@kent-tokyo/chematic 0.1.36 → 0.1.38

package/chematic_wasm.d.ts

@@ -730,6 +730,22 @@ export function get_bond_between(mol: MolHandle, atom1: number, atom2: number):
  */
 export function get_bond_info(mol: MolHandle, idx: number): string;
 
+/**
+ * Get bond length in Ångströms between two atoms from a SMILES string.
+ * Returns -1.0 if parsing fails or atom indices are out of range.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`: first atom index
+ * - `b`: second atom index
+ *
+ * # Example
+ * ```javascript
+ * const len = get_bond_length_json("CC", 0, 1);  // C-C single bond ≈ 1.54 Å
+ * ```
+ */
+export function get_bond_length_json(smiles: string, a: number, b: number): number;
+
 /**
  * All scalar molecular descriptors as a single JSON object.
  *
@@ -738,6 +754,21 @@ export function get_bond_info(mol: MolHandle, idx: number): string;
  */
 export function get_descriptors_json(mol: MolHandle): string;
 
+/**
+ * Get dihedral angle A—B—C—D in degrees from a SMILES string.
+ * Returns null (JSON null) if any atom index is out of range or atoms are collinear.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`, `b`, `c`, `d`: atom indices
+ *
+ * # Example
+ * ```javascript
+ * const dihedral = get_dihedral_json("CCCC", 0, 1, 2, 3);  // A-B-C-D
+ * ```
+ */
+export function get_dihedral_json(smiles: string, a: number, b: number, c: number, d: number): any;
+
 /**
  * Identify functional groups. Returns a JSON array of objects:
  * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
@@ -1074,6 +1105,24 @@ export function parse_smiles(s: string): MolHandle;
  */
 export function peoe_vsa_json(mol: MolHandle): string;
 
+/**
+ * Generate `count` random SMILES from a SMILES string using the given seed.
+ * Atoms are permuted based on xorshift64 RNG. Each variant should parse back
+ * to the same molecule. Returns a JSON array of SMILES strings.
+ *
+ * # Arguments
+ * - `smiles`: input SMILES string
+ * - `count`: number of variants to generate (capped at 100)
+ * - `seed`: xorshift64 seed
+ *
+ * # Example
+ * ```javascript
+ * const variants = random_smiles_json("CC(C)O", 5, 42);
+ * // variants: ["CC(C)O", "C(C)(O)C", ...]
+ * ```
+ */
+export function random_smiles_json(smiles: string, count: number, seed: bigint): string;
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  */
@@ -1180,6 +1229,23 @@ export function sdf_to_records_json(sdf: string): string;
  */
 export function sdf_to_smiles_json(sdf: string): string;
 
+/**
+ * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
+ * Rotates the D-side subtree around the B—C bond.
+ * Returns a JS error if parsing fails or atom indices are invalid.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`, `b`, `c`, `d`: atom indices
+ * - `angle_deg`: target dihedral angle in degrees
+ *
+ * # Example
+ * ```javascript
+ * const pdbBlock = set_dihedral_json("CCCC", 0, 1, 2, 3, 120.0);
+ * ```
+ */
+export function set_dihedral_json(smiles: string, a: number, b: number, c: number, d: number, angle_deg: number): string;
+
 /**
  * 3D shape descriptors as a JSON object.
  *
@@ -1424,7 +1490,9 @@ export interface InitOutput {
     readonly get_atom_info: (a: number, b: number) => [number, number];
     readonly get_bond_between: (a: number, b: number, c: number) => [number, number];
     readonly get_bond_info: (a: number, b: number) => [number, number];
+    readonly get_bond_length_json: (a: number, b: number, c: number, d: number) => number;
     readonly get_descriptors_json: (a: number) => [number, number];
+    readonly get_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number) => any;
     readonly identify_functional_groups: (a: number) => [number, number];
     readonly inchi_from_smiles: (a: number, b: number) => [number, number];
     readonly inchikey_from_smiles: (a: number, b: number) => [number, number];
@@ -1523,6 +1591,7 @@ export interface InitOutput {
     readonly parse_cxsmiles_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_smiles: (a: number, b: number) => [number, number, number];
     readonly peoe_vsa_json: (a: number) => [number, number];
+    readonly random_smiles_json: (a: number, b: number, c: number, d: bigint) => [number, number, number, number];
     readonly remove_hydrogens: (a: number) => number;
     readonly rgroup_decompose_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly run_md_json: (a: number, b: number, c: number) => [number, number];
@@ -1531,6 +1600,7 @@ export interface InitOutput {
     readonly sdf_from_records_json: (a: number, b: number, c: number, d: number, e: number, f: 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 set_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number, number];
     readonly shape_descriptors_json: (a: number) => [number, number];
     readonly slogp_vsa_json: (a: number) => [number, number];
     readonly smarts_match_atoms: (a: number, b: number, c: number) => [number, number, number, number];

package/chematic_wasm.js

@@ -1754,6 +1754,31 @@ export function get_bond_info(mol, idx) {
     }
 }
 
+/**
+ * Get bond length in Ångströms between two atoms from a SMILES string.
+ * Returns -1.0 if parsing fails or atom indices are out of range.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`: first atom index
+ * - `b`: second atom index
+ *
+ * # Example
+ * ```javascript
+ * const len = get_bond_length_json("CC", 0, 1);  // C-C single bond ≈ 1.54 Å
+ * ```
+ * @param {string} smiles
+ * @param {number} a
+ * @param {number} b
+ * @returns {number}
+ */
+export function get_bond_length_json(smiles, a, b) {
+    const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_bond_length_json(ptr0, len0, a, b);
+    return ret;
+}
+
 /**
  * All scalar molecular descriptors as a single JSON object.
  *
@@ -1776,6 +1801,32 @@ export function get_descriptors_json(mol) {
     }
 }
 
+/**
+ * Get dihedral angle A—B—C—D in degrees from a SMILES string.
+ * Returns null (JSON null) if any atom index is out of range or atoms are collinear.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`, `b`, `c`, `d`: atom indices
+ *
+ * # Example
+ * ```javascript
+ * const dihedral = get_dihedral_json("CCCC", 0, 1, 2, 3);  // A-B-C-D
+ * ```
+ * @param {string} smiles
+ * @param {number} a
+ * @param {number} b
+ * @param {number} c
+ * @param {number} d
+ * @returns {any}
+ */
+export function get_dihedral_json(smiles, a, b, c, d) {
+    const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.get_dihedral_json(ptr0, len0, a, b, c, d);
+    return ret;
+}
+
 /**
  * Identify functional groups. Returns a JSON array of objects:
  * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
@@ -2693,6 +2744,47 @@ export function peoe_vsa_json(mol) {
     }
 }
 
+/**
+ * Generate `count` random SMILES from a SMILES string using the given seed.
+ * Atoms are permuted based on xorshift64 RNG. Each variant should parse back
+ * to the same molecule. Returns a JSON array of SMILES strings.
+ *
+ * # Arguments
+ * - `smiles`: input SMILES string
+ * - `count`: number of variants to generate (capped at 100)
+ * - `seed`: xorshift64 seed
+ *
+ * # Example
+ * ```javascript
+ * const variants = random_smiles_json("CC(C)O", 5, 42);
+ * // variants: ["CC(C)O", "C(C)(O)C", ...]
+ * ```
+ * @param {string} smiles
+ * @param {number} count
+ * @param {bigint} seed
+ * @returns {string}
+ */
+export function random_smiles_json(smiles, count, seed) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.random_smiles_json(ptr0, len0, count, seed);
+        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);
+    }
+}
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  * @param {MolHandle} mol
@@ -2950,6 +3042,49 @@ export function sdf_to_smiles_json(sdf) {
     }
 }
 
+/**
+ * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
+ * Rotates the D-side subtree around the B—C bond.
+ * Returns a JS error if parsing fails or atom indices are invalid.
+ *
+ * # Arguments
+ * - `smiles`: SMILES string
+ * - `a`, `b`, `c`, `d`: atom indices
+ * - `angle_deg`: target dihedral angle in degrees
+ *
+ * # Example
+ * ```javascript
+ * const pdbBlock = set_dihedral_json("CCCC", 0, 1, 2, 3, 120.0);
+ * ```
+ * @param {string} smiles
+ * @param {number} a
+ * @param {number} b
+ * @param {number} c
+ * @param {number} d
+ * @param {number} angle_deg
+ * @returns {string}
+ */
+export function set_dihedral_json(smiles, a, b, c, d, angle_deg) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.set_dihedral_json(ptr0, len0, a, b, c, d, angle_deg);
+        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);
+    }
+}
+
 /**
  * 3D shape descriptors as a JSON object.
  *
@@ -3525,7 +3660,12 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbindgen_cast_0000000000000001: function(arg0, arg1) {
+        __wbindgen_cast_0000000000000001: function(arg0) {
+            // Cast intrinsic for `F64 -> Externref`.
+            const ret = arg0;
+            return ret;
+        },
+        __wbindgen_cast_0000000000000002: function(arg0, arg1) {
             // Cast intrinsic for `Ref(String) -> Externref`.
             const ret = getStringFromWasm0(arg0, arg1);
             return ret;

package/package.json

@@ -5,7 +5,7 @@
     "kent-tokyo <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "0.1.36",
+  "version": "0.1.38",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",