@molcrafts/molrs 0.0.1

package/molrs.d.ts

@@ -0,0 +1,555 @@
+/* tslint:disable */
+/* eslint-disable */
+
+/**
+ * A block containing columnar data.
+ */
+export class Block {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Gets an f32 column as Float32Array.
+     */
+    getColumnF32(key: string): Float32Array;
+    /**
+     * Gets an f32 column with shape (for compatibility).
+     */
+    getColumnF32WithShape(key: string): any;
+    /**
+     * Gets an i64 column.
+     */
+    getColumnI64(key: string): BigInt64Array;
+    /**
+     * Gets a string column.
+     */
+    getColumnStrings(key: string): Array<any> | undefined;
+    /**
+     * Gets a u32 column.
+     */
+    getColumnU32(key: string): Uint32Array;
+    /**
+     * Gets a u8 column.
+     */
+    getColumnU8(key: string): Uint8Array | undefined;
+    /**
+     * Gets column keys.
+     */
+    keys(): Array<any>;
+    /**
+     * Gets the number of columns.
+     */
+    len(): number;
+    /**
+     * Creates a new empty Block.
+     */
+    constructor();
+    /**
+     * Gets the number of rows.
+     */
+    nrows(): number;
+    /**
+     * Renames a column.
+     */
+    renameColumn(old_key: string, new_key: string): boolean;
+    /**
+     * Sets an f32 column.
+     */
+    setColumnF32(key: string, data: Float32Array, shape?: Uint32Array | null): void;
+    /**
+     * Sets an i64 column.
+     */
+    setColumnI64(key: string, data: BigInt64Array, _shape?: Uint32Array | null): void;
+    /**
+     * Sets a string column.
+     */
+    setColumnStrings(key: string, data: Array<any>, _shape?: Uint32Array | null): void;
+    /**
+     * Sets a u32 column.
+     */
+    setColumnU32(key: string, data: Uint32Array, _shape?: Uint32Array | null): void;
+    /**
+     * Sets a u8 column.
+     */
+    setColumnU8(key: string, data: Uint8Array, _shape?: Uint32Array | null): void;
+}
+
+/**
+ * Simulation box defining the periodic boundary conditions and coordinate transformations.
+ *
+ * Represents a parallelepiped defined by a 3x3 matrix `h` and an origin.
+ * Supports periodic boundary conditions (PBC) independently in x, y, z directions.
+ */
+export class Box {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Create a cubic box.
+     *
+     * # Arguments
+     * * `a` - Side length of the cube
+     * * `origin` - 3D origin vector as Float32Array with 3 elements
+     * * `pbc_x`, `pbc_y`, `pbc_z` - Periodic boundary conditions for each axis
+     */
+    static cube(a: number, origin: Float32Array, pbc_x: boolean, pbc_y: boolean, pbc_z: boolean): Box;
+    /**
+     * Calculate displacement vectors between two sets of coordinates.
+     *
+     * # Arguments
+     * * `a` - F32View with Nx3 coordinates
+     * * `b` - F32View with Nx3 coordinates
+     * * `minimum_image` - If true, apply minimum image convention
+     *
+     * # Returns
+     * F32View with Nx3 displacement vectors (b - a)
+     */
+    delta(a: F32View, b: F32View, minimum_image: boolean): F32View;
+    get_corners(): F32View;
+    /**
+     * Get the box edge lengths as F32View [lx, ly, lz].
+     */
+    lengths(): F32View;
+    /**
+     * Create a new box from a 3x3 matrix and origin.
+     *
+     * # Arguments
+     * * `h` - 3x3 matrix as Float32Array with 9 elements (row-major: [h00, h01, h02, h10, ...])
+     * * `origin` - 3D origin vector as Float32Array with 3 elements [x, y, z]
+     * * `pbc_x`, `pbc_y`, `pbc_z` - Periodic boundary conditions for each axis
+     */
+    constructor(h: Float32Array, origin: Float32Array, pbc_x: boolean, pbc_y: boolean, pbc_z: boolean);
+    /**
+     * Get the box origin as F32View [x, y, z].
+     */
+    origin(): F32View;
+    /**
+     * Create an orthorhombic box (rectangular box with axis-aligned edges).
+     *
+     * # Arguments
+     * * `lengths` - Box dimensions as Float32Array with 3 elements [lx, ly, lz]
+     * * `origin` - 3D origin vector as Float32Array with 3 elements
+     * * `pbc_x`, `pbc_y`, `pbc_z` - Periodic boundary conditions for each axis
+     */
+    static ortho(lengths: Float32Array, origin: Float32Array, pbc_x: boolean, pbc_y: boolean, pbc_z: boolean): Box;
+    /**
+     * Get the box tilt factors as F32View [xy, xz, yz].
+     */
+    tilts(): F32View;
+    /**
+     * Convert fractional coordinates to Cartesian coordinates.
+     *
+     * # Arguments
+     * * `coords` - F32View with Nx3 coordinates
+     *
+     * # Returns
+     * F32View with Nx3 Cartesian coordinates
+     */
+    to_cart(coords: F32View): F32View;
+    /**
+     * Convert Cartesian coordinates to fractional coordinates.
+     *
+     * # Arguments
+     * * `coords` - F32View with Nx3 coordinates
+     *
+     * # Returns
+     * F32View with Nx3 fractional coordinates
+     */
+    to_frac(coords: F32View): F32View;
+    /**
+     * Get the volume of the box.
+     */
+    volume(): number;
+    /**
+     * Wrap coordinates into the primary simulation box.
+     *
+     * # Arguments
+     * * `coords` - F32View with Nx3 coordinates
+     *
+     * # Returns
+     * F32View with Nx3 wrapped coordinates
+     */
+    wrap(coords: F32View): F32View;
+}
+
+/**
+ * Zero-copy view over f32 array data shared between JavaScript and Rust.
+ *
+ * `F32View` provides a safe wrapper around f32 arrays that can be accessed from both
+ * JavaScript and Rust without copying data. The data lives in WASM linear memory,
+ * and JavaScript can create typed array views over this memory using `ptr()` and `len()`.
+ *
+ * # Memory Model
+ *
+ * - Data is stored in `Vec<f32>` in WASM linear memory (Rust heap)
+ * - JavaScript creates `Float32Array` views using `ptr()` and `len()`
+ * - No copying occurs when JavaScript reads/writes via these views
+ * - **Important**: Pointers are only valid until WASM memory grows
+ *
+ * # Safety Considerations
+ *
+ * - Views should be short-lived (don't store across async boundaries)
+ * - JavaScript must not modify the underlying array while Rust holds a reference
+ * - WASM memory can grow/relocate, invalidating pointers
+ *
+ * # Example
+ *
+ * ```javascript
+ * // Create a view for 1000 atoms with 3D coordinates
+ * const view = new F32View([1000, 3]);
+ *
+ * // Access the data from JavaScript without copying
+ * const mem = new Float32Array(wasmMemory.buffer, view.ptr(), view.len());
+ * mem.set([1.0, 2.0, 3.0, ...]); // Write data
+ *
+ * // Pass to Rust for zero-copy processing
+ * const wrapped = box.wrap(view);
+ *
+ * // Read results without copying
+ * const result = new Float32Array(wasmMemory.buffer, wrapped.ptr(), wrapped.len());
+ * ```
+ */
+export class F32View {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Get the total number of elements in the view.
+     *
+     * Returns the product of all shape dimensions.
+     */
+    len(): number;
+    /**
+     * Create a new F32View with the given shape.
+     *
+     * Allocates a buffer in WASM linear memory with size = product of shape dimensions.
+     *
+     * # Arguments
+     *
+     * * `shape` - Dimensions of the array (e.g., `[1000, 3]` for Nx3 coordinates)
+     *
+     * # Example
+     *
+     * ```javascript
+     * const view = new F32View([100, 3]); // 100 atoms, 3D coordinates
+     * console.log(view.len()); // 300
+     * ```
+     */
+    constructor(shape: Uint32Array);
+    /**
+     * Get a pointer to the underlying data for zero-copy access from JavaScript.
+     *
+     * # Returns
+     *
+     * A raw pointer to the first element of the data buffer.
+     *
+     * # Safety
+     *
+     * The pointer is only valid until the next WASM memory allocation.
+     * JavaScript should create typed array views immediately and not store the pointer.
+     *
+     * # Example
+     *
+     * ```javascript
+     * const view = new F32View([10, 3]);
+     * const ptr = view.ptr();
+     * const arr = new Float32Array(wasmMemory.buffer, ptr, view.len());
+     * ```
+     */
+    ptr(): number;
+    /**
+     * Get the shape of the array (cloned for JS boundary).
+     */
+    shape(): Uint32Array;
+    /**
+     * Compute the sum of all elements (for testing).
+     *
+     * # Returns
+     *
+     * Sum of all elements in the view.
+     */
+    sum(): number;
+    /**
+     * Export the view data as a JavaScript Float32Array.
+     *
+     * Creates a new JavaScript array and copies the data.
+     * Use this for compatibility or when you need an owned JavaScript array.
+     *
+     * # Returns
+     *
+     * A new Float32Array containing a copy of the data.
+     *
+     * # Example
+     *
+     * ```javascript
+     * const view = new F32View([2, 3]);
+     * // ... populate view ...
+     * const arr = view.to_js_array(); // Copies data
+     * ```
+     */
+    to_js_array(): Float32Array;
+    /**
+     * Write data from a JavaScript Float32Array into this view.
+     *
+     * Copies data from the JavaScript array into WASM memory once.
+     * The array length must match the view's total size.
+     *
+     * # Arguments
+     *
+     * * `arr` - JavaScript Float32Array to copy from
+     *
+     * # Errors
+     *
+     * Returns an error if the array length doesn't match the view size.
+     *
+     * # Example
+     *
+     * ```javascript
+     * const view = new F32View([2, 3]);
+     * const data = new Float32Array([1, 2, 3, 4, 5, 6]);
+     * view.write_from(data);
+     * ```
+     */
+    write_from(arr: Float32Array): void;
+}
+
+/**
+ * A frame that contains blocks of data.
+ */
+export class Frame {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Clears all blocks from the frame.
+     */
+    clear(): void;
+    /**
+     * Creates a new block in this frame.
+     */
+    createBlock(key: string): Block;
+    /**
+     * Drops this frame from the store.
+     */
+    drop(): void;
+    /**
+     * Gets an existing block by key.
+     */
+    getBlock(key: string): Block | undefined;
+    /**
+     * Inserts a block into the frame (takes ownership).
+     */
+    insertBlock(key: string, block: Block): void;
+    /**
+     * Creates a new Frame.
+     */
+    constructor();
+    /**
+     * Removes a block from the frame.
+     */
+    removeBlock(key: string): void;
+    /**
+     * Renames a block in the frame.
+     */
+    renameBlock(old_key: string, new_key: string): boolean;
+    /**
+     * Renames a column in the specified block.
+     */
+    renameColumn(block_key: string, old_col_key: string, new_col_key: string): boolean;
+    /**
+     * Gets the simulation box (if any).
+     */
+    get simbox(): Box | undefined;
+    /**
+     * Sets the simulation box.
+     */
+    set simbox(value: Box | null | undefined);
+}
+
+/**
+ * LAMMPS data file reader for WASM
+ *
+ * # Example (JavaScript)
+ * ```js
+ * const reader = new LammpsReader(fileContent);
+ * const frame = reader.read(0);
+ * ```
+ */
+export class LammpsReader {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Returns the number of frames (always 1 for LAMMPS).
+     * @returns {number}
+     */
+    len(): number;
+    constructor(content: string);
+    /**
+     * Reads a frame at the given step.
+     * @param {number} step - Frame index (LAMMPS only supports single frame, so only step=0 is valid)
+     * @returns {Frame | undefined}
+     */
+    read(step: number): Frame | undefined;
+}
+
+/**
+ * PDB file reader for WASM
+ *
+ * # Example (JavaScript)
+ * ```js
+ * const reader = new PdbReader(fileContent);
+ * const frame = reader.read(0);
+ * ```
+ */
+export class PdbReader {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Returns the number of frames (always 1 for PDB).
+     * @returns {number}
+     */
+    len(): number;
+    constructor(content: string);
+    /**
+     * Reads a frame at the given step.
+     * @param {number} step - Frame index (PDB only supports single frame, so only step=0 is valid)
+     * @returns {Frame | undefined}
+     */
+    read(step: number): Frame | undefined;
+}
+
+/**
+ * XYZ/ExtXYZ file reader for WASM
+ *
+ * # Example (JavaScript)
+ * ```js
+ * const reader = new XyzReader(fileContent);
+ * const frame = reader.read(0);
+ * ```
+ */
+export class XyzReader {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Returns the number of frames in the file.
+     * @returns {number}
+     */
+    len(): number;
+    constructor(content: string);
+    /**
+     * Reads a frame at the given step.
+     * @param {number} step - Frame index
+     * @returns {Frame | undefined}
+     */
+    read(step: number): Frame | undefined;
+}
+
+/**
+ * Writes a frame to a string in the specified format.
+ *
+ * # Example (JavaScript)
+ * ```js
+ * const output = writeFrame(frame, "xyz");
+ * console.log(output); // XYZ format string
+ * ```
+ *
+ * @param {Frame} frame - Frame to write
+ * @param {string} format - Output format ("xyz" or "pdb")
+ * @returns {string} Formatted output
+ */
+export function writeFrame(frame: Frame, format: string): string;
+
+export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembly.Module;
+
+export interface InitOutput {
+    readonly memory: WebAssembly.Memory;
+    readonly __wbg_block_free: (a: number, b: number) => void;
+    readonly __wbg_frame_free: (a: number, b: number) => void;
+    readonly block_getColumnF32: (a: number, b: number, c: number) => [number, number, number];
+    readonly block_getColumnF32WithShape: (a: number, b: number, c: number) => [number, number, number];
+    readonly block_getColumnI64: (a: number, b: number, c: number) => [number, number, number];
+    readonly block_getColumnStrings: (a: number, b: number, c: number) => any;
+    readonly block_getColumnU32: (a: number, b: number, c: number) => [number, number, number];
+    readonly block_getColumnU8: (a: number, b: number, c: number) => any;
+    readonly block_keys: (a: number) => [number, number, number];
+    readonly block_len: (a: number) => [number, number, number];
+    readonly block_new: () => number;
+    readonly block_nrows: (a: number) => [number, number, number];
+    readonly block_renameColumn: (a: number, b: number, c: number, d: number, e: number) => [number, number, number];
+    readonly block_setColumnF32: (a: number, b: number, c: number, d: any, e: number) => [number, number];
+    readonly block_setColumnI64: (a: number, b: number, c: number, d: any, e: number) => [number, number];
+    readonly block_setColumnStrings: (a: number, b: number, c: number, d: any, e: number) => [number, number];
+    readonly block_setColumnU32: (a: number, b: number, c: number, d: any, e: number) => [number, number];
+    readonly block_setColumnU8: (a: number, b: number, c: number, d: any, e: number) => [number, number];
+    readonly frame_clear: (a: number) => [number, number];
+    readonly frame_createBlock: (a: number, b: number, c: number) => [number, number, number];
+    readonly frame_drop: (a: number) => [number, number];
+    readonly frame_getBlock: (a: number, b: number, c: number) => number;
+    readonly frame_insertBlock: (a: number, b: number, c: number, d: number) => [number, number];
+    readonly frame_new: () => number;
+    readonly frame_removeBlock: (a: number, b: number, c: number) => [number, number];
+    readonly frame_renameBlock: (a: number, b: number, c: number, d: number, e: number) => [number, number, number];
+    readonly frame_renameColumn: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number];
+    readonly frame_set_simbox: (a: number, b: number) => void;
+    readonly frame_simbox: (a: number) => number;
+    readonly __wbg_f32view_free: (a: number, b: number) => void;
+    readonly f32view_len: (a: number) => number;
+    readonly f32view_new: (a: number, b: number) => number;
+    readonly f32view_ptr: (a: number) => number;
+    readonly f32view_shape: (a: number) => [number, number];
+    readonly f32view_sum: (a: number) => number;
+    readonly f32view_to_js_array: (a: number) => any;
+    readonly f32view_write_from: (a: number, b: any) => [number, number];
+    readonly __wbg_lammpsreader_free: (a: number, b: number) => void;
+    readonly __wbg_pdbreader_free: (a: number, b: number) => void;
+    readonly __wbg_xyzreader_free: (a: number, b: number) => void;
+    readonly lammpsreader_len: (a: number) => [number, number, number];
+    readonly lammpsreader_new: (a: number, b: number) => number;
+    readonly lammpsreader_read: (a: number, b: number) => [number, number, number];
+    readonly pdbreader_len: (a: number) => [number, number, number];
+    readonly pdbreader_new: (a: number, b: number) => number;
+    readonly pdbreader_read: (a: number, b: number) => [number, number, number];
+    readonly xyzreader_len: (a: number) => [number, number, number];
+    readonly xyzreader_new: (a: number, b: number) => number;
+    readonly xyzreader_read: (a: number, b: number) => [number, number, number];
+    readonly __wbg_box_free: (a: number, b: number) => void;
+    readonly box_cube: (a: number, b: any, c: number, d: number, e: number) => [number, number, number];
+    readonly box_delta: (a: number, b: number, c: number, d: number) => [number, number, number];
+    readonly box_get_corners: (a: number) => number;
+    readonly box_lengths: (a: number) => number;
+    readonly box_new: (a: any, b: any, c: number, d: number, e: number) => [number, number, number];
+    readonly box_origin: (a: number) => number;
+    readonly box_ortho: (a: any, b: any, c: number, d: number, e: number) => [number, number, number];
+    readonly box_tilts: (a: number) => number;
+    readonly box_to_cart: (a: number, b: number) => [number, number, number];
+    readonly box_to_frac: (a: number, b: number) => [number, number, number];
+    readonly box_volume: (a: number) => number;
+    readonly box_wrap: (a: number, b: number) => [number, number, number];
+    readonly writeFrame: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly __wbindgen_malloc: (a: number, b: number) => number;
+    readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
+    readonly __wbindgen_exn_store: (a: number) => void;
+    readonly __externref_table_alloc: () => number;
+    readonly __wbindgen_externrefs: WebAssembly.Table;
+    readonly __externref_table_dealloc: (a: number) => void;
+    readonly __wbindgen_free: (a: number, b: number, c: number) => void;
+    readonly __wbindgen_start: () => void;
+}
+
+export type SyncInitInput = BufferSource | WebAssembly.Module;
+
+/**
+ * Instantiates the given `module`, which can either be bytes or
+ * a precompiled `WebAssembly.Module`.
+ *
+ * @param {{ module: SyncInitInput }} module - Passing `SyncInitInput` directly is deprecated.
+ *
+ * @returns {InitOutput}
+ */
+export function initSync(module: { module: SyncInitInput } | SyncInitInput): InitOutput;
+
+/**
+ * If `module_or_path` is {RequestInfo} or {URL}, makes a request and
+ * for everything else, calls `WebAssembly.instantiate` directly.
+ *
+ * @param {{ module_or_path: InitInput | Promise<InitInput> }} module_or_path - Passing `InitInput` directly is deprecated.
+ *
+ * @returns {Promise<InitOutput>}
+ */
+export default function __wbg_init (module_or_path?: { module_or_path: InitInput | Promise<InitInput> } | InitInput | Promise<InitInput>): Promise<InitOutput>;