@kent-tokyo/chematic 0.1.20 → 0.1.22

package/chematic_wasm.d.ts

@@ -380,6 +380,17 @@ export function butina_cluster_ecfp4_json(smiles_json: string, cutoff: number):
  */
 export function canonical_tautomer(mol: MolHandle): MolHandle;
 
+/**
+ * Parse all molecular fragments from a CDXML string.
+ *
+ * Returns a JSON array of SMILES strings, one per fragment:
+ * `["CC","c1ccccc1"]`
+ *
+ * Stereochemistry (wedge/dash bonds) is read from the `Display` attribute
+ * of bond elements.
+ */
+export function cdxml_to_smiles_json(cdxml: string): string;
+
 /**
  * CIP stereo assignments as a JSON array of `{atomIdx, cipCode}` objects.
  *
@@ -418,6 +429,15 @@ export function cpk_color(element_symbol: string): string;
  */
 export function depict_data_json(mol: MolHandle): string;
 
+/**
+ * Compute structured depiction data using caller-supplied 2D coordinates.
+ *
+ * `coords_json` — JSON array of `[x, y]` pairs, one per atom in order.
+ *
+ * Returns the same JSON format as `depict_data_json`.
+ */
+export function depict_data_with_coords_json(mol: MolHandle, coords_json: string): string;
+
 /**
  * Render a reaction SMILES string (e.g. `"CC(=O)O.CCO>>CC(=O)OCC.O"`) as a
  * single SVG showing reactants → products with `+` separators.
@@ -694,6 +714,14 @@ export function mcs_smiles_json(smiles_json: string): string;
  */
 export function mmp_pairs_json(smiles_json: string): string;
 
+/**
+ * Parse a MOL V2000 string and return 2D coordinates as a JSON array.
+ *
+ * Returns `[[x0,y0],[x1,y1],...]` in atom-insertion order.
+ * Coordinates are in Ångström as stored in the MOL file.
+ */
+export function mol_block_coords_json(mol_block: string): string;
+
 /**
  * Serialize a SMILES string directly to a MOL V2000 block with 2D coordinates.
  *
@@ -758,6 +786,21 @@ export function mol_next_atom_idx(mol: MolHandle): number;
  */
 export function mol_with_atom_added(mol: MolHandle, element_symbol: string): MolHandle;
 
+/**
+ * Return a new `MolHandle` with the formal charge of atom `idx` changed.
+ *
+ * Returns a JS error if `idx` is out of range.
+ */
+export function mol_with_atom_charge(mol: MolHandle, idx: number, charge: number): MolHandle;
+
+/**
+ * Return a new `MolHandle` with the element of atom `idx` changed.
+ *
+ * `element_symbol` — periodic-table symbol, e.g. `"N"`, `"O"`, `"Cl"`.
+ * Returns a JS error if `idx` is out of range or the symbol is unknown.
+ */
+export function mol_with_atom_element(mol: MolHandle, idx: number, element_symbol: string): MolHandle;
+
 /**
  * Return a new `MolHandle` with atom `idx` and all its bonds removed.
  *
@@ -1067,6 +1110,7 @@ export interface InitOutput {
     readonly brics_fragments_json: (a: number) => [number, number];
     readonly butina_cluster_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly canonical_tautomer: (a: number) => number;
+    readonly cdxml_to_smiles_json: (a: number, b: number) => [number, number, number, number];
     readonly cip_assignments_json: (a: number) => [number, number];
     readonly conformerhandle_add_generated_conformer: (a: number) => number;
     readonly conformerhandle_add_minimized_conformer: (a: number) => number;
@@ -1079,6 +1123,7 @@ export interface InitOutput {
     readonly conformerhandle_remove_conformer: (a: number, b: number) => number;
     readonly cpk_color: (a: number, b: number) => [number, number];
     readonly depict_data_json: (a: number) => [number, number];
+    readonly depict_data_with_coords_json: (a: number, b: number, c: number) => [number, number];
     readonly depict_reaction_svg: (a: number, b: number) => [number, number, number, number];
     readonly depict_svg_grid: (a: number, b: number, c: number) => [number, number];
     readonly depict_svg_grid_highlighted: (a: number, b: number, c: number, d: number, e: number) => [number, number];
@@ -1125,6 +1170,7 @@ export interface InitOutput {
     readonly maxmin_picks_ecfp4_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly mcs_smiles_json: (a: number, b: number) => [number, number, number, number];
     readonly mmp_pairs_json: (a: number, b: number) => [number, number, number, number];
+    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_from_cdxml: (a: number, b: number) => [number, number, number];
     readonly mol_from_cml: (a: number, b: number) => [number, number, number];
@@ -1134,6 +1180,8 @@ export interface InitOutput {
     readonly mol_from_xyz: (a: number, b: number) => [number, number, number];
     readonly mol_next_atom_idx: (a: number) => number;
     readonly mol_with_atom_added: (a: number, b: number, c: number) => [number, number, number];
+    readonly mol_with_atom_charge: (a: number, b: number, c: number) => [number, number, number];
+    readonly mol_with_atom_element: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly mol_with_atom_removed: (a: number, b: number) => [number, number, number];
     readonly mol_with_bond_added: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly mol_with_bond_removed: (a: number, b: number) => [number, number, number];

package/chematic_wasm.js

@@ -868,6 +868,38 @@ export function canonical_tautomer(mol) {
     return MolHandle.__wrap(ret);
 }
 
+/**
+ * Parse all molecular fragments from a CDXML string.
+ *
+ * Returns a JSON array of SMILES strings, one per fragment:
+ * `["CC","c1ccccc1"]`
+ *
+ * Stereochemistry (wedge/dash bonds) is read from the `Display` attribute
+ * of bond elements.
+ * @param {string} cdxml
+ * @returns {string}
+ */
+export function cdxml_to_smiles_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_to_smiles_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);
+    }
+}
+
 /**
  * CIP stereo assignments as a JSON array of `{atomIdx, cipCode}` objects.
  *
@@ -949,6 +981,32 @@ export function depict_data_json(mol) {
     }
 }
 
+/**
+ * Compute structured depiction data using caller-supplied 2D coordinates.
+ *
+ * `coords_json` — JSON array of `[x, y]` pairs, one per atom in order.
+ *
+ * Returns the same JSON format as `depict_data_json`.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @returns {string}
+ */
+export function depict_data_with_coords_json(mol, coords_json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.depict_data_with_coords_json(mol.__wbg_ptr, 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);
+    }
+}
+
 /**
  * Render a reaction SMILES string (e.g. `"CC(=O)O.CCO>>CC(=O)OCC.O"`) as a
  * single SVG showing reactants → products with `+` separators.
@@ -1668,6 +1726,35 @@ export function mmp_pairs_json(smiles_json) {
     }
 }
 
+/**
+ * Parse a MOL V2000 string and return 2D coordinates as a JSON array.
+ *
+ * Returns `[[x0,y0],[x1,y1],...]` in atom-insertion order.
+ * Coordinates are in Ångström as stored in the MOL file.
+ * @param {string} mol_block
+ * @returns {string}
+ */
+export function mol_block_coords_json(mol_block) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(mol_block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mol_block_coords_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);
+    }
+}
+
 /**
  * Serialize a SMILES string directly to a MOL V2000 block with 2D coordinates.
  *
@@ -1828,6 +1915,45 @@ export function mol_with_atom_added(mol, element_symbol) {
     return MolHandle.__wrap(ret[0]);
 }
 
+/**
+ * Return a new `MolHandle` with the formal charge of atom `idx` changed.
+ *
+ * Returns a JS error if `idx` is out of range.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @param {number} charge
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_charge(mol, idx, charge) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.mol_with_atom_charge(mol.__wbg_ptr, idx, charge);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
+/**
+ * Return a new `MolHandle` with the element of atom `idx` changed.
+ *
+ * `element_symbol` — periodic-table symbol, e.g. `"N"`, `"O"`, `"Cl"`.
+ * Returns a JS error if `idx` is out of range or the symbol is unknown.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @param {string} element_symbol
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_element(mol, idx, element_symbol) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(element_symbol, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_with_atom_element(mol.__wbg_ptr, idx, ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Return a new `MolHandle` with atom `idx` and all its bonds removed.
  *

package/package.json

@@ -4,8 +4,8 @@
   "collaborators": [
     "kent-tokyo <kent-tokyo@users.noreply.github.com>"
   ],
-  "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "0.1.20",
+  "description": "WebAssembly bindings for chematic \u2014 use chematic from JavaScript/TypeScript",
+  "version": "0.1.22",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",