@kent-tokyo/chematic 1.0.11 → 1.0.13

package/README.md

@@ -29,7 +29,8 @@ npm install @kent-tokyo/chematic
   deterministic input indices and partial/complete status; bounded malformed
   XYZ frames are grouped inline as rejected records when a later count-line
   boundary is recoverable (core file-backed readers remain fail-stop)
-- Bounded topology parsing for CML, ChemicalJSON (`mol_from_cjson`), MolJSON,
+- Bounded topology parsing for CML (`mol_from_cml_strict` provides the opt-in
+  non-empty, balanced, single-root boundary), ChemicalJSON (`mol_from_cjson`), MolJSON,
   CDXML, MOL2, and PDB/mmCIF
 - PDBx/mmCIF, PQR, QCSchema JSON, ORCA input/output, Gaussian Cube, OpenDX,
   and LAMMPS data/dump I/O (JSON-based bindings; see `format_io.rs`)
@@ -167,12 +168,54 @@ portable across native and `wasm32-unknown-unknown`
 precision across every JS engine, only that the value is finite, non-negative,
 and enforced correctly on all of them.
 
+## V3000 SGROUP syntax view
+
+`v3000_sgroups_json(block)` exposes bounded, typed SGROUP syntax without
+expanding polymer or Markush semantics. It preserves source order for unknown
+attributes and returns `kindToken` for unknown group kinds. Group IDs, parent
+references, atom references, and grouped-field counts are validated before
+JSON is returned.
+
+```js
+const groups = JSON.parse(v3000_sgroups_json(v3000Block));
+// [{ id, kind, parentId, atomIds, attributes, kindToken? }]
+```
+
+This is a syntax-level API; it does not claim polymer expansion, Markush
+interpretation, or cross-engine semantic compatibility.
+
 ## Bundle Size
 
-The optimized v1.0.10 candidate artifact was measured at **3.73 MB raw / 1.36 MB gzip**. Bundle size depends on features and toolchain; see [`benchmarks/2026-09-09-wasm-size-v1.0.10.md`](../../benchmarks/2026-09-09-wasm-size-v1.0.10.md) for exact tools, digest, and reproduction steps.
+The optimized v1.0.12 artifact was measured at **3.93 MB raw / 1.43 MB gzip**. Bundle size depends on features and toolchain; see [`benchmarks/2026-09-11-official-rdkit-js-v1.0.12.md`](../../benchmarks/2026-09-11-official-rdkit-js-v1.0.12.md) for exact tools, digest, and reproduction steps.
 
 PNG rasterization (`tiny_skia`) is excluded from the WASM build — use SVG output instead. All SVG depiction APIs remain fully available.
 
+## Versioned document binding boundary
+
+The `*_v1` document APIs provide a stable JSON boundary for downstream editors:
+
+```js
+const parsed = JSON.parse(reaction_document_json_v1(JSON.stringify(document)));
+const edited = JSON.parse(edit_reaction_document_json_v1(
+  JSON.stringify(parsed),
+  JSON.stringify({ kind: "set_step_condition", step_id: "step-1", key: "temperature", value: "25 C" }),
+));
+
+const cdxmlEnvelope = JSON.parse(cdxml_document_json_v1(cdxml));
+const cdxmlAgain = cdxml_document_from_json_v1(JSON.stringify(cdxmlEnvelope));
+```
+
+`cdxml_document_json_v1` retains the exact `source` string and returns a
+structural `document` summary with opaque objects and `diagnostics`. Use
+`edit_cdxml_document_json_v1` for bounded page/object edits; it reparses the
+result before returning. Errors are JSON-shaped with stable `code`, `path`, and
+`message` fields (`malformed_input`, `resource_limit`,
+`unsupported_construct`, `lossy_conversion`, or `serialization_error`).
+`reaction_document_to_rxn_v1` and `cdxml_document_projection_json_v1` reject
+lossy legacy projections with `lossy_conversion` diagnostics. These APIs do not claim
+mechanism correctness, product prediction, complete stoichiometry, or full
+ChemDraw/RXN compatibility.
+
 ## Building from source
 
 ```sh

package/chematic_wasm.d.ts

@@ -593,6 +593,11 @@ export function canonical_tautomer_with_blocked_atoms_json(mol: MolHandle, block
  */
 export function canonicalize_smiles_batch_json(smiles_batch: string, delimiter: string): string;
 
+/**
+ * Validate a versioned CDXML JSON envelope and serialize its exact source.
+ */
+export function cdxml_document_from_json_v1(document_json: string): string;
+
 /**
  * Parse a CDXML document while preserving page and presentation objects.
  * The returned JSON contains an opaque `raw_xml` for each object so unknown
@@ -600,6 +605,22 @@ export function canonicalize_smiles_batch_json(smiles_batch: string, delimiter:
  */
 export function cdxml_document_json(cdxml: string): string;
 
+/**
+ * Return a loss-preserving, versioned JSON envelope for a CDXML document.
+ *
+ * `source` is retained for exact re-serialization; `document` is the stable
+ * structural summary used by editors. Unknown objects remain in the summary
+ * and are listed under `document.diagnostics`.
+ */
+export function cdxml_document_json_v1(cdxml: string): string;
+
+/**
+ * Project a CDXML document to its first molecular fragment only when no
+ * presentation data would be lost. Unknown/presentation objects are reported
+ * as an explicit lossy conversion instead of being silently dropped.
+ */
+export function cdxml_document_projection_json_v1(cdxml: string): string;
+
 /**
  * Parse all molecular fragments from a CDXML string.
  *
@@ -872,6 +893,18 @@ export function ecfp_bitvec_custom(mol: MolHandle, radius: number, nbits: number
  */
 export function edit_cdxml_document_json(cdxml: string, edit_json: string): string;
 
+/**
+ * Apply a bounded CDXML edit to a versioned JSON envelope and return the
+ * updated envelope. The source is reparsed after editing, so paths and
+ * diagnostics cannot drift from the returned document summary.
+ */
+export function edit_cdxml_document_json_v1(document_json: string, edit_json: string): string;
+
+/**
+ * Apply a bounded, stable-ID reaction-document edit and return canonical JSON.
+ */
+export function edit_reaction_document_json_v1(document_json: string, edit_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
@@ -1456,7 +1489,7 @@ export function minimize_mmff94_lbfgs_json(mol: MolHandle, max_iter: number): st
  * `coords_json` — JSON array of `[x,y,z]` arrays (Å), one per atom.
  * `max_iter` — maximum iterations (0 = default 500).
  *
- * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool, "sound":bool, "worst_bond_length":float}`
+ * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool, "sound":bool, "worst_bond_length":float, "rejected_unsound_step":bool}`
  * or `{"error":"<msg>"}` on failure. `sound` is all-finite coordinates and
  * no bond stretched past a sane covalent-bond length — independent of
  * `converged`, since steepest descent often reports `converged:false` on
@@ -1619,6 +1652,14 @@ export function mol_from_cjson(json: string): MolHandle;
  */
 export function mol_from_cml(cml: string): MolHandle;
 
+/**
+ * Parse a structurally valid, non-empty CML string into a `MolHandle`.
+ *
+ * This opt-in strict boundary rejects missing/empty molecules and malformed
+ * XML while `mol_from_cml` retains its historical lenient behavior.
+ */
+export function mol_from_cml_strict(cml: string): MolHandle;
+
 /**
  * Parse a Gaussian Cube file and return a `MolHandle` (topology only --
  * element list, no bonds; Cube carries no bond table). Use
@@ -2167,6 +2208,21 @@ export function rdkit_rdk_bitvec(mol: MolHandle): Uint8Array;
  */
 export function rdkit_torsion_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * Validate and deterministically serialize a rich reaction document JSON.
+ *
+ * This is the versioned JSON boundary for WASM consumers. It preserves IDs,
+ * metadata, and provenance, and rejects malformed documents before returning
+ * JSON. Use [`edit_reaction_document_json_v1`] for bounded ID-addressed edits.
+ */
+export function reaction_document_json_v1(document_json: string): string;
+
+/**
+ * Convert a rich reaction document to legacy RXN V2000 with structured loss
+ * reporting. A lossy projection is never returned as if it were complete.
+ */
+export function reaction_document_to_rxn_v1(document_json: string): string;
+
 /**
  * Check whether a reaction SMILES matches a reaction SMARTS query.
  *
@@ -2237,6 +2293,17 @@ 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 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 polymer/query expansion is still out of
+ * scope, but the typed syntax view is available through
+ * [`v3000_sgroups_json`].
+ */
+export function roundtrip_mol_v3000_block(block: string): string;
+
 /**
  * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
  *
@@ -2345,6 +2412,11 @@ 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 +2544,14 @@ 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.
  */
@@ -2631,6 +2711,8 @@ export function topo_path_bitvec(mol: MolHandle): Uint8Array;
  */
 export function torsion_bitvec(mol: MolHandle): Uint8Array;
 
+export function v3000_sgroups_json(block: string): string;
+
 /**
  * Validate a vendor-neutral NMR spectrum JSON document without parsing a
  * vendor-specific raw file or predicting peaks.
@@ -2782,7 +2864,10 @@ export interface InitOutput {
     readonly canonical_tautomer: (a: number) => number;
     readonly canonical_tautomer_with_blocked_atoms_json: (a: number, b: number, c: 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];
+    readonly cdxml_document_json_v1: (a: number, b: number) => [number, number, number, number];
+    readonly cdxml_document_projection_json_v1: (a: number, b: number) => [number, number, number, number];
     readonly cdxml_to_smiles_json: (a: number, b: number) => [number, number, number, number];
     readonly charge_parent_json: (a: number) => [number, number];
     readonly chematic_version: () => [number, number];
@@ -2835,6 +2920,8 @@ export interface InitOutput {
     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 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 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];
@@ -2912,6 +2999,7 @@ export interface InitOutput {
     readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
     readonly mol_from_cjson: (a: number, b: number) => [number, number, number];
     readonly mol_from_cml: (a: number, b: number) => [number, number, number];
+    readonly mol_from_cml_strict: (a: number, b: number) => [number, number, number];
     readonly mol_from_cube: (a: number, b: number) => [number, number, number];
     readonly mol_from_extxyz: (a: number, b: number) => [number, number, number];
     readonly mol_from_mmcif: (a: number, b: number) => [number, number, number];
@@ -2936,7 +3024,6 @@ 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;
@@ -3049,11 +3136,14 @@ export interface InitOutput {
     readonly rdkit_path_bitvec: (a: number) => [number, number];
     readonly rdkit_rdk_bitvec: (a: number) => [number, number];
     readonly rdkit_torsion_bitvec: (a: number) => [number, number];
+    readonly reaction_document_json_v1: (a: number, b: number) => [number, number, number, number];
+    readonly reaction_document_to_rxn_v1: (a: number, b: number) => [number, number, number, number];
     readonly reaction_smarts_match: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly remove_hydrogens: (a: number) => number;
     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 +3155,7 @@ 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 +3170,8 @@ 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;
@@ -3104,6 +3195,7 @@ export interface InitOutput {
     readonly to_xyz: (a: number) => [number, number];
     readonly topo_path_bitvec: (a: number) => [number, number];
     readonly torsion_bitvec: (a: number) => [number, number];
+    readonly v3000_sgroups_json: (a: number, b: number) => [number, number, number, number];
     readonly validate_nmr_spectrum_json: (a: number, b: number) => [number, number];
     readonly virtual_screen_ecfp4_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly whim_descriptors_json: (a: number) => [number, number];
@@ -3121,6 +3213,8 @@ 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;
@@ -1401,6 +1401,32 @@ export function canonicalize_smiles_batch_json(smiles_batch, delimiter) {
     }
 }
 
+/**
+ * Validate a versioned CDXML JSON envelope and serialize its exact source.
+ * @param {string} document_json
+ * @returns {string}
+ */
+export function cdxml_document_from_json_v1(document_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.cdxml_document_from_json_v1(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);
+    }
+}
+
 /**
  * Parse a CDXML document while preserving page and presentation objects.
  * The returned JSON contains an opaque `raw_xml` for each object so unknown
@@ -1429,6 +1455,64 @@ export function cdxml_document_json(cdxml) {
     }
 }
 
+/**
+ * Return a loss-preserving, versioned JSON envelope for a CDXML document.
+ *
+ * `source` is retained for exact re-serialization; `document` is the stable
+ * structural summary used by editors. Unknown objects remain in the summary
+ * and are listed under `document.diagnostics`.
+ * @param {string} cdxml
+ * @returns {string}
+ */
+export function cdxml_document_json_v1(cdxml) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(cdxml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.cdxml_document_json_v1(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);
+    }
+}
+
+/**
+ * Project a CDXML document to its first molecular fragment only when no
+ * presentation data would be lost. Unknown/presentation objects are reported
+ * as an explicit lossy conversion instead of being silently dropped.
+ * @param {string} cdxml
+ * @returns {string}
+ */
+export function cdxml_document_projection_json_v1(cdxml) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(cdxml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.cdxml_document_projection_json_v1(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);
+    }
+}
+
 /**
  * Parse all molecular fragments from a CDXML string.
  *
@@ -2131,6 +2215,66 @@ export function edit_cdxml_document_json(cdxml, edit_json) {
     }
 }
 
+/**
+ * Apply a bounded CDXML edit to a versioned JSON envelope and return the
+ * updated envelope. The source is reparsed after editing, so paths and
+ * diagnostics cannot drift from the returned document summary.
+ * @param {string} document_json
+ * @param {string} edit_json
+ * @returns {string}
+ */
+export function edit_cdxml_document_json_v1(document_json, edit_json) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(edit_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.edit_cdxml_document_json_v1(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);
+    }
+}
+
+/**
+ * Apply a bounded, stable-ID reaction-document edit and return canonical JSON.
+ * @param {string} document_json
+ * @param {string} edit_json
+ * @returns {string}
+ */
+export function edit_reaction_document_json_v1(document_json, edit_json) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(edit_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.edit_reaction_document_json_v1(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);
+    }
+}
+
 /**
  * Run `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
  * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
@@ -3580,7 +3724,7 @@ export function minimize_mmff94_lbfgs_json(mol, max_iter) {
  * `coords_json` — JSON array of `[x,y,z]` arrays (Å), one per atom.
  * `max_iter` — maximum iterations (0 = default 500).
  *
- * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool, "sound":bool, "worst_bond_length":float}`
+ * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool, "sound":bool, "worst_bond_length":float, "rejected_unsound_step":bool}`
  * or `{"error":"<msg>"}` on failure. `sound` is all-finite coordinates and
  * no bond stretched past a sane covalent-bond length — independent of
  * `converged`, since steepest descent often reports `converged:false` on
@@ -4006,6 +4150,24 @@ export function mol_from_cml(cml) {
     return MolHandle.__wrap(ret[0]);
 }
 
+/**
+ * Parse a structurally valid, non-empty CML string into a `MolHandle`.
+ *
+ * This opt-in strict boundary rejects missing/empty molecules and malformed
+ * XML while `mol_from_cml` retains its historical lenient behavior.
+ * @param {string} cml
+ * @returns {MolHandle}
+ */
+export function mol_from_cml_strict(cml) {
+    const ptr0 = passStringToWasm0(cml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_cml_strict(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Parse a Gaussian Cube file and return a `MolHandle` (topology only --
  * element list, no bonds; Cube carries no bond table). Use
@@ -5055,7 +5217,7 @@ 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;
@@ -5478,6 +5640,63 @@ export function rdkit_torsion_bitvec(mol) {
     return v1;
 }
 
+/**
+ * Validate and deterministically serialize a rich reaction document JSON.
+ *
+ * This is the versioned JSON boundary for WASM consumers. It preserves IDs,
+ * metadata, and provenance, and rejects malformed documents before returning
+ * JSON. Use [`edit_reaction_document_json_v1`] for bounded ID-addressed edits.
+ * @param {string} document_json
+ * @returns {string}
+ */
+export function reaction_document_json_v1(document_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.reaction_document_json_v1(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);
+    }
+}
+
+/**
+ * Convert a rich reaction document to legacy RXN V2000 with structured loss
+ * reporting. A lossy projection is never returned as if it were complete.
+ * @param {string} document_json
+ * @returns {string}
+ */
+export function reaction_document_to_rxn_v1(document_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.reaction_document_to_rxn_v1(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);
+    }
+}
+
 /**
  * Check whether a reaction SMILES matches a reaction SMARTS query.
  *
@@ -5635,6 +5854,38 @@ export function ring_families_json(mol) {
     }
 }
 
+/**
+ * Parse and serialize a V3000 block while preserving 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 polymer/query expansion is still out of
+ * scope, but the typed syntax view is available through
+ * [`v3000_sgroups_json`].
+ * @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 +6212,37 @@ 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 +6660,29 @@ 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
@@ -6833,6 +7138,31 @@ export function torsion_bitvec(mol) {
     return v1;
 }
 
+/**
+ * @param {string} block
+ * @returns {string}
+ */
+export function v3000_sgroups_json(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.v3000_sgroups_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);
+    }
+}
+
 /**
  * Validate a vendor-neutral NMR spectrum JSON document without parsing a
  * vendor-specific raw file or predicting peaks.
@@ -7289,11 +7619,11 @@ 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 +7631,17 @@ 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 +7653,28 @@ 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 +7869,11 @@ 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": "1.0.13",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",