@molcrafts/molrs 0.0.12 → 0.0.13

package/molrs.d.ts

@@ -117,6 +117,50 @@ export class Block {
      * ```
      */
     copyColU32(key: string): Uint32Array;
+    /**
+     * Allocate a zero-filled float column at `key` with the given shape.
+     *
+     * Pair with [`viewColF`](Block::view_col_f) for zero-copy writes from JS:
+     *
+     * ```js
+     * block.createColF("x", [N]);            // allocate
+     * const view = block.viewColF("x");      // zero-copy view into the column
+     * for (let i = 0; i < N; i++) view[i] = src[i]; // direct write
+     * ```
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     * * `shape` - Shape of the column (e.g. `[N]` for 1D, `[N, 3]` for Nx3)
+     *
+     * # Errors
+     *
+     * Throws if the shape is empty, or if the leading dimension conflicts
+     * with existing columns in this block.
+     */
+    createColF(key: string, shape: Uint32Array): void;
+    /**
+     * Allocate a zero-filled i32 column at `key` with the given shape.
+     *
+     * See [`createColF`](Block::create_col_f) for the zero-copy write pattern.
+     *
+     * # Errors
+     *
+     * Throws if the shape is empty, or if the leading dimension conflicts
+     * with existing columns.
+     */
+    createColI32(key: string, shape: Uint32Array): void;
+    /**
+     * Allocate a zero-filled u32 column at `key` with the given shape.
+     *
+     * See [`createColF`](Block::create_col_f) for the zero-copy write pattern.
+     *
+     * # Errors
+     *
+     * Throws if the shape is empty, or if the leading dimension conflicts
+     * with existing columns.
+     */
+    createColU32(key: string, shape: Uint32Array): void;
     /**
      * Return the data type string for a column.
      *
@@ -1633,44 +1677,6 @@ export class InertiaTensor {
     constructor(masses?: Float64Array | null);
 }
 
-/**
- * LAMMPS dump trajectory file reader.
- *
- * Reads multi-frame LAMMPS dump files (the format produced by the
- * `dump` command). Each frame produces a [`Frame`] containing an
- * `"atoms"` block with columns matching the dump header (e.g.
- * `id`, `type`, `x`, `y`, `z`, `vx`, `vy`, `vz`).
- *
- * # Example (JavaScript)
- *
- * ```js
- * const reader = new LAMMPSDumpReader(dumpContent);
- * console.log(reader.len()); // number of timesteps
- * const frame = reader.read(0);
- * const atoms = frame.getBlock("atoms");
- * ```
- */
-export class LAMMPSDumpReader {
-    free(): void;
-    [Symbol.dispose](): void;
-    /**
-     * Check whether the file contains no frames.
-     */
-    isEmpty(): boolean;
-    /**
-     * Return the number of frames in the dump file.
-     */
-    len(): number;
-    /**
-     * Create a new LAMMPS dump reader from string content.
-     */
-    constructor(content: string);
-    /**
-     * Read a frame at the given step index.
-     */
-    read(step: number): Frame | undefined;
-}
-
 /**
  * LAMMPS data file reader.
  *
@@ -1754,6 +1760,44 @@ export class LAMMPSReader {
     read(step: number): Frame | undefined;
 }
 
+/**
+ * LAMMPS dump trajectory file reader.
+ *
+ * Reads multi-frame LAMMPS dump files (the format produced by the
+ * `dump` command). Each frame produces a [`Frame`] containing an
+ * `"atoms"` block with columns matching the dump header (e.g.
+ * `id`, `type`, `x`, `y`, `z`, `vx`, `vy`, `vz`).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const reader = new LAMMPSTrajReader(dumpContent);
+ * console.log(reader.len()); // number of timesteps
+ * const frame = reader.read(0);
+ * const atoms = frame.getBlock("atoms");
+ * ```
+ */
+export class LAMMPSTrajReader {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Check whether the file contains no frames.
+     */
+    isEmpty(): boolean;
+    /**
+     * Return the number of frames in the dump file.
+     */
+    len(): number;
+    /**
+     * Create a new LAMMPS dump reader from string content.
+     */
+    constructor(content: string);
+    /**
+     * Read a frame at the given step index.
+     */
+    read(step: number): Frame | undefined;
+}
+
 /**
  * Cell-list (linked-cell) based neighbor search.
  *

package/molrs.js

@@ -5,5 +5,5 @@ import { __wbg_set_wasm } from "./molrs_bg.js";
 __wbg_set_wasm(wasm);
 wasm.__wbindgen_start();
 export {
-    Block, Box, CenterOfMass, CenterOfMassResult, Cluster, ClusterCenters, ClusterResult, Frame, Grid, GyrationTensor, InertiaTensor, LAMMPSDumpReader, LAMMPSReader, LinkedCell, MSD, MSDResult, MolRecReader, NeighborList, PDBReader, RDF, RDFResult, RadiusOfGyration, SDFReader, SmilesIR, Topology, TopologyRingInfo, WasmArray, WasmKMeans, WasmPca2, WasmPcaResult, XYZReader, generate3D, parseSMILES, start, wasmMemory, writeFrame
+    Block, Box, CenterOfMass, CenterOfMassResult, Cluster, ClusterCenters, ClusterResult, Frame, Grid, GyrationTensor, InertiaTensor, LAMMPSReader, LAMMPSTrajReader, LinkedCell, MSD, MSDResult, MolRecReader, NeighborList, PDBReader, RDF, RDFResult, RadiusOfGyration, SDFReader, SmilesIR, Topology, TopologyRingInfo, WasmArray, WasmKMeans, WasmPca2, WasmPcaResult, XYZReader, generate3D, parseSMILES, start, wasmMemory, writeFrame
 } from "./molrs_bg.js";

package/molrs_bg.js

@@ -169,6 +169,83 @@ export class Block {
         }
         return takeFromExternrefTable0(ret[0]);
     }
+    /**
+     * Allocate a zero-filled float column at `key` with the given shape.
+     *
+     * Pair with [`viewColF`](Block::view_col_f) for zero-copy writes from JS:
+     *
+     * ```js
+     * block.createColF("x", [N]);            // allocate
+     * const view = block.viewColF("x");      // zero-copy view into the column
+     * for (let i = 0; i < N; i++) view[i] = src[i]; // direct write
+     * ```
+     *
+     * # Arguments
+     *
+     * * `key` - Column name
+     * * `shape` - Shape of the column (e.g. `[N]` for 1D, `[N, 3]` for Nx3)
+     *
+     * # Errors
+     *
+     * Throws if the shape is empty, or if the leading dimension conflicts
+     * with existing columns in this block.
+     * @param {string} key
+     * @param {Uint32Array} shape
+     */
+    createColF(key, shape) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(shape, wasm.__wbindgen_malloc_command_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.block_createColF(this.__wbg_ptr, ptr0, len0, ptr1, len1);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Allocate a zero-filled i32 column at `key` with the given shape.
+     *
+     * See [`createColF`](Block::create_col_f) for the zero-copy write pattern.
+     *
+     * # Errors
+     *
+     * Throws if the shape is empty, or if the leading dimension conflicts
+     * with existing columns.
+     * @param {string} key
+     * @param {Uint32Array} shape
+     */
+    createColI32(key, shape) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(shape, wasm.__wbindgen_malloc_command_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.block_createColI32(this.__wbg_ptr, ptr0, len0, ptr1, len1);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
+    /**
+     * Allocate a zero-filled u32 column at `key` with the given shape.
+     *
+     * See [`createColF`](Block::create_col_f) for the zero-copy write pattern.
+     *
+     * # Errors
+     *
+     * Throws if the shape is empty, or if the leading dimension conflicts
+     * with existing columns.
+     * @param {string} key
+     * @param {Uint32Array} shape
+     */
+    createColU32(key, shape) {
+        const ptr0 = passStringToWasm0(key, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(shape, wasm.__wbindgen_malloc_command_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.block_createColU32(this.__wbg_ptr, ptr0, len0, ptr1, len1);
+        if (ret[1]) {
+            throw takeFromExternrefTable0(ret[0]);
+        }
+    }
     /**
      * Return the data type string for a column.
      *
@@ -2455,83 +2532,6 @@ export class InertiaTensor {
 }
 if (Symbol.dispose) InertiaTensor.prototype[Symbol.dispose] = InertiaTensor.prototype.free;
 
-/**
- * LAMMPS dump trajectory file reader.
- *
- * Reads multi-frame LAMMPS dump files (the format produced by the
- * `dump` command). Each frame produces a [`Frame`] containing an
- * `"atoms"` block with columns matching the dump header (e.g.
- * `id`, `type`, `x`, `y`, `z`, `vx`, `vy`, `vz`).
- *
- * # Example (JavaScript)
- *
- * ```js
- * const reader = new LAMMPSDumpReader(dumpContent);
- * console.log(reader.len()); // number of timesteps
- * const frame = reader.read(0);
- * const atoms = frame.getBlock("atoms");
- * ```
- */
-export class LAMMPSDumpReader {
-    __destroy_into_raw() {
-        const ptr = this.__wbg_ptr;
-        this.__wbg_ptr = 0;
-        LAMMPSDumpReaderFinalization.unregister(this);
-        return ptr;
-    }
-    free() {
-        const ptr = this.__destroy_into_raw();
-        wasm.__wbg_lammpsdumpreader_free(ptr, 0);
-    }
-    /**
-     * Check whether the file contains no frames.
-     * @returns {boolean}
-     */
-    isEmpty() {
-        const ret = wasm.lammpsdumpreader_isEmpty(this.__wbg_ptr);
-        if (ret[2]) {
-            throw takeFromExternrefTable0(ret[1]);
-        }
-        return ret[0] !== 0;
-    }
-    /**
-     * Return the number of frames in the dump file.
-     * @returns {number}
-     */
-    len() {
-        const ret = wasm.lammpsdumpreader_len(this.__wbg_ptr);
-        if (ret[2]) {
-            throw takeFromExternrefTable0(ret[1]);
-        }
-        return ret[0] >>> 0;
-    }
-    /**
-     * Create a new LAMMPS dump reader from string content.
-     * @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.lammpsdumpreader_new(ptr0, len0);
-        this.__wbg_ptr = ret >>> 0;
-        LAMMPSDumpReaderFinalization.register(this, this.__wbg_ptr, this);
-        return this;
-    }
-    /**
-     * Read a frame at the given step index.
-     * @param {number} step
-     * @returns {Frame | undefined}
-     */
-    read(step) {
-        const ret = wasm.lammpsdumpreader_read(this.__wbg_ptr, step);
-        if (ret[2]) {
-            throw takeFromExternrefTable0(ret[1]);
-        }
-        return ret[0] === 0 ? undefined : Frame.__wrap(ret[0]);
-    }
-}
-if (Symbol.dispose) LAMMPSDumpReader.prototype[Symbol.dispose] = LAMMPSDumpReader.prototype.free;
-
 /**
  * LAMMPS data file reader.
  *
@@ -2654,6 +2654,83 @@ export class LAMMPSReader {
 }
 if (Symbol.dispose) LAMMPSReader.prototype[Symbol.dispose] = LAMMPSReader.prototype.free;
 
+/**
+ * LAMMPS dump trajectory file reader.
+ *
+ * Reads multi-frame LAMMPS dump files (the format produced by the
+ * `dump` command). Each frame produces a [`Frame`] containing an
+ * `"atoms"` block with columns matching the dump header (e.g.
+ * `id`, `type`, `x`, `y`, `z`, `vx`, `vy`, `vz`).
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * const reader = new LAMMPSTrajReader(dumpContent);
+ * console.log(reader.len()); // number of timesteps
+ * const frame = reader.read(0);
+ * const atoms = frame.getBlock("atoms");
+ * ```
+ */
+export class LAMMPSTrajReader {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        LAMMPSTrajReaderFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_lammpstrajreader_free(ptr, 0);
+    }
+    /**
+     * Check whether the file contains no frames.
+     * @returns {boolean}
+     */
+    isEmpty() {
+        const ret = wasm.lammpstrajreader_isEmpty(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] !== 0;
+    }
+    /**
+     * Return the number of frames in the dump file.
+     * @returns {number}
+     */
+    len() {
+        const ret = wasm.lammpstrajreader_len(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Create a new LAMMPS dump reader from string content.
+     * @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.lammpstrajreader_new(ptr0, len0);
+        this.__wbg_ptr = ret >>> 0;
+        LAMMPSTrajReaderFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Read a frame at the given step index.
+     * @param {number} step
+     * @returns {Frame | undefined}
+     */
+    read(step) {
+        const ret = wasm.lammpstrajreader_read(this.__wbg_ptr, step);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] === 0 ? undefined : Frame.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) LAMMPSTrajReader.prototype[Symbol.dispose] = LAMMPSTrajReader.prototype.free;
+
 /**
  * Cell-list (linked-cell) based neighbor search.
  *
@@ -5027,9 +5104,9 @@ const GyrationTensorFinalization = (typeof FinalizationRegistry === 'undefined')
 const InertiaTensorFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_inertiatensor_free(ptr >>> 0, 1));
-const LAMMPSDumpReaderFinalization = (typeof FinalizationRegistry === 'undefined')
+const LAMMPSTrajReaderFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
-    : new FinalizationRegistry(ptr => wasm.__wbg_lammpsdumpreader_free(ptr >>> 0, 1));
+    : new FinalizationRegistry(ptr => wasm.__wbg_lammpstrajreader_free(ptr >>> 0, 1));
 const LAMMPSReaderFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_lammpsreader_free(ptr >>> 0, 1));

package/package.json

@@ -5,7 +5,7 @@
     "MolCrafts"
   ],
   "description": "WASM bindings for molrs",
-  "version": "0.0.12",
+  "version": "0.0.13",
   "license": "BSD-3-Clause",
   "repository": {
     "type": "git",