@kent-tokyo/chematic 1.0.9 → 1.0.11

package/README.md

@@ -21,9 +21,16 @@ npm install @kent-tokyo/chematic
 - SA score: synthetic accessibility estimate [1, 10]
 - Functional group identification (Ertl 2017 IFG)
 - Canonical SMILES generation
-- ECFP4/6, AtomPair, Torsion, and path fingerprints with Tanimoto similarity
+- ECFP4/6, AtomPair, Torsion, path, and RDKit-compatible RDK fingerprints
+  with Tanimoto similarity
 - BRICS fragment count
-- SDF/MOL block parsing
+- SDF/MOL block parsing, including bounded resumable `sdf_records_batch_json`,
+  `xyz_frames_batch_json`, and `extxyz_frames_batch_json` manifests with
+  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,
+  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`)
 - Topological descriptors: Wiener index, Hall-Kier κ, χ connectivity indices, Bertz CT
@@ -68,7 +75,7 @@ console.log(mol.qed());                // drug-likeness score [0, 1]
 console.log(mol.exact_mass());         // ~180.042
 console.log(mol.hbd_count());          // 1
 console.log(mol.hba_count());          // 4
-console.log(mol.rotatable_bond_count()); // 3
+console.log(mol.rotatable_bond_count()); // 2 (RDKit Lipinski definition)
 console.log(mol.aromatic_ring_count()); // 1
 console.log(mol.lipinski_passes());     // true
 console.log(mol.canonical_smiles());    // canonical SMILES string
@@ -162,7 +169,7 @@ and enforced correctly on all of them.
 
 ## Bundle Size
 
-The optimized v1.0.9 candidate artifact was measured at **3.58 MB raw / 1.31 MB gzip**. Bundle size depends on features and toolchain; see [`benchmarks/2026-09-07-wasm-size-v1.0.9.md`](../../benchmarks/2026-09-07-wasm-size-v1.0.9.md) for exact tools, digest, and reproduction steps.
+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.
 
 PNG rasterization (`tiny_skia`) is excluded from the WASM build — use SVG output instead. All SVG depiction APIs remain fully available.
 

package/chematic_wasm.d.ts

@@ -974,6 +974,12 @@ export function estate_indices_json(mol: MolHandle): string;
  */
 export function extxyz_frame_json(text: string): string;
 
+/**
+ * Return one deterministic, resumable Extended-XYZ batch as a JSON manifest.
+ * Stopping before requesting the next offset is the cancellation boundary.
+ */
+export function extxyz_frames_batch_json(text: string, offset: number, batch_size: number): string;
+
 /**
  * FCFP4 (pharmacophore, radius-2) fingerprint as a bit-packed byte vector (256 bytes).
  */
@@ -1450,7 +1456,7 @@ 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}`
+ * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool, "sound":bool, "worst_bond_length":float}`
  * 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
@@ -1597,6 +1603,15 @@ export function mol_block_stereo_diagnostics_json(mol_block: string): string;
  */
 export function mol_from_cdxml(cdxml: string): MolHandle;
 
+/**
+ * Parse a ChemicalJSON (CJSON) string into a `MolHandle`.
+ *
+ * Coordinates and CJSON-specific metadata are intentionally not retained by
+ * this topology handle; use `convert_common_format` when a serialized CJSON
+ * round trip is required.
+ */
+export function mol_from_cjson(json: string): MolHandle;
+
 /**
  * Parse a CML string into a `MolHandle`.
  *
@@ -1665,6 +1680,21 @@ export function mol_from_orca_input(text: string): MolHandle;
  */
 export function mol_from_pdb(pdb: string): MolHandle;
 
+/**
+ * Strict PDB parser. Unlike [`mol_from_pdb`], malformed ATOM/HETATM fields
+ * return an error instead of producing a partially recovered molecule.
+ */
+export function mol_from_pdb_strict(pdb: string): MolHandle;
+
+/**
+ * Parse an AutoDock PDBQT block into a topology handle.
+ *
+ * Coordinates and partial charges are intentionally discarded, matching the
+ * Python `from_pdbqt` binding; use the Rust parser when those arrays are
+ * needed. Invalid records return a JS error instead of a partial molecule.
+ */
+export function mol_from_pdbqt(pdbqt: string): MolHandle;
+
 /**
  * Parse a PQR file and return a `MolHandle` (topology only -- element
  * list inferred per-atom, no bonds; PQR carries no connectivity). Use
@@ -1923,6 +1953,12 @@ export function pdb_coords_json(pdb: string): string;
  */
 export function peoe_vsa_json(mol: MolHandle): string;
 
+/**
+ * Fingerprint a serialized `PeriodicStructure`; invalid or oversized input
+ * returns a stable JSON error rather than being treated as a retrieval hit.
+ */
+export function periodic_structure_fingerprint_json(json: string, source: string): string;
+
 /**
  * Detect pharmacophore features for virtual screening and lead optimization.
  * Returns JSON array of features: [{type, atom_idx, neighbor_count}, ...]
@@ -1994,6 +2030,16 @@ export function pqr_to_json(text: string): string;
  */
 export function predict_pka_json(smiles: string): string;
 
+/**
+ * Run deterministic SVG publication preflight for a SMILES string.
+ *
+ * Returns a JSON `PreflightReport` with stable diagnostic paths and a
+ * deterministic input fingerprint. Font metrics are conservative estimates;
+ * the final browser/renderer remains authoritative for pixel-level validation.
+ * The input is capped at the same 1 MiB/10,000-atom limits as other WASM APIs.
+ */
+export function preflight_smiles_json(smiles: string, width: number, height: number): string;
+
 /**
  * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
  * `qcschema_molecule` document, in the SAME atom order
@@ -2099,6 +2145,38 @@ export function rdkit_ecfp_config_chiral_detail_json(mol: MolHandle, radius: num
  */
 export function rdkit_ecfp_config_detail_json(mol: MolHandle, radius: number, nbits: number): string;
 
+/**
+ * Compute the RDKit-compatible Daylight-like path fingerprint as a bit-packed
+ * byte vector (256 bytes = 2048 bits). This is the WASM counterpart of the
+ * Python `path_fp` operation and is intentionally separate from native
+ * `topo_path_bitvec`.
+ */
+export function rdkit_path_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * Compute the RDKit-compatible RDKFingerprint as a bit-packed byte vector
+ * (256 bytes = 2048 bits). This is separate from both the native
+ * `topo_path_bitvec` operation and the RDKit-compatible path operation.
+ */
+export function rdkit_rdk_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * Compute the opt-in RDKit-compatible hashed topological-torsion fingerprint
+ * as a bit-packed byte vector (256 bytes = 2048 bits). This remains separate
+ * from the native `torsion_bitvec` operation and its similarity semantics.
+ */
+export function rdkit_torsion_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * Check whether a reaction SMILES matches a reaction SMARTS query.
+ *
+ * The middle section of the query supports agent alternatives separated by
+ * `|`. This source-level API remains bounded and returns a typed JS error for
+ * invalid input; the generated Node artifact is updated separately when the
+ * wasm-bindgen toolchain is available.
+ */
+export function reaction_smarts_match(smarts: string, reaction_smiles: string): boolean;
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  */
@@ -2222,6 +2300,16 @@ export function screen_smiles_json(smiles_batch: string, delimiter: string): str
  */
 export function sdf_from_records_json(smiles_json: string, names_json: string, props_json: string): string;
 
+/**
+ * Return one deterministic, resumable SDF batch as a JSON manifest.
+ *
+ * `offset` is the zero-based input record to start at and `batch_size` is
+ * bounded by [`crate::WASM_MAX_BATCH_ITEMS`]. Invalid records stay inline as
+ * `status: "rejected"`; callers can stop requesting later batches to cancel
+ * work without a background queue or hidden buffering.
+ */
+export function sdf_records_batch_json(sdf: string, offset: number, batch_size: number): string;
+
 /**
  * Parse an SDF string and return a JSON array of record objects.
  *
@@ -2530,11 +2618,25 @@ export function to_qcschema_molecule_json(mol: MolHandle, coords_json: string, c
  */
 export function to_xyz(mol: MolHandle): string;
 
+/**
+ * Compute the native topological path fingerprint as a bit-packed byte vector
+ * (256 bytes = 2048 bits), using the default [`chematic_fp::TopoPathConfig`].
+ * This is the native `topo_path` operation, not the RDKit-compatible path
+ * fingerprint exposed by the separate `path_fp` Python method.
+ */
+export function topo_path_bitvec(mol: MolHandle): Uint8Array;
+
 /**
  * Torsion fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  */
 export function torsion_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * Validate a vendor-neutral NMR spectrum JSON document without parsing a
+ * vendor-specific raw file or predicting peaks.
+ */
+export function validate_nmr_spectrum_json(json: string): string;
+
 /**
  * Virtual screen a query SMILES against a database of SMILES using ECFP4 Tanimoto.
  *
@@ -2652,6 +2754,12 @@ export function xlogp3_json(mol: MolHandle): string;
  */
 export function xlogp3_per_atom_json(mol: MolHandle): string;
 
+/**
+ * Return one deterministic, resumable plain-XYZ batch as a JSON manifest.
+ * Stopping before requesting the next offset is the cancellation boundary.
+ */
+export function xyz_frames_batch_json(text: string, offset: number, batch_size: number): string;
+
 export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembly.Module;
 
 export interface InitOutput {
@@ -2735,6 +2843,7 @@ export interface InitOutput {
     readonly erg_vec_json: (a: number) => [number, number];
     readonly estate_indices_json: (a: number) => [number, number];
     readonly extxyz_frame_json: (a: number, b: number) => [number, number, number, number];
+    readonly extxyz_frames_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly fcfp4_bitvec: (a: number) => [number, number];
     readonly fcfp6_bitvec: (a: number) => [number, number];
     readonly find_reaction_center_json: (a: number, b: number) => [number, number];
@@ -2801,6 +2910,7 @@ export interface InitOutput {
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
     readonly mol_block_stereo_diagnostics_json: (a: number, b: number) => [number, number, number, number];
     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_cube: (a: number, b: number) => [number, number, number];
     readonly mol_from_extxyz: (a: number, b: number) => [number, number, number];
@@ -2808,6 +2918,8 @@ export interface InitOutput {
     readonly mol_from_moljson: (a: number, b: number) => [number, number, number];
     readonly mol_from_orca_input: (a: number, b: number) => [number, number, number];
     readonly mol_from_pdb: (a: number, b: number) => number;
+    readonly mol_from_pdb_strict: (a: number, b: number) => [number, number, number];
+    readonly mol_from_pdbqt: (a: number, b: number) => [number, number, number];
     readonly mol_from_pqr: (a: number, b: number) => [number, number, number];
     readonly mol_from_qcschema_molecule: (a: number, b: number) => [number, number, number];
     readonly mol_from_sdf_block: (a: number, b: number) => [number, number, number];
@@ -2914,6 +3026,7 @@ export interface InitOutput {
     readonly parse_smiles: (a: number, b: number) => [number, number, number];
     readonly pdb_coords_json: (a: number, b: number) => [number, number];
     readonly peoe_vsa_json: (a: number) => [number, number];
+    readonly periodic_structure_fingerprint_json: (a: number, b: number, c: number, d: number) => [number, number];
     readonly pharmacophore_features_json: (a: number) => [number, number];
     readonly pharmacophore_fp_2d_summary: (a: number) => [number, number];
     readonly pharmacophore_fp_3d_summary: (a: number) => [number, number];
@@ -2922,6 +3035,7 @@ export interface InitOutput {
     readonly pqr_infer_element: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number];
     readonly pqr_to_json: (a: number, b: number) => [number, number, number, number];
     readonly predict_pka_json: (a: number, b: number) => [number, number];
+    readonly preflight_smiles_json: (a: number, b: number, c: number, d: number) => [number, number];
     readonly qcschema_molecule_coords_json: (a: number, b: number) => [number, number, number, number];
     readonly qcschema_validate_atomic_input: (a: number, b: number) => [number, number, number, number];
     readonly qcschema_validate_atomic_result: (a: number, b: number) => [number, number, number, number];
@@ -2932,6 +3046,10 @@ export interface InitOutput {
     readonly rdkit_ecfp_config_chiral_bitvec: (a: number, b: number, c: number) => [number, number, number, number];
     readonly rdkit_ecfp_config_chiral_detail_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly rdkit_ecfp_config_detail_json: (a: number, b: number, c: number) => [number, number, number, number];
+    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_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];
@@ -2942,6 +3060,7 @@ export interface InitOutput {
     readonly sa_score: (a: number) => number;
     readonly screen_smiles_json: (a: number, b: number, c: number, d: number) => [number, number];
     readonly sdf_from_records_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
+    readonly sdf_records_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly sdf_to_records_json: (a: number, b: number) => [number, number];
     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];
@@ -2983,7 +3102,9 @@ export interface InitOutput {
     readonly to_moljson: (a: number) => [number, number];
     readonly to_qcschema_molecule_json: (a: number, b: number, c: number, d: number, e: bigint) => [number, number, number, number];
     readonly to_xyz: (a: number) => [number, number];
+    readonly topo_path_bitvec: (a: number) => [number, number];
     readonly torsion_bitvec: (a: 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];
     readonly whim_getaway_combined_json: (a: number) => [number, number];
@@ -2999,6 +3120,7 @@ export interface InitOutput {
     readonly write_smiles: (a: number) => [number, number];
     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 __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

@@ -2377,6 +2377,35 @@ export function extxyz_frame_json(text) {
     }
 }
 
+/**
+ * Return one deterministic, resumable Extended-XYZ batch as a JSON manifest.
+ * Stopping before requesting the next offset is the cancellation boundary.
+ * @param {string} text
+ * @param {number} offset
+ * @param {number} batch_size
+ * @returns {string}
+ */
+export function extxyz_frames_batch_json(text, offset, batch_size) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.extxyz_frames_batch_json(ptr0, len0, offset, batch_size);
+        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);
+    }
+}
+
 /**
  * FCFP4 (pharmacophore, radius-2) fingerprint as a bit-packed byte vector (256 bytes).
  * @param {MolHandle} mol
@@ -3551,7 +3580,7 @@ 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}`
+ * Returns JSON: `{"coords":[[x,y,z],...], "energy":float, "iterations":int, "converged":bool, "sound":bool, "worst_bond_length":float}`
  * 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
@@ -3941,6 +3970,25 @@ export function mol_from_cdxml(cdxml) {
     return MolHandle.__wrap(ret[0]);
 }
 
+/**
+ * Parse a ChemicalJSON (CJSON) string into a `MolHandle`.
+ *
+ * Coordinates and CJSON-specific metadata are intentionally not retained by
+ * this topology handle; use `convert_common_format` when a serialized CJSON
+ * round trip is required.
+ * @param {string} json
+ * @returns {MolHandle}
+ */
+export function mol_from_cjson(json) {
+    const ptr0 = passStringToWasm0(json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_cjson(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Parse a CML string into a `MolHandle`.
  *
@@ -4076,6 +4124,41 @@ export function mol_from_pdb(pdb) {
     return MolHandle.__wrap(ret);
 }
 
+/**
+ * Strict PDB parser. Unlike [`mol_from_pdb`], malformed ATOM/HETATM fields
+ * return an error instead of producing a partially recovered molecule.
+ * @param {string} pdb
+ * @returns {MolHandle}
+ */
+export function mol_from_pdb_strict(pdb) {
+    const ptr0 = passStringToWasm0(pdb, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_pdb_strict(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Parse an AutoDock PDBQT block into a topology handle.
+ *
+ * Coordinates and partial charges are intentionally discarded, matching the
+ * Python `from_pdbqt` binding; use the Rust parser when those arrays are
+ * needed. Invalid records return a JS error instead of a partial molecule.
+ * @param {string} pdbqt
+ * @returns {MolHandle}
+ */
+export function mol_from_pdbqt(pdbqt) {
+    const ptr0 = passStringToWasm0(pdbqt, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_pdbqt(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Parse a PQR file and return a `MolHandle` (topology only -- element
  * list inferred per-atom, no bonds; PQR carries no connectivity). Use
@@ -4800,6 +4883,30 @@ export function peoe_vsa_json(mol) {
     }
 }
 
+/**
+ * Fingerprint a serialized `PeriodicStructure`; invalid or oversized input
+ * returns a stable JSON error rather than being treated as a retrieval hit.
+ * @param {string} json
+ * @param {string} source
+ * @returns {string}
+ */
+export function periodic_structure_fingerprint_json(json, source) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(source, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.periodic_structure_fingerprint_json(ptr0, len0, ptr1, len1);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Detect pharmacophore features for virtual screening and lead optimization.
  * Returns JSON array of features: [{type, atom_idx, neighbor_count}, ...]
@@ -5006,6 +5113,33 @@ export function predict_pka_json(smiles) {
     }
 }
 
+/**
+ * Run deterministic SVG publication preflight for a SMILES string.
+ *
+ * Returns a JSON `PreflightReport` with stable diagnostic paths and a
+ * deterministic input fingerprint. Font metrics are conservative estimates;
+ * the final browser/renderer remains authoritative for pixel-level validation.
+ * The input is capped at the same 1 MiB/10,000-atom limits as other WASM APIs.
+ * @param {string} smiles
+ * @param {number} width
+ * @param {number} height
+ * @returns {string}
+ */
+export function preflight_smiles_json(smiles, width, height) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.preflight_smiles_json(ptr0, len0, width, height);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
 /**
  * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
  * `qcschema_molecule` document, in the SAME atom order
@@ -5298,6 +5432,75 @@ export function rdkit_ecfp_config_detail_json(mol, radius, nbits) {
     }
 }
 
+/**
+ * Compute the RDKit-compatible Daylight-like path fingerprint as a bit-packed
+ * byte vector (256 bytes = 2048 bits). This is the WASM counterpart of the
+ * Python `path_fp` operation and is intentionally separate from native
+ * `topo_path_bitvec`.
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function rdkit_path_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.rdkit_path_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Compute the RDKit-compatible RDKFingerprint as a bit-packed byte vector
+ * (256 bytes = 2048 bits). This is separate from both the native
+ * `topo_path_bitvec` operation and the RDKit-compatible path operation.
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function rdkit_rdk_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.rdkit_rdk_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Compute the opt-in RDKit-compatible hashed topological-torsion fingerprint
+ * as a bit-packed byte vector (256 bytes = 2048 bits). This remains separate
+ * from the native `torsion_bitvec` operation and its similarity semantics.
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function rdkit_torsion_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.rdkit_torsion_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Check whether a reaction SMILES matches a reaction SMARTS query.
+ *
+ * The middle section of the query supports agent alternatives separated by
+ * `|`. This source-level API remains bounded and returns a typed JS error for
+ * invalid input; the generated Node artifact is updated separately when the
+ * wasm-bindgen toolchain is available.
+ * @param {string} smarts
+ * @param {string} reaction_smiles
+ * @returns {boolean}
+ */
+export function reaction_smarts_match(smarts, reaction_smiles) {
+    const ptr0 = passStringToWasm0(smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ptr1 = passStringToWasm0(reaction_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len1 = WASM_VECTOR_LEN;
+    const ret = wasm.reaction_smarts_match(ptr0, len0, ptr1, len1);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0] !== 0;
+}
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  * @param {MolHandle} mol
@@ -5612,6 +5815,39 @@ export function sdf_from_records_json(smiles_json, names_json, props_json) {
     }
 }
 
+/**
+ * Return one deterministic, resumable SDF batch as a JSON manifest.
+ *
+ * `offset` is the zero-based input record to start at and `batch_size` is
+ * bounded by [`crate::WASM_MAX_BATCH_ITEMS`]. Invalid records stay inline as
+ * `status: "rejected"`; callers can stop requesting later batches to cancel
+ * work without a background queue or hidden buffering.
+ * @param {string} sdf
+ * @param {number} offset
+ * @param {number} batch_size
+ * @returns {string}
+ */
+export function sdf_records_batch_json(sdf, offset, batch_size) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(sdf, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.sdf_records_batch_json(ptr0, len0, offset, batch_size);
+        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 an SDF string and return a JSON array of record objects.
  *
@@ -6568,6 +6804,22 @@ export function to_xyz(mol) {
     }
 }
 
+/**
+ * Compute the native topological path fingerprint as a bit-packed byte vector
+ * (256 bytes = 2048 bits), using the default [`chematic_fp::TopoPathConfig`].
+ * This is the native `topo_path` operation, not the RDKit-compatible path
+ * fingerprint exposed by the separate `path_fp` Python method.
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function topo_path_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.topo_path_bitvec(mol.__wbg_ptr);
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
 /**
  * Torsion fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  * @param {MolHandle} mol
@@ -6581,6 +6833,27 @@ export function torsion_bitvec(mol) {
     return v1;
 }
 
+/**
+ * Validate a vendor-neutral NMR spectrum JSON document without parsing a
+ * vendor-specific raw file or predicting peaks.
+ * @param {string} json
+ * @returns {string}
+ */
+export function validate_nmr_spectrum_json(json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.validate_nmr_spectrum_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);
+    }
+}
+
 /**
  * Virtual screen a query SMILES against a database of SMILES using ECFP4 Tanimoto.
  *
@@ -6984,6 +7257,35 @@ export function xlogp3_per_atom_json(mol) {
         wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
     }
 }
+
+/**
+ * Return one deterministic, resumable plain-XYZ batch as a JSON manifest.
+ * Stopping before requesting the next offset is the cancellation boundary.
+ * @param {string} text
+ * @param {number} offset
+ * @param {number} batch_size
+ * @returns {string}
+ */
+export function xyz_frames_batch_json(text, offset, batch_size) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.xyz_frames_batch_json(ptr0, len0, offset, batch_size);
+        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);
+    }
+}
 function __wbg_get_imports() {
     const import0 = {
         __proto__: null,

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": "1.0.9",
+  "version": "1.0.11",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",