@kent-tokyo/chematic 0.49.0 → 1.0.3

package/chematic_wasm.d.ts

@@ -517,6 +517,8 @@ export function balance_check_json(reaction_smiles: string): string;
  *
  * Empty lines and invalid SMILES are silently skipped.
  * Returns the same card-grid HTML as Python's `chematic.report()`.
+ * The input is limited to 1 MiB, 1,024 non-empty records, and 10,000 atoms
+ * per successfully parsed molecule. Limit violations return an HTML error.
  *
  * ```js
  * const html = mod.batch_report_html("CCO\nc1ccccc1\nCC(=O)O");
@@ -582,6 +584,13 @@ export function canonical_tautomer(mol: MolHandle): MolHandle;
  */
 export function canonical_tautomer_with_blocked_atoms_json(mol: MolHandle, blocked_atom_indices_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
+ * ChemDraw extensions are never silently discarded.
+ */
+export function cdxml_document_json(cdxml: string): string;
+
 /**
  * Parse all molecular fragments from a CDXML string.
  *
@@ -638,6 +647,8 @@ export function cip_unresolved_json(mol: MolHandle): string;
 /**
  * Compare multiple SMILES strings (up to 256 by default).
  * Accepts a delimiter-separated list (e.g., newline or comma).
+ * The input is limited to 1 MiB, 1,024 records, and 10,000 atoms per parsed
+ * molecule.
  *
  * # Example (JS)
  * ```javascript
@@ -754,6 +765,9 @@ export function depict_reaction_svg(rxn_smiles: string): string;
  *
  * Lines that fail to parse are silently skipped.
  * `cols` controls the number of columns (each cell is 200×200 px).
+ * The input is limited to 1 MiB, 1,024 non-empty records, and 10,000 atoms
+ * per successfully parsed molecule. Limit violations return an empty SVG
+ * containing an error title.
  */
 export function depict_svg_grid(smiles_block: string, cols: number): string;
 
@@ -767,6 +781,9 @@ export function depict_svg_grid(smiles_block: string, cols: number): string;
  *
  * Invalid SMILES are rendered as empty cells; SMARTS parse failure returns an
  * unhighlighted grid (the SMARTS is silently ignored).
+ * The input is limited to 1 MiB, 1,024 non-empty records, and 10,000 atoms
+ * per successfully parsed molecule. Limit violations return an empty SVG
+ * containing an error title.
  */
 export function depict_svg_grid_highlighted(smiles_block: string, cols: number, match_smarts: string): string;
 
@@ -2081,7 +2098,7 @@ export function remove_hydrogens(mol: MolHandle): MolHandle;
  * APIs. This function changes nothing about the underlying algorithm; it
  * only serializes the result to JSON.
  *
- * `max_results` -- cap on returned disconnections (0 = unlimited).
+ * `max_results` -- cap on returned disconnections (0 = the WASM safety cap).
  *
  * `reaction_class` -- filter to a single reaction class, or `""` for all
  * classes. Valid values: `"AmideBond"`, `"Ester"`, `"Ether"`, `"CNBond"`,
@@ -2144,6 +2161,8 @@ export function sa_score(mol: MolHandle): number;
  * Screen a batch of SMILES strings (JSON string output).
  * Returns per-record results including pass/fail with error details.
  * Includes MaxMin diversity picking and Butina clustering by default.
+ * The input is limited to 1 MiB, 1,024 records, and 10,000 atoms per parsed
+ * molecule.
  *
  * # Example (JS)
  * ```javascript
@@ -2610,6 +2629,7 @@ export interface InitOutput {
     readonly butina_cluster_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly canonical_tautomer: (a: number) => number;
     readonly canonical_tautomer_with_blocked_atoms_json: (a: number, b: number, c: number) => [number, number];
+    readonly cdxml_document_json: (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];

package/chematic_wasm.js

@@ -1206,6 +1206,8 @@ export function balance_check_json(reaction_smiles) {
  *
  * Empty lines and invalid SMILES are silently skipped.
  * Returns the same card-grid HTML as Python's `chematic.report()`.
+ * The input is limited to 1 MiB, 1,024 non-empty records, and 10,000 atoms
+ * per successfully parsed molecule. Limit violations return an HTML error.
  *
  * ```js
  * const html = mod.batch_report_html("CCO\nc1ccccc1\nCC(=O)O");
@@ -1366,6 +1368,34 @@ export function canonical_tautomer_with_blocked_atoms_json(mol, blocked_atom_ind
     }
 }
 
+/**
+ * Parse a CDXML document while preserving page and presentation objects.
+ * The returned JSON contains an opaque `raw_xml` for each object so unknown
+ * ChemDraw extensions are never silently discarded.
+ * @param {string} cdxml
+ * @returns {string}
+ */
+export function cdxml_document_json(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(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.
  *
@@ -1511,6 +1541,8 @@ export function cip_unresolved_json(mol) {
 /**
  * Compare multiple SMILES strings (up to 256 by default).
  * Accepts a delimiter-separated list (e.g., newline or comma).
+ * The input is limited to 1 MiB, 1,024 records, and 10,000 atoms per parsed
+ * molecule.
  *
  * # Example (JS)
  * ```javascript
@@ -1826,6 +1858,9 @@ export function depict_reaction_svg(rxn_smiles) {
  *
  * Lines that fail to parse are silently skipped.
  * `cols` controls the number of columns (each cell is 200×200 px).
+ * The input is limited to 1 MiB, 1,024 non-empty records, and 10,000 atoms
+ * per successfully parsed molecule. Limit violations return an empty SVG
+ * containing an error title.
  * @param {string} smiles_block
  * @param {number} cols
  * @returns {string}
@@ -1855,6 +1890,9 @@ export function depict_svg_grid(smiles_block, cols) {
  *
  * Invalid SMILES are rendered as empty cells; SMARTS parse failure returns an
  * unhighlighted grid (the SMARTS is silently ignored).
+ * The input is limited to 1 MiB, 1,024 non-empty records, and 10,000 atoms
+ * per successfully parsed molecule. Limit violations return an empty SVG
+ * containing an error title.
  * @param {string} smiles_block
  * @param {number} cols
  * @param {string} match_smarts
@@ -5217,7 +5255,7 @@ export function remove_hydrogens(mol) {
  * APIs. This function changes nothing about the underlying algorithm; it
  * only serializes the result to JSON.
  *
- * `max_results` -- cap on returned disconnections (0 = unlimited).
+ * `max_results` -- cap on returned disconnections (0 = the WASM safety cap).
  *
  * `reaction_class` -- filter to a single reaction class, or `""` for all
  * classes. Valid values: `"AmideBond"`, `"Ester"`, `"Ether"`, `"CNBond"`,
@@ -5378,6 +5416,8 @@ export function sa_score(mol) {
  * Screen a batch of SMILES strings (JSON string output).
  * Returns per-record results including pass/fail with error details.
  * Includes MaxMin diversity picking and Butina clustering by default.
+ * The input is limited to 1 MiB, 1,024 records, and 10,000 atoms per parsed
+ * molecule.
  *
  * # Example (JS)
  * ```javascript

package/package.json

@@ -2,10 +2,10 @@
   "name": "@kent-tokyo/chematic",
   "type": "module",
   "collaborators": [
-    "kent-tokyo <kent-tokyo@users.noreply.github.com>"
+    "Kentaro Tanabe (kent-tokyo) <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "0.49.0",
+  "version": "1.0.3",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",