@molcrafts/molrs 0.0.1 → 0.0.4

package/molrs_bg.js

@@ -0,0 +1,4017 @@
+/**
+ * Axis-aligned bounding box spatial query for neighbor search.
+ *
+ * Builds a cell-list spatial index from a [`Frame`]'s atom positions
+ * and simulation box, then supports both self-queries (unique pairs
+ * within the reference set) and cross-queries (pairs between a
+ * query set and the reference set).
+ *
+ * All distances are in angstrom (A).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const nq = new AABBQuery(frame, 3.0); // cutoff = 3.0 A
+ * const selfPairs = nq.querySelf();      // unique pairs (i < j)
+ * const crossPairs = nq.query(otherFrame); // cross-query
+ *
+ * console.log(selfPairs.numPairs);
+ * ```
+ */
+export class AABBQuery {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        AABBQueryFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_aabbquery_free(ptr, 0);
+    }
+    /**
+     * Create a spatial query from a [`Frame`] with a given distance cutoff.
+     *
+     * The frame must have:
+     * - An `"atoms"` block with `x`, `y`, `z` (f32) columns
+     * - A `simbox` (simulation box) set on the frame
+     *
+     * # Arguments
+     *
+     * * `frame` - Reference frame with atom positions and simbox
+     * * `cutoff` - Maximum neighbor distance in angstrom (A)
+     *
+     * # Returns
+     *
+     * A new `AABBQuery` ready for `query()` or `querySelf()`.
+     *
+     * # Errors
+     *
+     * Throws if the frame has no `"atoms"` block, is missing `x`/`y`/`z`
+     * columns, or has no `simbox`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const nq = new AABBQuery(frame, 5.0);
+     * ```
+     * @param {Frame} frame
+     * @param {number} cutoff
+     */
+    constructor(frame, cutoff) {
+        _assertClass(frame, Frame);
+        const ret = wasm.aabbquery_new(frame.__wbg_ptr, cutoff);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        AABBQueryFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Cross-query: find all pairs where `i` indexes query points and
+     * `j` indexes the reference points (from the constructor frame).
+     *
+     * # Arguments
+     *
+     * * `query_frame` - Frame with query atom positions (must have
+     *   `"atoms"` block with `x`, `y`, `z` columns)
+     *
+     * # Returns
+     *
+     * A [`NeighborList`] containing all `(i, j, distance)` pairs
+     * within the cutoff.
+     *
+     * # Errors
+     *
+     * Throws if `query_frame` is missing required columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const crossPairs = nq.query(otherFrame);
+     * console.log(crossPairs.numPairs);
+     * ```
+     * @param {Frame} query_frame
+     * @returns {NeighborList}
+     */
+    query(query_frame) {
+        _assertClass(query_frame, Frame);
+        const ret = wasm.aabbquery_query(this.__wbg_ptr, query_frame.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return NeighborList.__wrap(ret[0]);
+    }
+    /**
+     * Self-query: find all unique pairs `(i < j)` within the reference
+     * point set (the frame used to construct this query).
+     *
+     * # Returns
+     *
+     * A [`NeighborList`] containing all unique pairs within the cutoff.
+     * The `isSelfQuery` property will be `true`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const pairs = nq.querySelf();
+     * console.log(pairs.isSelfQuery); // true
+     * console.log(pairs.numPairs);    // number of unique pairs
+     * ```
+     * @returns {NeighborList}
+     */
+    querySelf() {
+        const ret = wasm.aabbquery_querySelf(this.__wbg_ptr);
+        return NeighborList.__wrap(ret);
+    }
+}
+if (Symbol.dispose) AABBQuery.prototype[Symbol.dispose] = AABBQuery.prototype.free;
+
+/**
+ * Column-oriented data store with typed arrays.
+ *
+ * Each column is identified by a string key and has a fixed data type
+ * (`f32`, `i32`, `u32`, `string`). All columns in a block must have
+ * the same number of rows.
+ *
+ * # Supported column types
+ *
+ * | JS type | Rust type | dtype string | Setter | Getter (copy) | Getter (view) |
+ * |---------|-----------|-------------|--------|---------------|---------------|
+ * | `Float32Array` | `f32` | `"f32"` | `setColF32` | `copyColF32` | `viewColF32` |
+ * | `Int32Array` | `i32` | `"i32"` | `setColI32` | `copyColI32` | `viewColI32` |
+ * | `Uint32Array` | `u32` | `"u32"` | `setColU32` | `copyColU32` | `viewColU32` |
+ * | `Array<string>` | `String` | `"string"` | `setColStr` | `copyColStr` | -- |
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const block = new Block();
+ * block.setColF32("x", new Float32Array([1.0, 2.0, 3.0]));
+ * block.setColF32("y", new Float32Array([0.0, 0.0, 0.0]));
+ * console.log(block.nrows()); // 3
+ * console.log(block.keys());  // ["x", "y"]
+ *
+ * const x = block.copyColF32("x"); // owned copy, safe to keep
+ * ```
+ */
+export class Block {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(Block.prototype);
+        obj.__wbg_ptr = ptr;
+        BlockFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        BlockFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_block_free(ptr, 0);
+    }
+    /**
+     * Owned `Float32Array` copy of a column.
+     *
+     * Returns a new JS `Float32Array` that is an independent copy of
+     * the column data. Safe to store and use across allocations.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Returns
+     *
+     * An owned `Float32Array` copy of the column.
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `f32`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const x = block.copyColF32("x");
+     * console.log(x[0]); // 1.0
+     * ```
+     * @param {string} key
+     * @returns {Float32Array}
+     */
+    copyColF32(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_copyColF32(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Owned `Int32Array` copy of a column.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `i32`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const types = block.copyColI32("type_id");
+     * ```
+     * @param {string} key
+     * @returns {Int32Array}
+     */
+    copyColI32(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_copyColI32(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Owned `Array<string>` copy of a string column.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Returns
+     *
+     * A JS `Array` of strings.
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `string`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const symbols = block.copyColStr("symbol"); // ["C", "C", "O"]
+     * ```
+     * @param {string} key
+     * @returns {Array<any>}
+     */
+    copyColStr(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_copyColStr(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Owned `Uint32Array` copy of a column.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `u32`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const bondI = block.copyColU32("i");
+     * const bondJ = block.copyColU32("j");
+     * ```
+     * @param {string} key
+     * @returns {Uint32Array}
+     */
+    copyColU32(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_copyColU32(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Return the data type string for a column.
+     *
+     * Possible return values: `"f32"`, `"i32"`, `"u32"`, `"bool"`,
+     * `"string"`, `"u8"`. Returns `undefined` if the column does
+     * not exist.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Returns
+     *
+     * The dtype string, or `undefined` if the column is not found.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(block.dtype("x"));      // "f32"
+     * console.log(block.dtype("symbol")); // "string"
+     * ```
+     * @param {string} key
+     * @returns {string | undefined}
+     */
+    dtype(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_dtype(this.__wbg_ptr, ptr0, len0);
+        let v2;
+        if (ret[0] !== 0) {
+            v2 = getStringFromWasm0(ret[0], ret[1]).slice();
+            wasm.__wbindgen_free_command_export(ret[0], ret[1] * 1, 1);
+        }
+        return v2;
+    }
+    /**
+     * Check whether this block has zero columns.
+     *
+     * # Errors
+     *
+     * Throws if the block handle has been invalidated.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * if (block.isEmpty()) { /* no columns yet */ }
+     * ```
+     * @returns {boolean}
+     */
+    isEmpty() {
+        const ret = wasm.block_isEmpty(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Return all column names as a JS `Array<string>`.
+     *
+     * # Errors
+     *
+     * Throws if the block handle has been invalidated.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const names = block.keys(); // ["x", "y", "z", "symbol"]
+     * ```
+     * @returns {Array<any>}
+     */
+    keys() {
+        const ret = wasm.block_keys(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Return the number of columns in this block.
+     *
+     * # Errors
+     *
+     * Throws if the block handle has been invalidated.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(block.len()); // e.g., 3
+     * ```
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.block_len(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Create a new, standalone empty `Block`.
+     *
+     * The block is backed by its own temporary store. Prefer
+     * [`Frame.createBlock()`](crate::Frame::create_block) to create
+     * blocks that are immediately attached to a frame.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the internal store allocation fails.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const block = new Block();
+     * block.setColF32("values", new Float32Array([1, 2, 3]));
+     * ```
+     */
+    constructor() {
+        const ret = wasm.block_new();
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        BlockFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Return the number of rows (shared across all columns).
+     *
+     * Returns `0` if the block has no columns.
+     *
+     * # Errors
+     *
+     * Throws if the block handle has been invalidated.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(block.nrows()); // e.g., 100
+     * ```
+     * @returns {number}
+     */
+    nrows() {
+        const ret = wasm.block_nrows(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Rename a column from `old_key` to `new_key`.
+     *
+     * # Arguments
+     *
+     * * `old_key` - Current column name
+     * * `new_key` - New column name
+     *
+     * # Returns
+     *
+     * `true` if the column was found and renamed, `false` otherwise.
+     *
+     * # Errors
+     *
+     * Throws if the block handle has been invalidated.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * block.renameColumn("element", "symbol"); // true
+     * ```
+     * @param {string} old_key
+     * @param {string} new_key
+     * @returns {boolean}
+     */
+    renameColumn(old_key, new_key) {
+        const ptr0 = passStringToWasm0(old_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(new_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.block_renameColumn(this.__wbg_ptr, ptr0, len0, ptr1, len1);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Set a float column from a `Float32Array`.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name (e.g., `"x"`, `"mass"`, `"charge"`)
+     * * `data` - `Float32Array` with the column values
+     * * `shape` - Optional shape array for multi-dimensional data
+     *   (e.g., `[N, 3]` for an Nx3 matrix stored flat). If omitted,
+     *   the data is stored as a 1D column.
+     *
+     * # Errors
+     *
+     * Throws if `shape` product does not match `data.length`, or if
+     * the resulting row count is inconsistent with existing columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * block.setColF32("x", new Float32Array([1.0, 2.0, 3.0]));
+     * // Multi-dimensional: 2 rows x 3 columns
+     * block.setColF32("pos", new Float32Array([1,2,3, 4,5,6]), [2, 3]);
+     * ```
+     * @param {string} key
+     * @param {Float32Array} data
+     * @param {Uint32Array | null} [shape]
+     */
+    setColF32(key, data, shape) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        var ptr1 = isLikeNone(shape) ? 0 : passArray32ToWasm0(shape, wasm.__wbindgen_malloc_command_export);
+        var len1 = WASM_VECTOR_LEN;
+        const ret = wasm.block_setColF32(this.__wbg_ptr, ptr0, len0, data, ptr1, len1);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Set a signed integer column from an `Int32Array`.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     * * `data` - `Int32Array` with the column values
+     *
+     * # Errors
+     *
+     * Throws if the row count is inconsistent with existing columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * block.setColI32("charge_sign", new Int32Array([1, -1, 0]));
+     * ```
+     * @param {string} key
+     * @param {Int32Array} data
+     */
+    setColI32(key, data) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_setColI32(this.__wbg_ptr, ptr0, len0, data);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Set a string column from a JS `Array<string>`.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name (e.g., `"symbol"`, `"name"`)
+     * * `data` - JS `Array` where every element must be a string
+     *
+     * # Errors
+     *
+     * Throws if any element is not a string, or if the row count is
+     * inconsistent with existing columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * atoms.setColStr("symbol", ["C", "C", "O"]);
+     * ```
+     * @param {string} key
+     * @param {Array<any>} data
+     */
+    setColStr(key, data) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_setColStr(this.__wbg_ptr, ptr0, len0, data);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Set an unsigned integer column from a `Uint32Array`.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name (e.g., `"i"`, `"j"` for bond indices)
+     * * `data` - `Uint32Array` with the column values
+     *
+     * # Errors
+     *
+     * Throws if the row count is inconsistent with existing columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * // Bond topology: atom indices
+     * bonds.setColU32("i", new Uint32Array([0, 1]));
+     * bonds.setColU32("j", new Uint32Array([1, 2]));
+     * ```
+     * @param {string} key
+     * @param {Uint32Array} data
+     */
+    setColU32(key, data) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_setColU32(this.__wbg_ptr, ptr0, len0, data);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Zero-copy `Float32Array` view into WASM linear memory.
+     *
+     * Returns a view backed directly by the block's storage in WASM
+     * memory. This avoids copying but the view becomes **invalid**
+     * if WASM linear memory grows (due to any allocation).
+     *
+     * Use [`copyColF32`](Block::copy_col_f32) for a safe, long-lived copy.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Returns
+     *
+     * A `Float32Array` view into WASM memory.
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `f32`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const view = block.viewColF32("x"); // zero-copy, use immediately
+     * const copy = block.copyColF32("x"); // safe to keep
+     * ```
+     * @param {string} key
+     * @returns {Float32Array}
+     */
+    viewColF32(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_viewColF32(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Zero-copy `Int32Array` view into WASM linear memory.
+     *
+     * **Warning**: invalidated if WASM linear memory grows.
+     * Use [`copyColI32`](Block::copy_col_i32) for a safe copy.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `i32`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const view = block.viewColI32("type_id");
+     * ```
+     * @param {string} key
+     * @returns {Int32Array}
+     */
+    viewColI32(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_viewColI32(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Zero-copy `Uint32Array` view into WASM linear memory.
+     *
+     * **Warning**: invalidated if WASM linear memory grows.
+     * Use [`copyColU32`](Block::copy_col_u32) for a safe copy.
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     *
+     * # Errors
+     *
+     * Throws if the column does not exist or is not of type `u32`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const view = block.viewColU32("i");
+     * ```
+     * @param {string} key
+     * @returns {Uint32Array}
+     */
+    viewColU32(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.block_viewColU32(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+}
+if (Symbol.dispose) Block.prototype[Symbol.dispose] = Block.prototype.free;
+
+/**
+ * Simulation box defining periodic boundary conditions and coordinate
+ * transformations.
+ *
+ * Represents a parallelepiped defined by a 3x3 matrix `h` and an
+ * origin point. Supports periodic boundary conditions (PBC)
+ * independently in x, y, z directions.
+ *
+ * Exported as `Box` in JavaScript.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const h = new Float32Array([10, 0, 0, 0, 10, 0, 0, 0, 10]);
+ * const origin = new Float32Array([0, 0, 0]);
+ * const box = new Box(h, origin, true, true, true);
+ * console.log(box.volume()); // 1000.0
+ * console.log(box.lengths().toCopy()); // [10, 10, 10]
+ * ```
+ */
+export class Box {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(Box.prototype);
+        obj.__wbg_ptr = ptr;
+        BoxFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        BoxFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_box_free(ptr, 0);
+    }
+    /**
+     * Create a cubic box with equal side lengths.
+     *
+     * # Arguments
+     *
+     * * `a` - Side length of the cube in angstrom (A)
+     * * `origin` - 3D origin vector as `Float32Array` with 3 elements
+     *   `[x, y, z]` in angstrom
+     * * `pbc_x` - Enable periodic boundary in x direction
+     * * `pbc_y` - Enable periodic boundary in y direction
+     * * `pbc_z` - Enable periodic boundary in z direction
+     *
+     * # Returns
+     *
+     * A new cubic `Box` with side length `a`.
+     *
+     * # Errors
+     *
+     * Throws if `origin` does not have 3 elements.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const origin = new Float32Array([0, 0, 0]);
+     * const box = Box.cube(10.0, origin, true, true, true);
+     * console.log(box.volume()); // 1000.0
+     * ```
+     * @param {number} a
+     * @param {Float32Array} origin
+     * @param {boolean} pbc_x
+     * @param {boolean} pbc_y
+     * @param {boolean} pbc_z
+     * @returns {Box}
+     */
+    static cube(a, origin, pbc_x, pbc_y, pbc_z) {
+        const ret = wasm.box_cube(a, origin, pbc_x, pbc_y, pbc_z);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return Box.__wrap(ret[0]);
+    }
+    /**
+     * Calculate displacement vectors between two sets of coordinates.
+     *
+     * Computes `delta = b - a` for each pair of points. When
+     * `minimum_image` is `true`, the minimum-image convention is
+     * applied so that the displacement uses the shortest vector
+     * under periodic boundary conditions.
+     *
+     * # Arguments
+     *
+     * * `a` - `WasmArray` with shape `[N, 3]` (reference positions in A)
+     * * `b` - `WasmArray` with shape `[N, 3]` (target positions in A)
+     * * `minimum_image` - If `true`, apply minimum image convention
+     *   for PBC-enabled axes
+     *
+     * # Returns
+     *
+     * `WasmArray` with shape `[N, 3]` containing displacement vectors
+     * `(b - a)` in angstrom (A).
+     *
+     * # Errors
+     *
+     * Throws if `a` or `b` does not have shape `[N, 3]`, or if the
+     * two arrays have different numbers of rows.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const a = WasmArray.from(new Float32Array([1,1,1]), [1,3]);
+     * const b = WasmArray.from(new Float32Array([9,9,9]), [1,3]);
+     * const d = box.delta(a, b, true); // minimum-image displacement
+     * ```
+     * @param {WasmArray} a
+     * @param {WasmArray} b
+     * @param {boolean} minimum_image
+     * @returns {WasmArray}
+     */
+    delta(a, b, minimum_image) {
+        _assertClass(a, WasmArray);
+        _assertClass(b, WasmArray);
+        const ret = wasm.box_delta(this.__wbg_ptr, a.__wbg_ptr, b.__wbg_ptr, minimum_image);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return WasmArray.__wrap(ret[0]);
+    }
+    /**
+     * Calculate displacement vectors and write the result directly into
+     * a [`Block`] column.
+     *
+     * This is an allocation-efficient alternative to [`delta`](Box::delta).
+     *
+     * # Arguments
+     *
+     * * `a` - `WasmArray` with shape `[N, 3]` (reference positions in A)
+     * * `b` - `WasmArray` with shape `[N, 3]` (target positions in A)
+     * * `minimum_image` - If `true`, apply minimum image convention
+     * * `out_block` - Target [`Block`] to write the result into
+     * * `out_key` - Column name for the result (f32, shape `[N, 3]`)
+     *
+     * # Errors
+     *
+     * Throws if shapes are invalid or if the block write fails.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * box.deltaToBlock(a, b, true, outBlock, "displacements");
+     * ```
+     * @param {WasmArray} a
+     * @param {WasmArray} b
+     * @param {boolean} minimum_image
+     * @param {Block} out_block
+     * @param {string} out_key
+     */
+    deltaToBlock(a, b, minimum_image, out_block, out_key) {
+        _assertClass(a, WasmArray);
+        _assertClass(b, WasmArray);
+        _assertClass(out_block, Block);
+        const ptr0 = passStringToWasm0(out_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.box_deltaToBlock(this.__wbg_ptr, a.__wbg_ptr, b.__wbg_ptr, minimum_image, out_block.__wbg_ptr, ptr0, len0);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Return the 8 corner vertices of the parallelepiped.
+     *
+     * # Returns
+     *
+     * `WasmArray` with shape `[8, 3]` containing the corner
+     * coordinates in angstrom (A). The flat array has 24 elements.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const corners = box.getCorners();
+     * console.log(corners.len()); // 24 (8 corners x 3 coords)
+     * ```
+     * @returns {WasmArray}
+     */
+    get_corners() {
+        const ret = wasm.box_get_corners(this.__wbg_ptr);
+        return WasmArray.__wrap(ret);
+    }
+    /**
+     * Return the box edge lengths as a `WasmArray` with shape `[3]`.
+     *
+     * For orthorhombic boxes these are `[lx, ly, lz]`. For triclinic
+     * boxes these are the lengths of the three cell vectors.
+     *
+     * # Returns
+     *
+     * `WasmArray` containing `[lx, ly, lz]` in angstrom (A).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const L = box.lengths().toCopy(); // Float32Array [10, 10, 10]
+     * ```
+     * @returns {WasmArray}
+     */
+    lengths() {
+        const ret = wasm.box_lengths(this.__wbg_ptr);
+        return WasmArray.__wrap(ret);
+    }
+    /**
+     * Create a new box from a 3x3 cell matrix and origin.
+     *
+     * # Arguments
+     *
+     * * `h` - 3x3 cell matrix as `Float32Array` with 9 elements in
+     *   row-major order: `[h00, h01, h02, h10, h11, h12, h20, h21, h22]`.
+     *   All values in angstrom (A).
+     * * `origin` - 3D origin vector as `Float32Array` with 3 elements
+     *   `[x, y, z]` in angstrom.
+     * * `pbc_x` - Enable periodic boundary in x direction
+     * * `pbc_y` - Enable periodic boundary in y direction
+     * * `pbc_z` - Enable periodic boundary in z direction
+     *
+     * # Returns
+     *
+     * A new `Box` instance.
+     *
+     * # Errors
+     *
+     * Throws if `h` does not have 9 elements or `origin` does not have
+     * 3 elements, or if the matrix is singular.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * // Triclinic box
+     * const h = new Float32Array([10, 2, 0, 0, 10, 0, 0, 0, 10]);
+     * const origin = new Float32Array([0, 0, 0]);
+     * const box = new Box(h, origin, true, true, true);
+     * ```
+     * @param {Float32Array} h
+     * @param {Float32Array} origin
+     * @param {boolean} pbc_x
+     * @param {boolean} pbc_y
+     * @param {boolean} pbc_z
+     */
+    constructor(h, origin, pbc_x, pbc_y, pbc_z) {
+        const ret = wasm.box_new(h, origin, pbc_x, pbc_y, pbc_z);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        BoxFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Return the box origin as a `WasmArray` with shape `[3]`.
+     *
+     * The origin is the lower-left corner of the box in angstrom (A).
+     *
+     * # Returns
+     *
+     * `WasmArray` containing `[ox, oy, oz]` in angstrom.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const o = box.origin().toCopy(); // Float32Array [0, 0, 0]
+     * ```
+     * @returns {WasmArray}
+     */
+    origin() {
+        const ret = wasm.box_origin(this.__wbg_ptr);
+        return WasmArray.__wrap(ret);
+    }
+    /**
+     * Create an orthorhombic (rectangular) box with axis-aligned edges.
+     *
+     * # Arguments
+     *
+     * * `lengths` - Box dimensions as `Float32Array` with 3 elements
+     *   `[lx, ly, lz]` in angstrom (A)
+     * * `origin` - 3D origin vector as `Float32Array` with 3 elements
+     *   `[x, y, z]` in angstrom
+     * * `pbc_x` - Enable periodic boundary in x direction
+     * * `pbc_y` - Enable periodic boundary in y direction
+     * * `pbc_z` - Enable periodic boundary in z direction
+     *
+     * # Returns
+     *
+     * A new orthorhombic `Box`.
+     *
+     * # Errors
+     *
+     * Throws if `lengths` or `origin` does not have 3 elements.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const origin = new Float32Array([0, 0, 0]);
+     * const box = Box.ortho(new Float32Array([10, 20, 30]), origin, true, true, true);
+     * console.log(box.volume()); // 6000.0
+     * ```
+     * @param {Float32Array} lengths
+     * @param {Float32Array} origin
+     * @param {boolean} pbc_x
+     * @param {boolean} pbc_y
+     * @param {boolean} pbc_z
+     * @returns {Box}
+     */
+    static ortho(lengths, origin, pbc_x, pbc_y, pbc_z) {
+        const ret = wasm.box_ortho(lengths, origin, pbc_x, pbc_y, pbc_z);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return Box.__wrap(ret[0]);
+    }
+    /**
+     * Return the box tilt factors as a `WasmArray` with shape `[3]`.
+     *
+     * Tilt factors `[xy, xz, yz]` define the off-diagonal elements
+     * of the cell matrix (LAMMPS convention). For orthorhombic boxes
+     * all tilts are zero.
+     *
+     * # Returns
+     *
+     * `WasmArray` containing `[xy, xz, yz]` (dimensionless ratios
+     * multiplied by the corresponding box length, so effectively in A).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const t = box.tilts().toCopy(); // Float32Array [0, 0, 0]
+     * ```
+     * @returns {WasmArray}
+     */
+    tilts() {
+        const ret = wasm.box_tilts(this.__wbg_ptr);
+        return WasmArray.__wrap(ret);
+    }
+    /**
+     * Convert fractional to Cartesian coordinates and write the result
+     * directly into a [`Block`] column.
+     *
+     * # Arguments
+     *
+     * * `coords` - `WasmArray` with shape `[N, 3]` (fractional, dimensionless)
+     * * `out_block` - Target [`Block`]
+     * * `out_key` - Column name for the result (f32, shape `[N, 3]`)
+     *
+     * # Errors
+     *
+     * Throws if `coords` does not have shape `[N, 3]`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * box.toCartToBlock(fracCoords, outBlock, "cart_coords");
+     * ```
+     * @param {WasmArray} coords
+     * @param {Block} out_block
+     * @param {string} out_key
+     */
+    toCartToBlock(coords, out_block, out_key) {
+        _assertClass(coords, WasmArray);
+        _assertClass(out_block, Block);
+        const ptr0 = passStringToWasm0(out_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.box_toCartToBlock(this.__wbg_ptr, coords.__wbg_ptr, out_block.__wbg_ptr, ptr0, len0);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Convert Cartesian to fractional coordinates and write the result
+     * directly into a [`Block`] column.
+     *
+     * # Arguments
+     *
+     * * `coords` - `WasmArray` with shape `[N, 3]` (Cartesian, A)
+     * * `out_block` - Target [`Block`]
+     * * `out_key` - Column name for the result (f32, shape `[N, 3]`)
+     *
+     * # Errors
+     *
+     * Throws if `coords` does not have shape `[N, 3]`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * box.toFracToBlock(cartCoords, outBlock, "frac_coords");
+     * ```
+     * @param {WasmArray} coords
+     * @param {Block} out_block
+     * @param {string} out_key
+     */
+    toFracToBlock(coords, out_block, out_key) {
+        _assertClass(coords, WasmArray);
+        _assertClass(out_block, Block);
+        const ptr0 = passStringToWasm0(out_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.box_toFracToBlock(this.__wbg_ptr, coords.__wbg_ptr, out_block.__wbg_ptr, ptr0, len0);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Convert fractional coordinates to Cartesian coordinates.
+     *
+     * # Arguments
+     *
+     * * `coords` - `WasmArray` with shape `[N, 3]` containing
+     *   fractional coordinates (dimensionless)
+     *
+     * # Returns
+     *
+     * `WasmArray` with shape `[N, 3]` containing Cartesian coordinates
+     * in angstrom (A).
+     *
+     * # Errors
+     *
+     * Throws if `coords` does not have shape `[N, 3]`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frac = WasmArray.from(new Float32Array([0.5, 0.5, 0.5]), [1, 3]);
+     * const cart = box.toCart(frac);
+     * console.log(cart.toCopy()); // [5, 5, 5] for a 10x10x10 box
+     * ```
+     * @param {WasmArray} coords
+     * @returns {WasmArray}
+     */
+    to_cart(coords) {
+        _assertClass(coords, WasmArray);
+        const ret = wasm.box_to_cart(this.__wbg_ptr, coords.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return WasmArray.__wrap(ret[0]);
+    }
+    /**
+     * Convert Cartesian coordinates to fractional coordinates.
+     *
+     * Fractional coordinates are in the range [0, 1) for atoms
+     * inside the primary image of the box.
+     *
+     * # Arguments
+     *
+     * * `coords` - `WasmArray` with shape `[N, 3]` containing
+     *   Cartesian coordinates in angstrom (A)
+     *
+     * # Returns
+     *
+     * `WasmArray` with shape `[N, 3]` containing fractional coordinates
+     * (dimensionless).
+     *
+     * # Errors
+     *
+     * Throws if `coords` does not have shape `[N, 3]`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const cart = WasmArray.from(new Float32Array([5, 5, 5]), [1, 3]);
+     * const frac = box.toFrac(cart);
+     * console.log(frac.toCopy()); // [0.5, 0.5, 0.5] for a 10x10x10 box
+     * ```
+     * @param {WasmArray} coords
+     * @returns {WasmArray}
+     */
+    to_frac(coords) {
+        _assertClass(coords, WasmArray);
+        const ret = wasm.box_to_frac(this.__wbg_ptr, coords.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return WasmArray.__wrap(ret[0]);
+    }
+    /**
+     * Return the box volume in cubic angstrom (A^3).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(box.volume()); // e.g., 1000.0
+     * ```
+     * @returns {number}
+     */
+    volume() {
+        const ret = wasm.box_volume(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Wrap Cartesian coordinates into the primary image of the box.
+     *
+     * Atoms outside the box are translated back into the primary image
+     * using the periodic boundary conditions. Only axes with PBC
+     * enabled are wrapped.
+     *
+     * # Arguments
+     *
+     * * `coords` - `WasmArray` with shape `[N, 3]` containing
+     *   Cartesian coordinates in angstrom (A)
+     *
+     * # Returns
+     *
+     * `WasmArray` with shape `[N, 3]` containing wrapped coordinates
+     * in angstrom (A).
+     *
+     * # Errors
+     *
+     * Throws if `coords` does not have shape `[N, 3]`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const pos = WasmArray.from(new Float32Array([12, -1, 5]), [1, 3]);
+     * const wrapped = box.wrap(pos); // wraps into [0, lx) x [0, ly) x [0, lz)
+     * ```
+     * @param {WasmArray} coords
+     * @returns {WasmArray}
+     */
+    wrap(coords) {
+        _assertClass(coords, WasmArray);
+        const ret = wasm.box_wrap(this.__wbg_ptr, coords.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return WasmArray.__wrap(ret[0]);
+    }
+    /**
+     * Wrap coordinates and write the result directly into a [`Block`] column.
+     *
+     * This is an allocation-efficient alternative to [`wrap`](Box::wrap)
+     * that avoids creating an intermediate `WasmArray`.
+     *
+     * # Arguments
+     *
+     * * `coords` - `WasmArray` with shape `[N, 3]` containing
+     *   Cartesian coordinates in angstrom (A)
+     * * `out_block` - Target [`Block`] to write the result into
+     * * `out_key` - Column name for the result (f32, shape `[N, 3]`)
+     *
+     * # Errors
+     *
+     * Throws if `coords` does not have shape `[N, 3]` or if the
+     * block write fails.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * box.wrapToBlock(coords, outBlock, "wrapped_pos");
+     * ```
+     * @param {WasmArray} coords
+     * @param {Block} out_block
+     * @param {string} out_key
+     */
+    wrapToBlock(coords, out_block, out_key) {
+        _assertClass(coords, WasmArray);
+        _assertClass(out_block, Block);
+        const ptr0 = passStringToWasm0(out_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.box_wrapToBlock(this.__wbg_ptr, coords.__wbg_ptr, out_block.__wbg_ptr, ptr0, len0);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+}
+if (Symbol.dispose) Box.prototype[Symbol.dispose] = Box.prototype.free;
+
+/**
+ * Distance-based cluster analysis using BFS on the neighbor graph.
+ *
+ * Particles that are connected (directly or transitively) through
+ * neighbor-list pairs are grouped into clusters. Clusters smaller
+ * than `minClusterSize` are filtered out (their particles get
+ * cluster ID = -1).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const ns = new NeighborSearch(2.0);
+ * const nlist = ns.build(frame);
+ *
+ * const cluster = new Cluster(5); // min 5 particles per cluster
+ * const result = cluster.compute(frame, nlist);
+ *
+ * console.log(result.numClusters);     // number of valid clusters
+ * console.log(result.clusterIdx());    // Int32Array, per-particle IDs
+ * console.log(result.clusterSizes());  // Uint32Array, size of each cluster
+ * ```
+ */
+export class Cluster {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        ClusterFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_cluster_free(ptr, 0);
+    }
+    /**
+     * Run cluster analysis on a frame with pre-built neighbor pairs.
+     *
+     * # Arguments
+     *
+     * * `frame` - Frame with atom positions
+     * * `neighbors` - Pre-built [`NeighborList`] defining connectivity
+     *
+     * # Returns
+     *
+     * A [`ClusterResult`] with per-particle cluster IDs and cluster sizes.
+     *
+     * # Errors
+     *
+     * Throws if the frame cannot be cloned or the analysis fails.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const result = cluster.compute(frame, nlist);
+     * ```
+     * @param {Frame} frame
+     * @param {NeighborList} neighbors
+     * @returns {ClusterResult}
+     */
+    compute(frame, neighbors) {
+        _assertClass(frame, Frame);
+        _assertClass(neighbors, NeighborList);
+        const ret = wasm.cluster_compute(this.__wbg_ptr, frame.__wbg_ptr, neighbors.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ClusterResult.__wrap(ret[0]);
+    }
+    /**
+     * Create a cluster analysis with a minimum cluster size filter.
+     *
+     * # Arguments
+     *
+     * * `min_cluster_size` - Minimum number of particles for a cluster
+     *   to be considered valid. Clusters with fewer particles are
+     *   discarded (their particles get cluster ID = -1).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const cluster = new Cluster(5); // ignore clusters < 5 particles
+     * ```
+     * @param {number} min_cluster_size
+     */
+    constructor(min_cluster_size) {
+        const ret = wasm.cluster_new(min_cluster_size);
+        this.__wbg_ptr = ret >>> 0;
+        ClusterFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) Cluster.prototype[Symbol.dispose] = Cluster.prototype.free;
+
+/**
+ * Result of a distance-based cluster analysis.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const result = cluster.compute(frame, nlist);
+ * console.log(result.numClusters);       // number
+ *
+ * const ids   = result.clusterIdx();     // Int32Array (per-particle)
+ * const sizes = result.clusterSizes();   // Uint32Array (per-cluster)
+ *
+ * // Particles in filtered-out clusters have id = -1
+ * for (let i = 0; i < ids.length; i++) {
+ *   if (ids[i] === -1) console.log(`Particle ${i} not in any valid cluster`);
+ * }
+ * ```
+ */
+export class ClusterResult {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(ClusterResult.prototype);
+        obj.__wbg_ptr = ptr;
+        ClusterResultFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        ClusterResultFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_clusterresult_free(ptr, 0);
+    }
+    /**
+     * Per-particle cluster ID assignment as `Int32Array`.
+     *
+     * `clusterIdx()[i]` is the cluster ID for particle `i`.
+     * Particles in clusters smaller than `minClusterSize` are
+     * assigned ID = -1 (filtered out).
+     *
+     * Cluster IDs are zero-based and contiguous: `0, 1, ..., numClusters-1`.
+     * @returns {Int32Array}
+     */
+    clusterIdx() {
+        const ret = wasm.clusterresult_clusterIdx(this.__wbg_ptr);
+        var v1 = getArrayI32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Size (particle count) of each valid cluster as `Uint32Array`.
+     *
+     * `clusterSizes()[c]` is the number of particles in cluster `c`.
+     * Length equals `numClusters`.
+     * @returns {Uint32Array}
+     */
+    clusterSizes() {
+        const ret = wasm.clusterresult_clusterSizes(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Number of valid clusters found (after min-size filtering).
+     * @returns {number}
+     */
+    get numClusters() {
+        const ret = wasm.clusterresult_numClusters(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+}
+if (Symbol.dispose) ClusterResult.prototype[Symbol.dispose] = ClusterResult.prototype.free;
+
+/**
+ * Hierarchical data container mapping string keys to typed [`Block`]s.
+ *
+ * A `Frame` owns a set of named blocks (column stores) and an optional
+ * simulation box ([`Box`](super::region::simbox::Box)). This is the
+ * primary interchange type for molecular data in the WASM API.
+ *
+ * # Conventions
+ *
+ * - The `"atoms"` block should contain per-atom properties: `symbol`
+ *   (string), `x`/`y`/`z` (f32, coordinates in angstrom), and optionally
+ *   `mass` (f32, atomic mass units) and `charge` (f32, elementary charges).
+ * - The `"bonds"` block should contain bond topology: `i`/`j` (u32,
+ *   zero-based atom indices) and `order` (f32, bond order: 1.0 = single,
+ *   1.5 = aromatic, 2.0 = double, 3.0 = triple).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const frame = new Frame();
+ * const atoms = frame.createBlock("atoms");
+ * atoms.setColF32("x", new Float32Array([0.0, 1.54]));
+ * ```
+ */
+export class Frame {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(Frame.prototype);
+        obj.__wbg_ptr = ptr;
+        FrameFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        FrameFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_frame_free(ptr, 0);
+    }
+    /**
+     * Remove all blocks from this frame (but keep the frame alive).
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the frame has already been dropped.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * frame.clear();
+     * ```
+     */
+    clear() {
+        const ret = wasm.frame_clear(this.__wbg_ptr);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Create a new empty [`Block`] and register it under `key`.
+     *
+     * If a block with the same key already exists it is replaced.
+     *
+     * # Arguments
+     *
+     * * `key` - Block name (e.g., `"atoms"`, `"bonds"`)
+     *
+     * # Returns
+     *
+     * A mutable [`Block`] handle that can be used to add columns.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the underlying store operation fails
+     * (e.g., the frame has been dropped).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const atoms = frame.createBlock("atoms");
+     * atoms.setColF32("x", new Float32Array([1.0, 2.0]));
+     * ```
+     * @param {string} key
+     * @returns {Block}
+     */
+    createBlock(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.frame_createBlock(this.__wbg_ptr, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return Block.__wrap(ret[0]);
+    }
+    /**
+     * Explicitly release this frame and all its blocks from the store.
+     *
+     * After calling `drop()`, any subsequent operations on this frame
+     * or its blocks will throw. This is optional -- the frame will also
+     * be released when garbage-collected by the JS engine.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the frame was already dropped.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * frame.drop();
+     * // frame.clear() would now throw
+     * ```
+     */
+    drop() {
+        const ret = wasm.frame_drop(this.__wbg_ptr);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Retrieve an existing [`Block`] by name.
+     *
+     * # Arguments
+     *
+     * * `key` - Block name to look up
+     *
+     * # Returns
+     *
+     * The [`Block`] if found, or `undefined` if no block with that key
+     * exists in this frame.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const atoms = frame.getBlock("atoms");
+     * if (atoms) {
+     *   const x = atoms.copyColF32("x");
+     * }
+     * ```
+     * @param {string} key
+     * @returns {Block | undefined}
+     */
+    getBlock(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.frame_getBlock(this.__wbg_ptr, ptr0, len0);
+        return ret === 0 ? undefined : Block.__wrap(ret);
+    }
+    /**
+     * Insert a block by deep-copying its data into this frame's store.
+     *
+     * This is useful for transferring a block from one frame to another.
+     * The source block's data is cloned; subsequent modifications to the
+     * source will not affect this frame.
+     *
+     * # Arguments
+     *
+     * * `key` - Name under which to store the block
+     * * `block` - The source [`Block`] whose data will be copied
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if either the source block or the
+     * destination frame handle is invalid.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const otherFrame = new Frame();
+     * const atoms = otherFrame.createBlock("atoms");
+     * // ... populate atoms ...
+     * frame.insertBlock("atoms", atoms);
+     * ```
+     * @param {string} key
+     * @param {Block} block
+     */
+    insertBlock(key, block) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        _assertClass(block, Block);
+        var ptr1 = block.__destroy_into_raw();
+        const ret = wasm.frame_insertBlock(this.__wbg_ptr, ptr0, len0, ptr1);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Create a new, empty `Frame` with no blocks and no simulation box.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frame = new Frame();
+     * ```
+     */
+    constructor() {
+        const ret = wasm.frame_new();
+        this.__wbg_ptr = ret >>> 0;
+        FrameFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Remove a block by name.
+     *
+     * # Arguments
+     *
+     * * `key` - Block name to remove
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the frame has been dropped or the
+     * key does not exist.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * frame.removeBlock("bonds");
+     * ```
+     * @param {string} key
+     */
+    removeBlock(key) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.frame_removeBlock(this.__wbg_ptr, ptr0, len0);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Rename a block from `old_key` to `new_key`.
+     *
+     * # Arguments
+     *
+     * * `old_key` - Current block name
+     * * `new_key` - New block name
+     *
+     * # Returns
+     *
+     * `true` if the block was found and renamed, `false` if `old_key`
+     * did not exist.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the frame has been dropped.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * frame.renameBlock("atoms", "particles");
+     * ```
+     * @param {string} old_key
+     * @param {string} new_key
+     * @returns {boolean}
+     */
+    renameBlock(old_key, new_key) {
+        const ptr0 = passStringToWasm0(old_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(new_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.frame_renameBlock(this.__wbg_ptr, ptr0, len0, ptr1, len1);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Rename a column within a specific block.
+     *
+     * # Arguments
+     *
+     * * `block_key` - Name of the block containing the column
+     * * `old_col` - Current column name
+     * * `new_col` - New column name
+     *
+     * # Returns
+     *
+     * `true` if the column was found and renamed, `false` if
+     * `old_col` did not exist in the block.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the frame or block does not exist.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * frame.renameColumn("atoms", "element", "symbol");
+     * ```
+     * @param {string} block_key
+     * @param {string} old_col
+     * @param {string} new_col
+     * @returns {boolean}
+     */
+    renameColumn(block_key, old_col, new_col) {
+        const ptr0 = passStringToWasm0(block_key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(old_col, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passStringToWasm0(new_col, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len2 = WASM_VECTOR_LEN;
+        const ret = wasm.frame_renameColumn(this.__wbg_ptr, ptr0, len0, ptr1, len1, ptr2, len2);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Attach or detach a simulation box.
+     *
+     * Pass a [`Box`](super::region::simbox::Box) to attach, or
+     * `undefined`/`null` to detach.
+     *
+     * # Arguments
+     *
+     * * `simbox` - The simulation box, or `undefined`/`null` to remove it
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the frame has been dropped.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const origin = new Float32Array([0, 0, 0]);
+     * frame.simbox = Box.cube(10.0, origin, true, true, true);
+     * ```
+     * @param {Box | null} [simbox]
+     */
+    set simbox(simbox) {
+        let ptr0 = 0;
+        if (!isLikeNone(simbox)) {
+            _assertClass(simbox, Box);
+            ptr0 = simbox.__destroy_into_raw();
+        }
+        const ret = wasm.frame_set_simbox(this.__wbg_ptr, ptr0);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Get the simulation box attached to this frame (if any).
+     *
+     * # Returns
+     *
+     * The [`Box`](super::region::simbox::Box) if one has been set,
+     * or `undefined` otherwise.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const box = frame.simbox;
+     * if (box) {
+     *   console.log("Volume:", box.volume());
+     * }
+     * ```
+     * @returns {Box | undefined}
+     */
+    get simbox() {
+        const ret = wasm.frame_simbox(this.__wbg_ptr);
+        return ret === 0 ? undefined : Box.__wrap(ret);
+    }
+}
+if (Symbol.dispose) Frame.prototype[Symbol.dispose] = Frame.prototype.free;
+
+/**
+ * LAMMPS data file reader.
+ *
+ * Reads LAMMPS data files (the format written by `write_data`). The
+ * reader produces a [`Frame`] containing:
+ *
+ * - `"atoms"` block: `type` (i32), `x`, `y`, `z` (f32, angstrom),
+ *   and optionally `charge` (f32)
+ * - `"bonds"` block (if present): `i`, `j` (u32), `type` (i32)
+ * - Simulation box (`simbox`) with PBC
+ *
+ * Only a single frame is supported (`step = 0`).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const reader = new LAMMPSReader(dataFileContent);
+ * const frame = reader.read(0);
+ * const atoms = frame.getBlock("atoms");
+ * const bonds = frame.getBlock("bonds");
+ * const box   = frame.simbox;
+ * ```
+ */
+export class LAMMPSReader {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        LAMMPSReaderFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_lammpsreader_free(ptr, 0);
+    }
+    /**
+     * Check whether the file contains no valid frames.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     * @returns {boolean}
+     */
+    isEmpty() {
+        const ret = wasm.lammpsreader_isEmpty(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Return the number of frames (always 0 or 1 for LAMMPS data files).
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.lammpsreader_len(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Create a new LAMMPS data file reader from string content.
+     *
+     * # Arguments
+     *
+     * * `content` - The full text content of a LAMMPS data file
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const reader = new LAMMPSReader(dataFileString);
+     * ```
+     * @param {string} content
+     */
+    constructor(content) {
+        const ptr0 = passStringToWasm0(content, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.lammpsreader_new(ptr0, len0);
+        this.__wbg_ptr = ret >>> 0;
+        LAMMPSReaderFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Read the frame at the given step index.
+     *
+     * LAMMPS data files contain a single configuration, so only
+     * `step = 0` is valid. Passing any other step returns `undefined`.
+     *
+     * # Arguments
+     *
+     * * `step` - Frame index (must be `0`)
+     *
+     * # Returns
+     *
+     * A [`Frame`] with atoms, optional bonds, and simbox, or `undefined`.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frame = reader.read(0);
+     * ```
+     * @param {number} step
+     * @returns {Frame | undefined}
+     */
+    read(step) {
+        const ret = wasm.lammpsreader_read(this.__wbg_ptr, step);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] === 0 ? undefined : Frame.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) LAMMPSReader.prototype[Symbol.dispose] = LAMMPSReader.prototype.free;
+
+/**
+ * Mean squared displacement (MSD) relative to a reference configuration.
+ *
+ * Computes MSD = <|r(t) - r(0)|^2> for each particle and the
+ * system average. Useful for measuring diffusion coefficients
+ * via the Einstein relation D = MSD / (6t).
+ *
+ * All distances are in angstrom (A), so MSD is in A^2.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const msd = MSD.fromReference(refFrame);
+ *
+ * for (let t = 0; t < nFrames; t++) {
+ *   const frame = reader.read(t);
+ *   const result = msd.compute(frame);
+ *   console.log(`t=${t}: MSD = ${result.mean} A^2`);
+ * }
+ * ```
+ *
+ * # References
+ *
+ * - Einstein, A. (1905). *Annalen der Physik*, 322(8), 549-560.
+ */
+export class MSD {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(MSD.prototype);
+        obj.__wbg_ptr = ptr;
+        MSDFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        MSDFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_msd_free(ptr, 0);
+    }
+    /**
+     * Compute MSD for a frame relative to the stored reference.
+     *
+     * # Arguments
+     *
+     * * `frame` - Current frame with `"atoms"` block containing
+     *   `x`, `y`, `z` (f32) columns
+     *
+     * # Returns
+     *
+     * An [`MSDResult`] with per-particle and system-average MSD
+     * values in A^2.
+     *
+     * # Errors
+     *
+     * Throws if the frame is missing required columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const result = msd.compute(currentFrame);
+     * console.log(result.mean); // system-average MSD in A^2
+     * ```
+     * @param {Frame} frame
+     * @returns {MSDResult}
+     */
+    compute(frame) {
+        _assertClass(frame, Frame);
+        const ret = wasm.msd_compute(this.__wbg_ptr, frame.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return MSDResult.__wrap(ret[0]);
+    }
+    /**
+     * Create an MSD analysis from a reference (t=0) frame.
+     *
+     * The reference frame's `"atoms"` block must have `x`, `y`, `z`
+     * (f32) columns. These positions are stored internally and used
+     * as the baseline for all subsequent `compute()` calls.
+     *
+     * # Arguments
+     *
+     * * `ref_frame` - Reference frame (typically the initial
+     *   configuration at t=0)
+     *
+     * # Returns
+     *
+     * A new `MSD` instance.
+     *
+     * # Errors
+     *
+     * Throws if the frame is missing required columns.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const msd = MSD.fromReference(initialFrame);
+     * ```
+     * @param {Frame} ref_frame
+     * @returns {MSD}
+     */
+    static fromReference(ref_frame) {
+        _assertClass(ref_frame, Frame);
+        const ret = wasm.msd_fromReference(ref_frame.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return MSD.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) MSD.prototype[Symbol.dispose] = MSD.prototype.free;
+
+/**
+ * Result of a mean squared displacement computation.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const result = msd.compute(frame);
+ * console.log(result.mean);              // number (A^2)
+ * console.log(result.perParticle());     // Float32Array (A^2)
+ * ```
+ */
+export class MSDResult {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(MSDResult.prototype);
+        obj.__wbg_ptr = ptr;
+        MSDResultFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        MSDResultFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_msdresult_free(ptr, 0);
+    }
+    /**
+     * System-average mean squared displacement in A^2.
+     *
+     * This is the arithmetic mean of all per-particle squared
+     * displacements: `mean = sum(|r_i(t) - r_i(0)|^2) / N`.
+     * @returns {number}
+     */
+    get mean() {
+        const ret = wasm.msdresult_mean(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Per-particle squared displacements as `Float32Array` in A^2.
+     *
+     * `perParticle()[i]` is `|r_i(t) - r_i(0)|^2` for particle `i`.
+     * Length equals the number of atoms.
+     * @returns {Float32Array}
+     */
+    perParticle() {
+        const ret = wasm.msdresult_perParticle(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+}
+if (Symbol.dispose) MSDResult.prototype[Symbol.dispose] = MSDResult.prototype.free;
+
+/**
+ * Result of a neighbor search: all atom pairs within a distance cutoff.
+ *
+ * Contains pair indices, distances, and squared distances for every
+ * neighbor pair found. This object is produced by [`AABBQuery`] or
+ * [`NeighborSearch`] and consumed by analysis classes like [`RDF`]
+ * and [`Cluster`].
+ *
+ * # Properties
+ *
+ * | Property | Type | Description |
+ * |----------|------|-------------|
+ * | `numPairs` | `number` | Total number of neighbor pairs |
+ * | `numPoints` | `number` | Number of reference points |
+ * | `numQueryPoints` | `number` | Number of query points |
+ * | `isSelfQuery` | `boolean` | Whether this is a self-query result |
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const nlist = nq.querySelf();
+ * console.log(nlist.numPairs);
+ *
+ * const i = nlist.queryPointIndices(); // Uint32Array
+ * const j = nlist.pointIndices();      // Uint32Array
+ * const d = nlist.distances();         // Float32Array (in A)
+ * ```
+ */
+export class NeighborList {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(NeighborList.prototype);
+        obj.__wbg_ptr = ptr;
+        NeighborListFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        NeighborListFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_neighborlist_free(ptr, 0);
+    }
+    /**
+     * Squared pairwise distances in A^2, as a `Float32Array`.
+     *
+     * More efficient than `distances()` when you only need to
+     * compare or threshold distances.
+     * @returns {Float32Array}
+     */
+    distSq() {
+        const ret = wasm.neighborlist_distSq(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Pairwise distances in angstrom (A), as a `Float32Array`.
+     *
+     * `distances()[k]` is the distance between query point
+     * `queryPointIndices()[k]` and reference point `pointIndices()[k]`.
+     * @returns {Float32Array}
+     */
+    distances() {
+        const ret = wasm.neighborlist_distances(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * **Deprecated**: Use `queryPointIndices()` instead.
+     *
+     * First particle index per pair as `Uint32Array`.
+     * @returns {Uint32Array}
+     */
+    idxI() {
+        const ret = wasm.neighborlist_idxI(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * **Deprecated**: Use `pointIndices()` instead.
+     *
+     * Second particle index per pair as `Uint32Array`.
+     * @returns {Uint32Array}
+     */
+    idxJ() {
+        const ret = wasm.neighborlist_idxJ(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Whether this result came from a self-query (`querySelf()`).
+     *
+     * In self-queries, only unique pairs `(i < j)` are reported.
+     * @returns {boolean}
+     */
+    get isSelfQuery() {
+        const ret = wasm.neighborlist_isSelfQuery(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Total number of neighbor pairs found.
+     * @returns {number}
+     */
+    get numPairs() {
+        const ret = wasm.neighborlist_numPairs(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of reference (target) points in the search.
+     * @returns {number}
+     */
+    get numPoints() {
+        const ret = wasm.neighborlist_numPoints(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Number of query points in the search.
+     *
+     * For self-queries, this equals `numPoints`.
+     * @returns {number}
+     */
+    get numQueryPoints() {
+        const ret = wasm.neighborlist_numQueryPoints(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Reference point indices (`j`) for each pair, as a `Uint32Array`.
+     * @returns {Uint32Array}
+     */
+    pointIndices() {
+        const ret = wasm.neighborlist_pointIndices(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Query point indices (`i`) for each pair, as a `Uint32Array`.
+     *
+     * The `k`-th pair connects query point `queryPointIndices()[k]`
+     * to reference point `pointIndices()[k]`.
+     * @returns {Uint32Array}
+     */
+    queryPointIndices() {
+        const ret = wasm.neighborlist_queryPointIndices(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+}
+if (Symbol.dispose) NeighborList.prototype[Symbol.dispose] = NeighborList.prototype.free;
+
+/**
+ * **Deprecated**: backward-compatible alias for [`NeighborList`].
+ *
+ * Use [`NeighborList`] instead. This type is kept only for API
+ * compatibility with older code.
+ */
+export class NeighborResult {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        NeighborResultFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_neighborresult_free(ptr, 0);
+    }
+    /**
+     * Squared pairwise distances in A^2 as `Float32Array`.
+     * @returns {Float32Array}
+     */
+    distSq() {
+        const ret = wasm.neighborresult_distSq(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * First particle index per pair as `Uint32Array`.
+     * @returns {Uint32Array}
+     */
+    idxI() {
+        const ret = wasm.neighborresult_idxI(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Second particle index per pair as `Uint32Array`.
+     * @returns {Uint32Array}
+     */
+    idxJ() {
+        const ret = wasm.neighborresult_idxJ(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Total number of neighbor pairs found.
+     * @returns {number}
+     */
+    get numPairs() {
+        const ret = wasm.neighborresult_numPairs(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+}
+if (Symbol.dispose) NeighborResult.prototype[Symbol.dispose] = NeighborResult.prototype.free;
+
+/**
+ * Neighbor search using the cell-list (link-cell) algorithm.
+ *
+ * This is a simpler, backward-compatible interface compared to
+ * [`AABBQuery`]. It performs a self-query in a single `build()` call.
+ *
+ * Prefer [`AABBQuery`] for more flexibility (cross-queries, reusable
+ * spatial index).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const ns = new NeighborSearch(3.0); // cutoff = 3.0 A
+ * const nbrs = ns.build(frame);
+ * console.log(nbrs.numPairs);
+ * ```
+ */
+export class NeighborSearch {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        NeighborSearchFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_neighborsearch_free(ptr, 0);
+    }
+    /**
+     * Build a neighbor list from a [`Frame`].
+     *
+     * Performs a self-query: finds all unique pairs `(i < j)` of atoms
+     * within the cutoff distance, using the cell-list algorithm.
+     *
+     * The frame must have:
+     * - An `"atoms"` block with `x`, `y`, `z` (f32) columns
+     * - A `simbox` (simulation box) set on the frame
+     *
+     * # Arguments
+     *
+     * * `frame` - Frame with atom positions and simbox
+     *
+     * # Returns
+     *
+     * A [`NeighborList`] containing all pairs within the cutoff.
+     *
+     * # Errors
+     *
+     * Throws if the frame is missing required data.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const nbrs = ns.build(frame);
+     * const dists = nbrs.distances(); // Float32Array
+     * ```
+     * @param {Frame} frame
+     * @returns {NeighborList}
+     */
+    build(frame) {
+        _assertClass(frame, Frame);
+        const ret = wasm.neighborsearch_build(this.__wbg_ptr, frame.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return NeighborList.__wrap(ret[0]);
+    }
+    /**
+     * Create a neighbor search with the given distance cutoff.
+     *
+     * # Arguments
+     *
+     * * `cutoff` - Maximum neighbor distance in angstrom (A)
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const ns = new NeighborSearch(5.0);
+     * ```
+     * @param {number} cutoff
+     */
+    constructor(cutoff) {
+        const ret = wasm.neighborsearch_new(cutoff);
+        this.__wbg_ptr = ret >>> 0;
+        NeighborSearchFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) NeighborSearch.prototype[Symbol.dispose] = NeighborSearch.prototype.free;
+
+/**
+ * Protein Data Bank (PDB) file reader.
+ *
+ * PDB files contain a single molecular structure. The reader produces
+ * a [`Frame`] with an `"atoms"` block containing columns such as
+ * `name` (string), `resname` (string), `x`, `y`, `z` (f32, angstrom),
+ * and optionally `occupancy` and `bfactor` (f32).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const reader = new PDBReader(pdbContent);
+ * const frame = reader.read(0);
+ * const atoms = frame.getBlock("atoms");
+ * const names = atoms.copyColStr("name"); // ["CA", "CB", ...]
+ * const x = atoms.copyColF32("x");
+ * ```
+ */
+export class PDBReader {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        PDBReaderFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_pdbreader_free(ptr, 0);
+    }
+    /**
+     * Check whether the file contains no valid frames.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     * @returns {boolean}
+     */
+    isEmpty() {
+        const ret = wasm.pdbreader_isEmpty(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Return the number of frames (always 0 or 1 for PDB files).
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.pdbreader_len(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Create a new PDB reader from a string containing the file content.
+     *
+     * # Arguments
+     *
+     * * `content` - The full text content of a PDB file
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const reader = new PDBReader(pdbString);
+     * ```
+     * @param {string} content
+     */
+    constructor(content) {
+        const ptr0 = passStringToWasm0(content, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.pdbreader_new(ptr0, len0);
+        this.__wbg_ptr = ret >>> 0;
+        PDBReaderFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Read the frame at the given step index.
+     *
+     * PDB files contain a single structure, so only `step = 0` is
+     * valid. Passing any other step returns `undefined`.
+     *
+     * # Arguments
+     *
+     * * `step` - Frame index (must be `0` for PDB files)
+     *
+     * # Returns
+     *
+     * A [`Frame`] if `step == 0` and the file is valid, or `undefined`.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frame = reader.read(0);
+     * ```
+     * @param {number} step
+     * @returns {Frame | undefined}
+     */
+    read(step) {
+        const ret = wasm.pdbreader_read(this.__wbg_ptr, step);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] === 0 ? undefined : Frame.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) PDBReader.prototype[Symbol.dispose] = PDBReader.prototype.free;
+
+/**
+ * Radial distribution function g(r) analysis.
+ *
+ * Computes the pair correlation function by binning neighbor-pair
+ * distances into a histogram and normalizing by the ideal-gas
+ * density (spherical shell volume normalization).
+ *
+ * # Algorithm
+ *
+ * g(r) = n(r) / (rho * V_shell(r) * N_ref)
+ *
+ * where `n(r)` is the pair count in bin `r`, `rho` is the number
+ * density, and `V_shell(r)` is the shell volume for that bin.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const nq = new AABBQuery(frame, 5.0);
+ * const nlist = nq.querySelf();
+ *
+ * const rdf = new RDF(100, 5.0);
+ * const result = rdf.compute(frame, nlist);
+ *
+ * const r  = result.binCenters();  // Float32Array, bin centers in A
+ * const gr = result.rdf();         // Float32Array, g(r) values
+ * ```
+ */
+export class RDF {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        RDFFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_rdf_free(ptr, 0);
+    }
+    /**
+     * Compute the RDF from a pre-built neighbor list.
+     *
+     * The frame is needed to read the simulation box volume for
+     * normalization.
+     *
+     * # Arguments
+     *
+     * * `frame` - Frame with a `simbox` set (for volume normalization)
+     * * `neighbors` - Pre-built [`NeighborList`] from [`AABBQuery`]
+     *   or [`NeighborSearch`]
+     *
+     * # Returns
+     *
+     * An [`RDFResult`] containing bin centers, g(r) values, and raw
+     * pair counts.
+     *
+     * # Errors
+     *
+     * Throws if the frame cannot be cloned or the computation fails.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const result = rdf.compute(frame, nlist);
+     * const gr = result.rdf(); // Float32Array
+     * ```
+     * @param {Frame} frame
+     * @param {NeighborList} neighbors
+     * @returns {RDFResult}
+     */
+    compute(frame, neighbors) {
+        _assertClass(frame, Frame);
+        _assertClass(neighbors, NeighborList);
+        const ret = wasm.rdf_compute(this.__wbg_ptr, frame.__wbg_ptr, neighbors.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RDFResult.__wrap(ret[0]);
+    }
+    /**
+     * Create a new RDF analysis with specified binning.
+     *
+     * # Arguments
+     *
+     * * `n_bins` - Number of histogram bins
+     * * `r_max` - Maximum radial distance in angstrom (A). Should
+     *   match or be less than the neighbor-search cutoff.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const rdf = new RDF(100, 5.0); // 100 bins up to 5 A
+     * ```
+     * @param {number} n_bins
+     * @param {number} r_max
+     */
+    constructor(n_bins, r_max) {
+        const ret = wasm.rdf_new(n_bins, r_max);
+        this.__wbg_ptr = ret >>> 0;
+        RDFFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) RDF.prototype[Symbol.dispose] = RDF.prototype.free;
+
+/**
+ * Result of a radial distribution function computation.
+ *
+ * Contains the binned g(r) values, bin geometry, raw pair counts,
+ * and normalization metadata.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const result = rdf.compute(frame, nlist);
+ * const r  = result.binCenters();  // Float32Array [0.025, 0.075, ...]
+ * const gr = result.rdf();         // Float32Array, normalized g(r)
+ * const nr = result.pairCounts();  // Float32Array, raw counts
+ * console.log("Volume:", result.volume, "A^3");
+ * console.log("N_ref:", result.numPoints);
+ * ```
+ */
+export class RDFResult {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(RDFResult.prototype);
+        obj.__wbg_ptr = ptr;
+        RDFResultFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        RDFResultFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_rdfresult_free(ptr, 0);
+    }
+    /**
+     * Bin center positions as `Float32Array` in angstrom (A).
+     *
+     * Length equals `n_bins` (the value passed to the `RDF` constructor).
+     * @returns {Float32Array}
+     */
+    binCenters() {
+        const ret = wasm.rdfresult_binCenters(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Bin edge positions as `Float32Array` in angstrom (A).
+     *
+     * Length is `n_bins + 1` (one more than bin centers).
+     * @returns {Float32Array}
+     */
+    binEdges() {
+        const ret = wasm.rdfresult_binEdges(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Number of reference points used in the normalization.
+     * @returns {number}
+     */
+    get numPoints() {
+        const ret = wasm.rdfresult_numPoints(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Raw (un-normalized) pair counts per bin as `Float32Array`.
+     * @returns {Float32Array}
+     */
+    pairCounts() {
+        const ret = wasm.rdfresult_pairCounts(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Normalized g(r) values as `Float32Array` (dimensionless).
+     *
+     * A uniform ideal gas has g(r) = 1.0 everywhere. Peaks indicate
+     * preferred interatomic distances (coordination shells).
+     * @returns {Float32Array}
+     */
+    rdf() {
+        const ret = wasm.rdfresult_rdf(this.__wbg_ptr);
+        var v1 = getArrayF32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Simulation box volume used in the normalization, in A^3.
+     * @returns {number}
+     */
+    get volume() {
+        const ret = wasm.rdfresult_volume(this.__wbg_ptr);
+        return ret;
+    }
+}
+if (Symbol.dispose) RDFResult.prototype[Symbol.dispose] = RDFResult.prototype.free;
+
+/**
+ * Reader for Zarr V3 simulation archives.
+ *
+ * Wraps [`SimulationStore`] from `molrs-core` for reading trajectory
+ * frames and system metadata from an in-memory Zarr store. The store
+ * is populated from a `Map<string, Uint8Array>` of file paths to
+ * binary content.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const files = new Map();
+ * files.set("zarr.json", new Uint8Array([...]));
+ * files.set("system/.zarray", new Uint8Array([...]));
+ * // ... etc.
+ *
+ * const reader = new SimulationReader(files);
+ * const frame = reader.readFrame(0);
+ * ```
+ */
+export class SimulationReader {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        SimulationReaderFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_simulationreader_free(ptr, 0);
+    }
+    /**
+     * Return the number of atoms in the system topology.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(reader.countAtoms()); // e.g., 256
+     * ```
+     * @returns {number}
+     */
+    countAtoms() {
+        const ret = wasm.simulationreader_countAtoms(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Return the number of trajectory frames in the archive.
+     *
+     * Returns `0` if no trajectory data is present.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on I/O errors.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(reader.countFrames()); // e.g., 1000
+     * ```
+     * @returns {number}
+     */
+    countFrames() {
+        const ret = wasm.simulationreader_countFrames(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Create a reader from a map of file paths to binary content.
+     *
+     * The map keys are relative paths within the Zarr archive
+     * (e.g., `"zarr.json"`, `"system/.zarray"`). Values are the
+     * raw bytes of each file as `Uint8Array`.
+     *
+     * # Arguments
+     *
+     * * `files` - `Map<string, Uint8Array>` mapping archive paths
+     *   to their binary content
+     *
+     * # Returns
+     *
+     * A new `SimulationReader` ready to read frames.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the archive cannot be opened
+     * (e.g., missing required metadata files).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const reader = new SimulationReader(filesMap);
+     * ```
+     * @param {Map<any, any>} files
+     */
+    constructor(files) {
+        const ret = wasm.simulationreader_new(files);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        SimulationReaderFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Read a trajectory frame at the given time index.
+     *
+     * The returned [`Frame`] merges the static system topology
+     * (atoms, bonds) with the per-frame trajectory data (positions,
+     * velocities, etc.) at time step `t`.
+     *
+     * # Arguments
+     *
+     * * `t` - Zero-based time step index
+     *
+     * # Returns
+     *
+     * A [`Frame`] with merged system + trajectory data, or `undefined`
+     * if no trajectory is present.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on I/O or deserialization errors.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frame = reader.readFrame(0);
+     * if (frame) {
+     *   const x = frame.getBlock("atoms").copyColF32("x");
+     * }
+     * ```
+     * @param {number} t
+     * @returns {Frame | undefined}
+     */
+    readFrame(t) {
+        const ret = wasm.simulationreader_readFrame(this.__wbg_ptr, t);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] === 0 ? undefined : Frame.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) SimulationReader.prototype[Symbol.dispose] = SimulationReader.prototype.free;
+
+/**
+ * Intermediate representation of a parsed SMILES string.
+ *
+ * Holds the molecular graph(s) parsed from a SMILES string. A single
+ * SMILES string can encode multiple disconnected molecules separated
+ * by `.` (e.g., `"[Na+].[Cl-]"`).
+ *
+ * Call [`toFrame()`](WasmSmilesIR::to_frame) to convert to a [`Frame`]
+ * with `"atoms"` and `"bonds"` blocks.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const ir = parseSMILES("CCO");
+ * console.log(ir.nComponents); // 1
+ *
+ * const frame = ir.toFrame();
+ * const atoms = frame.getBlock("atoms");
+ * console.log(atoms.copyColStr("symbol")); // ["C", "C", "O", "H", ...]
+ * ```
+ */
+export class SmilesIR {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(SmilesIR.prototype);
+        obj.__wbg_ptr = ptr;
+        SmilesIRFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        SmilesIRFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_smilesir_free(ptr, 0);
+    }
+    /**
+     * Return the number of disconnected components in the SMILES.
+     *
+     * Components are separated by `.` in the SMILES string. For
+     * example, `"[Na+].[Cl-]"` has 2 components.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const ir = parseSMILES("[Na+].[Cl-]");
+     * console.log(ir.nComponents); // 2
+     * ```
+     * @returns {number}
+     */
+    get nComponents() {
+        const ret = wasm.smilesir_nComponents(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Convert the intermediate representation to a [`Frame`].
+     *
+     * The resulting frame contains:
+     *
+     * - `"atoms"` block: `symbol` (string), and implicit hydrogens
+     *   are added. No 3D coordinates are present -- use
+     *   [`generate3D`](crate::generate_3d_wasm) to embed coordinates.
+     * - `"bonds"` block: `i`, `j` (u32, zero-based atom indices),
+     *   `order` (f32, bond order: 1.0 = single, 1.5 = aromatic,
+     *   2.0 = double, 3.0 = triple).
+     *
+     * # Returns
+     *
+     * A new [`Frame`] with atoms and bonds.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the conversion fails (e.g.,
+     * invalid valence).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frame = ir.toFrame();
+     * const bonds = frame.getBlock("bonds");
+     * const order = bonds.copyColF32("order");
+     * ```
+     * @returns {Frame}
+     */
+    toFrame() {
+        const ret = wasm.smilesir_toFrame(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return Frame.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) SmilesIR.prototype[Symbol.dispose] = SmilesIR.prototype.free;
+
+/**
+ * Owned f32 array with ndarray-compatible shape metadata.
+ *
+ * Stores a flat `Vec<f32>` together with a shape descriptor (e.g.,
+ * `[N, 3]` for an Nx3 coordinate matrix). Used for passing
+ * multi-dimensional numeric data across the WASM boundary.
+ *
+ * # Memory layout
+ *
+ * Data is stored in row-major (C) order, matching ndarray's default
+ * and JavaScript's `Float32Array` convention.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * // Create a 2x3 zero array
+ * const arr = new WasmArray([2, 3]);
+ * arr.writeFrom(new Float32Array([1,2,3, 4,5,6]));
+ *
+ * // Or from existing data
+ * const arr2 = WasmArray.from(new Float32Array([1,2,3]), [1, 3]);
+ *
+ * // Get data back
+ * const copy = arr.toCopy();       // safe owned copy
+ * const view = arr.toTypedArray(); // zero-copy (invalidated on alloc)
+ * ```
+ */
+export class WasmArray {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(WasmArray.prototype);
+        obj.__wbg_ptr = ptr;
+        WasmArrayFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        WasmArrayFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_wasmarray_free(ptr, 0);
+    }
+    /**
+     * Return the data type string. Always `"float"` for `WasmArray`.
+     * @returns {string}
+     */
+    dtype() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.wasmarray_dtype(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free_command_export(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Create a `WasmArray` from an existing JS `Float32Array`.
+     *
+     * # Arguments
+     *
+     * * `data` - Source `Float32Array`
+     * * `shape` - Optional shape. If omitted, defaults to `[data.length]` (1D).
+     *
+     * # Returns
+     *
+     * A new `WasmArray` owning a copy of the data.
+     *
+     * # Errors
+     *
+     * Throws if `shape` product does not equal `data.length`.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const arr = WasmArray.from(new Float32Array([1,2,3,4,5,6]), [2, 3]);
+     * console.log(arr.shape()); // [2, 3]
+     * ```
+     * @param {Float32Array} data
+     * @param {Uint32Array | null} [shape]
+     * @returns {WasmArray}
+     */
+    static from(data, shape) {
+        var ptr0 = isLikeNone(shape) ? 0 : passArray32ToWasm0(shape, wasm.__wbindgen_malloc_command_export);
+        var len0 = WASM_VECTOR_LEN;
+        const ret = wasm.wasmarray_from(data, ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return WasmArray.__wrap(ret[0]);
+    }
+    /**
+     * Check whether the array contains no elements.
+     * @returns {boolean}
+     */
+    is_empty() {
+        const ret = wasm.wasmarray_is_empty(this.__wbg_ptr);
+        return ret !== 0;
+    }
+    /**
+     * Return the total number of elements (product of all shape dimensions).
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const arr = new WasmArray([10, 3]);
+     * console.log(arr.len()); // 30
+     * ```
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.wasmarray_len(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Create a zero-initialized array with the given shape.
+     *
+     * The total number of elements is the product of all dimensions.
+     *
+     * # Arguments
+     *
+     * * `shape` - Array of dimension sizes (e.g., `[10, 3]` for 10 rows x 3 columns)
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const coords = new WasmArray([100, 3]); // 100 atoms, 3D
+     * console.log(coords.len()); // 300
+     * ```
+     * @param {Uint32Array} shape
+     */
+    constructor(shape) {
+        const ptr0 = passArray32ToWasm0(shape, wasm.__wbindgen_malloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.wasmarray_new(ptr0, len0);
+        this.__wbg_ptr = ret >>> 0;
+        WasmArrayFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Return a raw pointer to the underlying data buffer.
+     *
+     * This is intended for advanced interop with other WASM modules
+     * that need direct memory access. The pointer is only valid as
+     * long as this `WasmArray` is alive and no WASM memory growth
+     * has occurred.
+     * @returns {number}
+     */
+    ptr() {
+        const ret = wasm.wasmarray_ptr(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Return a copy of the shape metadata as a JS array.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const s = arr.shape(); // e.g., [10, 3]
+     * ```
+     * @returns {Uint32Array}
+     */
+    shape() {
+        const ret = wasm.wasmarray_shape(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free_command_export(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Compute the sum of all elements.
+     *
+     * Primarily useful for quick sanity checks and testing.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const arr = WasmArray.from(new Float32Array([1, 2, 3]));
+     * console.log(arr.sum()); // 6.0
+     * ```
+     * @returns {number}
+     */
+    sum() {
+        const ret = wasm.wasmarray_sum(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Create an owned JS `Float32Array` copy of the data.
+     *
+     * The returned array is an independent copy that is safe to store
+     * and use regardless of subsequent WASM memory operations.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const copy = arr.toCopy(); // safe to keep indefinitely
+     * ```
+     * @returns {Float32Array}
+     */
+    toCopy() {
+        const ret = wasm.wasmarray_toCopy(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Zero-copy `Float32Array` view over this array's backing storage.
+     *
+     * **Warning**: The returned view becomes **invalid** if WASM linear
+     * memory grows (due to any allocation). Use [`toCopy`](WasmArray::to_copy)
+     * if you need to keep the data.
+     *
+     * # Safety (internal)
+     *
+     * Uses `Float32Array::view` which creates an unowned view into
+     * WASM memory. The view must not outlive the `WasmArray` and must
+     * not be used after any allocation that could trigger memory growth.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const view = arr.toTypedArray(); // use immediately
+     * // Do NOT allocate between view creation and use
+     * ```
+     * @returns {Float32Array}
+     */
+    toTypedArray() {
+        const ret = wasm.wasmarray_toTypedArray(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Overwrite the array contents from a JS `Float32Array`.
+     *
+     * The source array must have exactly the same number of elements
+     * as this `WasmArray` (i.e., the shape is preserved).
+     *
+     * # Arguments
+     *
+     * * `arr` - Source `Float32Array` with matching length
+     *
+     * # Errors
+     *
+     * Throws if `arr.length` does not match this array's element count.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const wa = new WasmArray([3]);
+     * wa.writeFrom(new Float32Array([1.0, 2.0, 3.0]));
+     * ```
+     * @param {Float32Array} arr
+     */
+    write_from(arr) {
+        const ret = wasm.wasmarray_write_from(this.__wbg_ptr, arr);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+}
+if (Symbol.dispose) WasmArray.prototype[Symbol.dispose] = WasmArray.prototype.free;
+
+/**
+ * XYZ / Extended XYZ file reader.
+ *
+ * Supports multi-frame trajectory files. Each frame produces a
+ * [`Frame`] with an `"atoms"` block containing `element` (string)
+ * and `x`, `y`, `z` (f32, coordinates in angstrom) columns.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const content = await file.text(); // read file in browser
+ * const reader = new XYZReader(content);
+ * console.log(reader.len()); // number of frames
+ *
+ * const frame = reader.read(0); // first frame
+ * const atoms = frame.getBlock("atoms");
+ * const x = atoms.copyColF32("x");
+ * ```
+ */
+export class XYZReader {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        XYZReaderFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_xyzreader_free(ptr, 0);
+    }
+    /**
+     * Check whether the file contains no frames.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the file cannot be scanned.
+     * @returns {boolean}
+     */
+    isEmpty() {
+        const ret = wasm.xyzreader_isEmpty(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Return the number of frames in the file.
+     *
+     * # Returns
+     *
+     * The total frame count.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string if the file cannot be scanned.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * console.log(reader.len()); // e.g., 100
+     * ```
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.xyzreader_len(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Create a new XYZ reader from a string containing the file content.
+     *
+     * # Arguments
+     *
+     * * `content` - The full text content of an XYZ or Extended XYZ file
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const reader = new XYZReader(fileContent);
+     * ```
+     * @param {string} content
+     */
+    constructor(content) {
+        const ptr0 = passStringToWasm0(content, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.xyzreader_new(ptr0, len0);
+        this.__wbg_ptr = ret >>> 0;
+        XYZReaderFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Read a frame at the given step index.
+     *
+     * # Arguments
+     *
+     * * `step` - Zero-based frame index
+     *
+     * # Returns
+     *
+     * A [`Frame`] if the step exists, or `undefined` if `step` is
+     * out of range.
+     *
+     * # Errors
+     *
+     * Throws a `JsValue` string on parse errors.
+     *
+     * # Example (JavaScript)
+     *
+     * ```js
+     * const frame = reader.read(0);
+     * if (frame) {
+     *   const atoms = frame.getBlock("atoms");
+     * }
+     * ```
+     * @param {number} step
+     * @returns {Frame | undefined}
+     */
+    read(step) {
+        const ret = wasm.xyzreader_read(this.__wbg_ptr, step);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] === 0 ? undefined : Frame.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) XYZReader.prototype[Symbol.dispose] = XYZReader.prototype.free;
+
+/**
+ * Generate 3D coordinates for a molecular [`Frame`].
+ *
+ * The input frame must have an `"atoms"` block with a `"symbol"`
+ * string column (element symbols like `"C"`, `"N"`, `"O"`). A
+ * `"bonds"` block with `i`, `j` (u32) and `order` (f32) columns
+ * is required for correct geometry.
+ *
+ * Returns a **new** [`Frame`] with 3D coordinates added as `x`, `y`,
+ * `z` (f32, angstrom) columns in the `"atoms"` block.
+ *
+ * # Arguments
+ *
+ * * `frame` - Input molecular frame with atoms and bonds (from
+ *   [`parseSMILES`](crate::parse_smiles) or file readers)
+ * * `speed` - Quality/speed preset:
+ *   - `"fast"` -- minimal refinement, suitable for visualization
+ *   - `"medium"` (default) -- balanced quality/speed
+ *   - `"better"` -- thorough conformer search, best geometry
+ * * `seed` - Optional RNG seed (`u32`) for reproducibility. If
+ *   omitted, a random seed is used.
+ *
+ * # Returns
+ *
+ * A new [`Frame`] with 3D coordinates. The original frame is
+ * not modified.
+ *
+ * # Errors
+ *
+ * Throws a `JsValue` string if:
+ * - The frame has no `"atoms"` block or is missing required columns
+ * - The molecular graph has invalid valences or topology
+ * - The 3D embedding fails to converge
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const ir = parseSMILES("c1ccccc1"); // benzene
+ * const frame2d = ir.toFrame();
+ * const frame3d = generate3D(frame2d, "fast", 42);
+ *
+ * const atoms = frame3d.getBlock("atoms");
+ * const x = atoms.copyColF32("x"); // Float32Array with 3D x-coords
+ * const y = atoms.copyColF32("y");
+ * const z = atoms.copyColF32("z");
+ * ```
+ * @param {Frame} frame
+ * @param {string | null} [speed]
+ * @param {number | null} [seed]
+ * @returns {Frame}
+ */
+export function generate3D(frame, speed, seed) {
+    _assertClass(frame, Frame);
+    var ptr0 = isLikeNone(speed) ? 0 : passStringToWasm0(speed, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+    var len0 = WASM_VECTOR_LEN;
+    const ret = wasm.generate3D(frame.__wbg_ptr, ptr0, len0, isLikeNone(seed) ? 0x100000001 : (seed) >>> 0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return Frame.__wrap(ret[0]);
+}
+
+/**
+ * Parse a SMILES notation string into an intermediate representation.
+ *
+ * Supports standard SMILES features including ring closures,
+ * branching, stereochemistry markers, and aromatic atoms.
+ *
+ * # Arguments
+ *
+ * * `smiles` - SMILES notation string (e.g., `"CCO"` for ethanol,
+ *   `"c1ccccc1"` for benzene, `"[Na+].[Cl-]"` for NaCl)
+ *
+ * # Returns
+ *
+ * A [`SmilesIR`](WasmSmilesIR) object. Call `.toFrame()` to convert
+ * to a [`Frame`] with atoms and bonds blocks.
+ *
+ * # Errors
+ *
+ * Throws a `JsValue` string if the SMILES string is malformed
+ * (e.g., unmatched ring closure digits, invalid atom symbols).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const ir = parseSMILES("CCO");
+ * const frame = ir.toFrame();
+ * const mol3d = generate3D(frame, "fast");
+ * ```
+ * @param {string} smiles
+ * @returns {SmilesIR}
+ */
+export function parseSMILES(smiles) {
+    const ptr0 = passStringToWasm0(smiles, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.parseSMILES(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return SmilesIR.__wrap(ret[0]);
+}
+
+/**
+ * WASM module entry point. Installs the panic hook so that Rust panics
+ * are forwarded to the browser console as readable stack traces.
+ */
+export function start() {
+    wasm.start();
+}
+
+/**
+ * Return a handle to the WASM linear memory.
+ *
+ * Useful for advanced interop where JS code needs direct access to the
+ * WASM memory buffer (e.g., for zero-copy typed-array views).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const mem = wasmMemory();
+ * const buf = new Float32Array(mem.buffer, ptr, len);
+ * ```
+ * @returns {WebAssembly.Memory}
+ */
+export function wasmMemory() {
+    const ret = wasm.wasmMemory();
+    return ret;
+}
+
+/**
+ * Serialize a [`Frame`] to a string in the specified format.
+ *
+ * The frame must have an `"atoms"` block with at least an element/name
+ * string column and `x`, `y`, `z` float columns (coordinates in
+ * angstrom).
+ *
+ * # Arguments
+ *
+ * * `frame` - The [`Frame`] to write
+ * * `format` - Output format string: `"xyz"` or `"pdb"`
+ *   (case-insensitive)
+ *
+ * # Returns
+ *
+ * The formatted file content as a string.
+ *
+ * # Errors
+ *
+ * Throws a `JsValue` string if:
+ * - The format is not recognized
+ * - The frame is missing required columns
+ * - The writer encounters an error
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const xyzStr = writeFrame(frame, "xyz");
+ * console.log(xyzStr);
+ * // 2
+ * //
+ * // H  0.000000  0.000000  0.000000
+ * // O  1.000000  0.000000  0.500000
+ *
+ * const pdbStr = writeFrame(frame, "pdb");
+ * // download or display the PDB string
+ * ```
+ * @param {Frame} frame
+ * @param {string} format
+ * @returns {string}
+ */
+export function writeFrame(frame, format) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        _assertClass(frame, Frame);
+        const ptr0 = passStringToWasm0(format, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.writeFrame(frame.__wbg_ptr, 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_command_export(deferred3_0, deferred3_1, 1);
+    }
+}
+export function __wbg___wbindgen_debug_string_5398f5bb970e0daa(arg0, arg1) {
+    const ret = debugString(arg1);
+    const ptr1 = passStringToWasm0(ret, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+    const len1 = WASM_VECTOR_LEN;
+    getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
+    getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
+}
+export function __wbg___wbindgen_memory_edb3f01e3930bbf6() {
+    const ret = wasm.memory;
+    return ret;
+}
+export function __wbg___wbindgen_string_get_395e606bd0ee4427(arg0, arg1) {
+    const obj = arg1;
+    const ret = typeof(obj) === 'string' ? obj : undefined;
+    var ptr1 = isLikeNone(ret) ? 0 : passStringToWasm0(ret, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+    var len1 = WASM_VECTOR_LEN;
+    getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
+    getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
+}
+export function __wbg___wbindgen_throw_6ddd609b62940d55(arg0, arg1) {
+    throw new Error(getStringFromWasm0(arg0, arg1));
+}
+export function __wbg_done_08ce71ee07e3bd17(arg0) {
+    const ret = arg0.done;
+    return ret;
+}
+export function __wbg_error_a6fa202b58aa1cd3(arg0, arg1) {
+    let deferred0_0;
+    let deferred0_1;
+    try {
+        deferred0_0 = arg0;
+        deferred0_1 = arg1;
+        console.error(getStringFromWasm0(arg0, arg1));
+    } finally {
+        wasm.__wbindgen_free_command_export(deferred0_0, deferred0_1, 1);
+    }
+}
+export function __wbg_getRandomValues_3f44b700395062e5() { return handleError(function (arg0, arg1) {
+    globalThis.crypto.getRandomValues(getArrayU8FromWasm0(arg0, arg1));
+}, arguments); }
+export function __wbg_get_10ee87d86a58fb49(arg0, arg1) {
+    const ret = arg0.get(arg1);
+    return ret;
+}
+export function __wbg_get_unchecked_329cfe50afab7352(arg0, arg1) {
+    const ret = arg0[arg1 >>> 0];
+    return ret;
+}
+export function __wbg_keys_3fff7686656d707e(arg0) {
+    const ret = arg0.keys();
+    return ret;
+}
+export function __wbg_length_259ee9d041e381ad(arg0) {
+    const ret = arg0.length;
+    return ret;
+}
+export function __wbg_length_27280eca2d70010e(arg0) {
+    const ret = arg0.length;
+    return ret;
+}
+export function __wbg_length_76eefdd571f24b00(arg0) {
+    const ret = arg0.length;
+    return ret;
+}
+export function __wbg_length_b3416cf66a5452c8(arg0) {
+    const ret = arg0.length;
+    return ret;
+}
+export function __wbg_length_ea16607d7b61445b(arg0) {
+    const ret = arg0.length;
+    return ret;
+}
+export function __wbg_new_227d7c05414eb861() {
+    const ret = new Error();
+    return ret;
+}
+export function __wbg_new_5f486cdf45a04d78(arg0) {
+    const ret = new Uint8Array(arg0);
+    return ret;
+}
+export function __wbg_new_a70fbab9066b301f() {
+    const ret = new Array();
+    return ret;
+}
+export function __wbg_new_from_slice_898ac63cbd46f332(arg0, arg1) {
+    const ret = new Uint32Array(getArrayU32FromWasm0(arg0, arg1));
+    return ret;
+}
+export function __wbg_new_from_slice_c62f8165d6102476(arg0, arg1) {
+    const ret = new Int32Array(getArrayI32FromWasm0(arg0, arg1));
+    return ret;
+}
+export function __wbg_new_from_slice_ff2c15e8e05ffdfc(arg0, arg1) {
+    const ret = new Float32Array(getArrayF32FromWasm0(arg0, arg1));
+    return ret;
+}
+export function __wbg_next_11b99ee6237339e3() { return handleError(function (arg0) {
+    const ret = arg0.next();
+    return ret;
+}, arguments); }
+export function __wbg_prototypesetcall_247ac4333d4d3cb4(arg0, arg1, arg2) {
+    Float32Array.prototype.set.call(getArrayF32FromWasm0(arg0, arg1), arg2);
+}
+export function __wbg_prototypesetcall_52ca14fb142bc37b(arg0, arg1, arg2) {
+    Int32Array.prototype.set.call(getArrayI32FromWasm0(arg0, arg1), arg2);
+}
+export function __wbg_prototypesetcall_d62e5099504357e6(arg0, arg1, arg2) {
+    Uint8Array.prototype.set.call(getArrayU8FromWasm0(arg0, arg1), arg2);
+}
+export function __wbg_prototypesetcall_f04613188bde902d(arg0, arg1, arg2) {
+    Uint32Array.prototype.set.call(getArrayU32FromWasm0(arg0, arg1), arg2);
+}
+export function __wbg_push_e87b0e732085a946(arg0, arg1) {
+    const ret = arg0.push(arg1);
+    return ret;
+}
+export function __wbg_stack_3b0d974bbf31e44f(arg0, arg1) {
+    const ret = arg1.stack;
+    const ptr1 = passStringToWasm0(ret, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+    const len1 = WASM_VECTOR_LEN;
+    getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
+    getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
+}
+export function __wbg_value_21fc78aab0322612(arg0) {
+    const ret = arg0.value;
+    return ret;
+}
+export function __wbindgen_cast_0000000000000001(arg0, arg1) {
+    // Cast intrinsic for `Ref(Slice(F32)) -> NamedExternref("Float32Array")`.
+    const ret = getArrayF32FromWasm0(arg0, arg1);
+    return ret;
+}
+export function __wbindgen_cast_0000000000000002(arg0, arg1) {
+    // Cast intrinsic for `Ref(Slice(I32)) -> NamedExternref("Int32Array")`.
+    const ret = getArrayI32FromWasm0(arg0, arg1);
+    return ret;
+}
+export function __wbindgen_cast_0000000000000003(arg0, arg1) {
+    // Cast intrinsic for `Ref(Slice(U32)) -> NamedExternref("Uint32Array")`.
+    const ret = getArrayU32FromWasm0(arg0, arg1);
+    return ret;
+}
+export function __wbindgen_cast_0000000000000004(arg0, arg1) {
+    // Cast intrinsic for `Ref(String) -> Externref`.
+    const ret = getStringFromWasm0(arg0, arg1);
+    return ret;
+}
+export function __wbindgen_init_externref_table() {
+    const table = wasm.__wbindgen_externrefs;
+    const offset = table.grow(4);
+    table.set(0, undefined);
+    table.set(offset + 0, undefined);
+    table.set(offset + 1, null);
+    table.set(offset + 2, true);
+    table.set(offset + 3, false);
+}
+const AABBQueryFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_aabbquery_free(ptr >>> 0, 1));
+const BlockFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_block_free(ptr >>> 0, 1));
+const BoxFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_box_free(ptr >>> 0, 1));
+const ClusterFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_cluster_free(ptr >>> 0, 1));
+const ClusterResultFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_clusterresult_free(ptr >>> 0, 1));
+const FrameFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_frame_free(ptr >>> 0, 1));
+const LAMMPSReaderFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_lammpsreader_free(ptr >>> 0, 1));
+const MSDFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_msd_free(ptr >>> 0, 1));
+const MSDResultFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_msdresult_free(ptr >>> 0, 1));
+const NeighborListFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_neighborlist_free(ptr >>> 0, 1));
+const NeighborResultFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_neighborresult_free(ptr >>> 0, 1));
+const NeighborSearchFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_neighborsearch_free(ptr >>> 0, 1));
+const PDBReaderFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_pdbreader_free(ptr >>> 0, 1));
+const RDFFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_rdf_free(ptr >>> 0, 1));
+const RDFResultFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_rdfresult_free(ptr >>> 0, 1));
+const SimulationReaderFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_simulationreader_free(ptr >>> 0, 1));
+const WasmArrayFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_wasmarray_free(ptr >>> 0, 1));
+const SmilesIRFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_smilesir_free(ptr >>> 0, 1));
+const XYZReaderFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_xyzreader_free(ptr >>> 0, 1));
+
+function addToExternrefTable0(obj) {
+    const idx = wasm.__externref_table_alloc_command_export();
+    wasm.__wbindgen_externrefs.set(idx, obj);
+    return idx;
+}
+
+function _assertClass(instance, klass) {
+    if (!(instance instanceof klass)) {
+        throw new Error(`expected instance of ${klass.name}`);
+    }
+}
+
+function debugString(val) {
+    // primitive types
+    const type = typeof val;
+    if (type == 'number' || type == 'boolean' || val == null) {
+        return  `${val}`;
+    }
+    if (type == 'string') {
+        return `"${val}"`;
+    }
+    if (type == 'symbol') {
+        const description = val.description;
+        if (description == null) {
+            return 'Symbol';
+        } else {
+            return `Symbol(${description})`;
+        }
+    }
+    if (type == 'function') {
+        const name = val.name;
+        if (typeof name == 'string' && name.length > 0) {
+            return `Function(${name})`;
+        } else {
+            return 'Function';
+        }
+    }
+    // objects
+    if (Array.isArray(val)) {
+        const length = val.length;
+        let debug = '[';
+        if (length > 0) {
+            debug += debugString(val[0]);
+        }
+        for(let i = 1; i < length; i++) {
+            debug += ', ' + debugString(val[i]);
+        }
+        debug += ']';
+        return debug;
+    }
+    // Test for built-in
+    const builtInMatches = /\[object ([^\]]+)\]/.exec(toString.call(val));
+    let className;
+    if (builtInMatches && builtInMatches.length > 1) {
+        className = builtInMatches[1];
+    } else {
+        // Failed to match the standard '[object ClassName]'
+        return toString.call(val);
+    }
+    if (className == 'Object') {
+        // we're a user defined class or Object
+        // JSON.stringify avoids problems with cycles, and is generally much
+        // easier than looping through ownProperties of `val`.
+        try {
+            return 'Object(' + JSON.stringify(val) + ')';
+        } catch (_) {
+            return 'Object';
+        }
+    }
+    // errors
+    if (val instanceof Error) {
+        return `${val.name}: ${val.message}\n${val.stack}`;
+    }
+    // TODO we could test for more things here, like `Set`s and `Map`s.
+    return className;
+}
+
+function getArrayF32FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getFloat32ArrayMemory0().subarray(ptr / 4, ptr / 4 + len);
+}
+
+function getArrayI32FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getInt32ArrayMemory0().subarray(ptr / 4, ptr / 4 + len);
+}
+
+function getArrayU32FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getUint32ArrayMemory0().subarray(ptr / 4, ptr / 4 + len);
+}
+
+function getArrayU8FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
+}
+
+let cachedDataViewMemory0 = null;
+function getDataViewMemory0() {
+    if (cachedDataViewMemory0 === null || cachedDataViewMemory0.buffer.detached === true || (cachedDataViewMemory0.buffer.detached === undefined && cachedDataViewMemory0.buffer !== wasm.memory.buffer)) {
+        cachedDataViewMemory0 = new DataView(wasm.memory.buffer);
+    }
+    return cachedDataViewMemory0;
+}
+
+let cachedFloat32ArrayMemory0 = null;
+function getFloat32ArrayMemory0() {
+    if (cachedFloat32ArrayMemory0 === null || cachedFloat32ArrayMemory0.byteLength === 0) {
+        cachedFloat32ArrayMemory0 = new Float32Array(wasm.memory.buffer);
+    }
+    return cachedFloat32ArrayMemory0;
+}
+
+let cachedInt32ArrayMemory0 = null;
+function getInt32ArrayMemory0() {
+    if (cachedInt32ArrayMemory0 === null || cachedInt32ArrayMemory0.byteLength === 0) {
+        cachedInt32ArrayMemory0 = new Int32Array(wasm.memory.buffer);
+    }
+    return cachedInt32ArrayMemory0;
+}
+
+function getStringFromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return decodeText(ptr, len);
+}
+
+let cachedUint32ArrayMemory0 = null;
+function getUint32ArrayMemory0() {
+    if (cachedUint32ArrayMemory0 === null || cachedUint32ArrayMemory0.byteLength === 0) {
+        cachedUint32ArrayMemory0 = new Uint32Array(wasm.memory.buffer);
+    }
+    return cachedUint32ArrayMemory0;
+}
+
+let cachedUint8ArrayMemory0 = null;
+function getUint8ArrayMemory0() {
+    if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
+        cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
+    }
+    return cachedUint8ArrayMemory0;
+}
+
+function handleError(f, args) {
+    try {
+        return f.apply(this, args);
+    } catch (e) {
+        const idx = addToExternrefTable0(e);
+        wasm.__wbindgen_exn_store_command_export(idx);
+    }
+}
+
+function isLikeNone(x) {
+    return x === undefined || x === null;
+}
+
+function passArray32ToWasm0(arg, malloc) {
+    const ptr = malloc(arg.length * 4, 4) >>> 0;
+    getUint32ArrayMemory0().set(arg, ptr / 4);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+
+function passStringToWasm0(arg, malloc, realloc) {
+    if (realloc === undefined) {
+        const buf = cachedTextEncoder.encode(arg);
+        const ptr = malloc(buf.length, 1) >>> 0;
+        getUint8ArrayMemory0().subarray(ptr, ptr + buf.length).set(buf);
+        WASM_VECTOR_LEN = buf.length;
+        return ptr;
+    }
+
+    let len = arg.length;
+    let ptr = malloc(len, 1) >>> 0;
+
+    const mem = getUint8ArrayMemory0();
+
+    let offset = 0;
+
+    for (; offset < len; offset++) {
+        const code = arg.charCodeAt(offset);
+        if (code > 0x7F) break;
+        mem[ptr + offset] = code;
+    }
+    if (offset !== len) {
+        if (offset !== 0) {
+            arg = arg.slice(offset);
+        }
+        ptr = realloc(ptr, len, len = offset + arg.length * 3, 1) >>> 0;
+        const view = getUint8ArrayMemory0().subarray(ptr + offset, ptr + len);
+        const ret = cachedTextEncoder.encodeInto(arg, view);
+
+        offset += ret.written;
+        ptr = realloc(ptr, len, offset, 1) >>> 0;
+    }
+
+    WASM_VECTOR_LEN = offset;
+    return ptr;
+}
+
+function takeFromExternrefTable0(idx) {
+    const value = wasm.__wbindgen_externrefs.get(idx);
+    wasm.__externref_table_dealloc_command_export(idx);
+    return value;
+}
+
+let cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+cachedTextDecoder.decode();
+const MAX_SAFARI_DECODE_BYTES = 2146435072;
+let numBytesDecoded = 0;
+function decodeText(ptr, len) {
+    numBytesDecoded += len;
+    if (numBytesDecoded >= MAX_SAFARI_DECODE_BYTES) {
+        cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+        cachedTextDecoder.decode();
+        numBytesDecoded = len;
+    }
+    return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
+}
+
+const cachedTextEncoder = new TextEncoder();
+
+if (!('encodeInto' in cachedTextEncoder)) {
+    cachedTextEncoder.encodeInto = function (arg, view) {
+        const buf = cachedTextEncoder.encode(arg);
+        view.set(buf);
+        return {
+            read: arg.length,
+            written: buf.length
+        };
+    };
+}
+
+let WASM_VECTOR_LEN = 0;
+
+
+let wasm;
+export function __wbg_set_wasm(val) {
+    wasm = val;
+}