@kent-tokyo/chematic 1.0.10 → 1.0.11

package/README.md

@@ -29,6 +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,
+  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
@@ -73,7 +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
@@ -167,7 +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

@@ -1603,6 +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`.
  *
@@ -1671,6 +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
@@ -2143,6 +2167,16 @@ export function rdkit_rdk_bitvec(mol: MolHandle): Uint8Array;
  */
 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.
  */
@@ -2876,6 +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];
@@ -2883,6 +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];
@@ -3012,6 +3049,7 @@ 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_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];

package/chematic_wasm.js

@@ -3970,6 +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`.
  *
@@ -4105,6 +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
@@ -5424,6 +5478,29 @@ export function rdkit_torsion_bitvec(mol) {
     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

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": "1.0.10",
+  "version": "1.0.11",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",