@kent-tokyo/chematic 1.0.34 → 1.0.36

package/README.md

@@ -4,7 +4,7 @@ WebAssembly bindings for [chematic](https://github.com/kent-tokyo/chematic), a p
 
 Published to npm as [`@kent-tokyo/chematic`](https://www.npmjs.com/package/@kent-tokyo/chematic).
 
-The current workspace line is 1.0.34. The binding keeps bounded parsing,
+The current workspace line is 1.0.36. The binding keeps bounded parsing,
 typed failures, and opt-in `embed_pipeline_v2_json`; 3D/MMFF94 behavior remains
 Experimental and is not a claim of full RDKit parity.
 

package/chematic_wasm.d.ts

@@ -756,8 +756,11 @@ export function chematic_version(): string;
  * but merges the accurate engine's tetrahedral R/S (~99.6% oracle-stable agreement,
  * see `docs/rfcs/cip_accurate_rfc.md`) with legacy's E/Z and allene answers (the accurate
  * engine computes neither). Atoms it can't resolve are omitted here -- see
- * [`cip_unresolved_json`] -- never a silently-guessed label. Returns `"null"` on an
- * internal engine error (budget-independent computations should not normally hit this).
+ * [`cip_unresolved_json`] -- never a silently-guessed label. A phosphorus on an
+ * unsaturated ring (cyclophosphazene) gets RDKit's CIPLabeler label, which flips
+ * with the ring's Kekulé spelling; its object carries `"kekuleDependent": true`.
+ * Returns `"null"` on an internal engine error (budget-independent computations
+ * should not normally hit this).
  */
 export function cip_assignments_accurate_json(mol: MolHandle): string;
 
@@ -1746,6 +1749,13 @@ export function mol_block_from_smiles(smiles: string): string;
  */
 export function mol_block_stereo_diagnostics_json(mol_block: string): string;
 
+/**
+ * The stereo [`to_mol_block`] does not carry, as JSON:
+ * `{"centres": [atom...], "double_bonds": [bond...],
+ * "non_tetrahedral_centres": [atom...], "stereo_groups_dropped": bool}`.
+ */
+export function mol_block_stereo_loss_json(mol: MolHandle): string;
+
 /**
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
@@ -2827,9 +2837,20 @@ export function to_extxyz_json(mol: MolHandle, coords_json: string, options_json
  *
  * Atom positions are computed via the same layout engine used for SVG depiction
  * and converted to Ångström units (`1.5 Å` per bond).
+ *
+ * A molecule with stereo gets the MOL writer's stereo layout (E/Z set by
+ * the geometry, one checked wedge per centre); a centre or E/Z bond that
+ * layout cannot express is lost silently here. Use [`to_mol_block_strict`]
+ * to get an error instead, or [`mol_block_stereo_loss_json`] for the list.
  */
 export function to_mol_block(mol: MolHandle): string;
 
+/**
+ * [`to_mol_block`] that fails, naming the lost centres and bonds, when the
+ * block would not carry all of the molecule's stereo.
+ */
+export function to_mol_block_strict(mol: MolHandle): string;
+
 /**
  * Serialise a `MolHandle` to MOL V3000 format with 2D coordinates.
  */
@@ -3182,6 +3203,7 @@ export interface InitOutput {
     readonly mol_block_coords_json: (a: number, b: number) => [number, number, number, number];
     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_block_stereo_loss_json: (a: 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];
@@ -3393,6 +3415,7 @@ export interface InitOutput {
     readonly to_cml: (a: number) => [number, number];
     readonly to_extxyz_json: (a: number, b: number, c: number, d: number, e: number) => [number, number, number, number];
     readonly to_mol_block: (a: number) => [number, number];
+    readonly to_mol_block_strict: (a: number) => [number, number, number, number];
     readonly to_mol_v3000_block: (a: number) => [number, number];
     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];

package/chematic_wasm.js

@@ -1891,8 +1891,11 @@ export function chematic_version() {
  * but merges the accurate engine's tetrahedral R/S (~99.6% oracle-stable agreement,
  * see `docs/rfcs/cip_accurate_rfc.md`) with legacy's E/Z and allene answers (the accurate
  * engine computes neither). Atoms it can't resolve are omitted here -- see
- * [`cip_unresolved_json`] -- never a silently-guessed label. Returns `"null"` on an
- * internal engine error (budget-independent computations should not normally hit this).
+ * [`cip_unresolved_json`] -- never a silently-guessed label. A phosphorus on an
+ * unsaturated ring (cyclophosphazene) gets RDKit's CIPLabeler label, which flips
+ * with the ring's Kekulé spelling; its object carries `"kekuleDependent": true`.
+ * Returns `"null"` on an internal engine error (budget-independent computations
+ * should not normally hit this).
  * @param {MolHandle} mol
  * @returns {string}
  */
@@ -4424,6 +4427,27 @@ export function mol_block_stereo_diagnostics_json(mol_block) {
     }
 }
 
+/**
+ * The stereo [`to_mol_block`] does not carry, as JSON:
+ * `{"centres": [atom...], "double_bonds": [bond...],
+ * "non_tetrahedral_centres": [atom...], "stereo_groups_dropped": bool}`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function mol_block_stereo_loss_json(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.mol_block_stereo_loss_json(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
 /**
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
@@ -7427,6 +7451,11 @@ export function to_extxyz_json(mol, coords_json, options_json) {
  *
  * Atom positions are computed via the same layout engine used for SVG depiction
  * and converted to Ångström units (`1.5 Å` per bond).
+ *
+ * A molecule with stereo gets the MOL writer's stereo layout (E/Z set by
+ * the geometry, one checked wedge per centre); a centre or E/Z bond that
+ * layout cannot express is lost silently here. Use [`to_mol_block_strict`]
+ * to get an error instead, or [`mol_block_stereo_loss_json`] for the list.
  * @param {MolHandle} mol
  * @returns {string}
  */
@@ -7444,6 +7473,32 @@ export function to_mol_block(mol) {
     }
 }
 
+/**
+ * [`to_mol_block`] that fails, naming the lost centres and bonds, when the
+ * block would not carry all of the molecule's stereo.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function to_mol_block_strict(mol) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.to_mol_block_strict(mol.__wbg_ptr);
+        var ptr1 = ret[0];
+        var len1 = ret[1];
+        if (ret[3]) {
+            ptr1 = 0; len1 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred2_0 = ptr1;
+        deferred2_1 = len1;
+        return getStringFromWasm0(ptr1, len1);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
 /**
  * Serialise a `MolHandle` to MOL V3000 format with 2D coordinates.
  * @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": "1.0.34",
+  "version": "1.0.36",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",