command(model_json: string, command_json: st
  */
 export function semantic_expand_json(base_smiles: string, model_json: string): string;
 
+/**
+ * Expand a validated semantic model with explicit finite atom/repeat budgets.
+ */
+export function semantic_expand_json_with_limits(base_smiles: string, model_json: string, max_atoms: number, max_repeat_count: number): string;
+
 /**
  * Validate and normalize a typed Markush/polymer semantic model JSON.
  */
@@ -2472,6 +2488,14 @@ export function start(): void;
  */
 export function stereo_parent_json(mol: MolHandle): string;
 
+/**
+ * Analyze a rich reaction document's explicit atom/isotope inventory and
+ * formal charges. The returned JSON includes evidence scope, per-step
+ * diagnostics, and a status that does not imply chemical completeness.
+ * Returns `error:<msg>` when the document or a component is invalid.
+ */
+export function stoichiometry_report_json(document_json: string): string;
+
 /**
  * Compute the composed Super Parent with explicit resource limits.
  */
@@ -2936,7 +2960,6 @@ 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_bbb_passes: (a: number) => number;
     readonly molhandle_bbb_score: (a: number) => number;
     readonly molhandle_bertz_ct: (a: number) => number;
@@ -3054,6 +3077,7 @@ export interface InitOutput {
     readonly retro_disconnect_json: (a: number, b: number, c: number, d: number) => [number, number, 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 roundtrip_mol_v3000_block: (a: number, b: number) => [number, number, number, number];
     readonly run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly rxn_document_from_rxn: (a: number, b: number) => [number, number, number, number];
     readonly rxn_document_to_rxn: (a: number, b: number) => [number, number, number, number];
@@ -3065,6 +3089,7 @@ export interface InitOutput {
     readonly sdf_to_smiles_json: (a: number, b: number) => [number, number];
     readonly semantic_apply_json_command: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     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_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];
@@ -3079,8 +3104,8 @@ 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];
     readonly super_parent_report_json: (a: number, b: number, c: number, d: number, e: bigint) => [number, number];
     readonly tanimoto_atom_pair: (a: number, b: number) => number;
@@ -3121,6 +3146,8 @@ 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]);
+            v1 = getStringFromWasm0(ret[0], ret[1]).slice();
             wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
         }
         return v1;
@@ -5055,7 +5055,7 @@ 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]);
+        v4 = getStringFromWasm0(ret[0], ret[1]).slice();
         wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
     }
     return v4;
@@ -5635,6 +5635,38 @@ export function ring_families_json(mol) {
     }
 }
 
+/**
+ * Parse and serialize a V3000 block while preserving opaque V3000 metadata.
+ *
+ * Unlike the topology-only [`mol_from_v3000_block`] + [`to_mol_v3000_block`]
+ * pair, this explicit round-trip API retains `SGROUP` logical lines and
+ * `COLLECTION` stereo groups. SGROUP semantics remain opaque until the core
+ * molecule model grows a typed representation; the API therefore preserves
+ * bytes at the logical-line level without claiming polymer/query semantics.
+ * @param {string} block
+ * @returns {string}
+ */
+export function roundtrip_mol_v3000_block(block) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.roundtrip_mol_v3000_block(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);
+    }
+}
+
 /**
  * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
  *
@@ -5961,6 +5993,37 @@ export function semantic_expand_json(base_smiles, model_json) {
     }
 }
 
+/**
+ * Expand a validated semantic model with explicit finite atom/repeat budgets.
+ * @param {string} base_smiles
+ * @param {string} model_json
+ * @param {number} max_atoms
+ * @param {number} max_repeat_count
+ * @returns {string}
+ */
+export function semantic_expand_json_with_limits(base_smiles, model_json, max_atoms, max_repeat_count) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(base_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(model_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.semantic_expand_json_with_limits(ptr0, len0, ptr1, len1, max_atoms, max_repeat_count);
+        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);
+    }
+}
+
 /**
  * Validate and normalize a typed Markush/polymer semantic model JSON.
  * @param {string} model_json
@@ -6378,6 +6441,29 @@ export function stereo_parent_json(mol) {
     }
 }
 
+/**
+ * Analyze a rich reaction document's explicit atom/isotope inventory and
+ * formal charges. The returned JSON includes evidence scope, per-step
+ * diagnostics, and a status that does not imply chemical completeness.
+ * Returns `error:<msg>` when the document or a component is invalid.
+ * @param {string} document_json
+ * @returns {string}
+ */
+export function stoichiometry_report_json(document_json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.stoichiometry_report_json(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);
+    }
+}
+
 /**
  * Compute the composed Super Parent with explicit resource limits.
  * @param {MolHandle} mol
@@ -7289,11 +7375,11 @@ export function xyz_frames_batch_json(text, offset, batch_size) {
 function __wbg_get_imports() {
     const import0 = {
         __proto__: null,
-        __wbg___wbindgen_is_undefined_8c687d0b90d5b524: function(arg0) {
+        __wbg___wbindgen_is_undefined_35bb9f4c7fd651d5: function(arg0) {
             const ret = arg0 === undefined;
             return ret;
         },
-        __wbg___wbindgen_string_get_92ab86bb19cbc12f: function(arg0, arg1) {
+        __wbg___wbindgen_string_get_d109740c0d18f4d7: 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);
@@ -7301,17 +7387,17 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_throw_5d9e815e6fdf150f: function(arg0, arg1) {
+        __wbg___wbindgen_throw_9c31b086c2b26051: function(arg0, arg1) {
             throw new Error(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_error_756c5934221e6fee: function(arg0) {
+        __wbg_error_f085d7e62279b703: function(arg0) {
             console.error(arg0);
         },
-        __wbg_new_from_slice_3b4c7f1456059f80: function(arg0, arg1) {
+        __wbg_new_from_slice_02962bf7778cf945: function(arg0, arg1) {
             const ret = new Float64Array(getArrayF64FromWasm0(arg0, arg1));
             return ret;
         },
-        __wbg_new_from_slice_a500ec81601be48f: function(arg0, arg1) {
+        __wbg_new_from_slice_f92bf65e9a895613: function(arg0, arg1) {
             const ret = new Uint32Array(getArrayU32FromWasm0(arg0, arg1));
             return ret;
         },
@@ -7323,28 +7409,28 @@ function __wbg_get_imports() {
             const ret = arg0.performance;
             return ret;
         },
-        __wbg_static_accessor_GLOBAL_8eb4cd83130a11a0: function() {
-            const ret = typeof global === 'undefined' ? null : global;
+        __wbg_static_accessor_GLOBAL_THIS_02344c9b09eb08a9: function() {
+            const ret = typeof globalThis === 'undefined' ? null : globalThis;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbg_static_accessor_GLOBAL_THIS_1e7044f654e934db: function() {
-            const ret = typeof globalThis === 'undefined' ? null : globalThis;
+        __wbg_static_accessor_GLOBAL_ac6d4ac874d5cd54: function() {
+            const ret = typeof global === 'undefined' ? null : global;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbg_static_accessor_SELF_d8b50611246a6d92: function() {
+        __wbg_static_accessor_SELF_9b2406c23aeb2023: function() {
             const ret = typeof self === 'undefined' ? null : self;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbg_static_accessor_WINDOW_fd0bc376bf0f8b42: function() {
+        __wbg_static_accessor_WINDOW_b34d2126934e16ba: function() {
             const ret = typeof window === 'undefined' ? null : window;
             return isLikeNone(ret) ? 0 : addToExternrefTable0(ret);
         },
-        __wbindgen_generic_0000000000000001: function(arg0) {
+        __wbindgen_cast_0000000000000001: function(arg0) {
             // Cast intrinsic for `F64 -> Externref`.
             const ret = arg0;
             return ret;
         },
-        __wbindgen_generic_0000000000000002: function(arg0, arg1) {
+        __wbindgen_cast_0000000000000002: function(arg0, arg1) {
             // Cast intrinsic for `Ref(String) -> Externref`.
             const ret = getStringFromWasm0(arg0, arg1);
             return ret;
@@ -7539,15 +7625,11 @@ 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 = expectedResponseType(module.type);
+                const validResponse = module.ok && 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": "1.0.11",
+  "version": "1.0.12",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",