@molcrafts/molrs 0.0.17 → 0.1.1

package/README.md

@@ -78,7 +78,7 @@ Frames without a simulation box are supported — a non-periodic bounding box is
 | `bonds` | `i`, `j` | `u32` | Atom indices |
 | `bonds` | `order` | `F` | Bond order (1.0, 1.5, 2.0, 3.0) |
 
-`F` is the workspace float type from `molrs-core` — always `f64`.
+`F` is the molrs core float type — always `f64`.
 
 ## Build from source
 

package/molrs.d.ts

@@ -2048,7 +2048,7 @@ export class MSD {
      */
     reset(): void;
     /**
-     * Run the stateless [`molrs_compute::MSD`] over every fed frame and
+     * Run the stateless [`molrs::compute::MSD`] over every fed frame and
      * return the per-frame time series.
      *
      * The first frame is always the reference, so `results()[0].mean ≈ 0`.
@@ -2317,7 +2317,7 @@ export class RDF {
      *
      * Use this for non-periodic systems or to override the box volume.
      * Internally wraps the supplied volume as a cubic SimBox since the
-     * underlying [`molrs_compute::RDF`] pulls its normalization volume from
+     * underlying [`molrs::compute::RDF`] pulls its normalization volume from
      * `frame.simbox`.
      *
      * # Arguments
@@ -2884,7 +2884,7 @@ export class WasmArray {
 }
 
 /**
- * Wrapper for [`molrs_compute::kmeans::KMeans`].
+ * Wrapper for [`molrs::compute::kmeans::KMeans`].
  *
  * # Example (JavaScript)
  *
@@ -3210,7 +3210,7 @@ export class WasmLammpsDumpStream {
 }
 
 /**
- * Stateless wrapper for [`molrs_compute::pca::Pca2`].
+ * Stateless wrapper for [`molrs::compute::pca::Pca2`].
  *
  * All configuration lives on [`fitTransform`](Self::fit_transform).
  *
@@ -3786,6 +3786,24 @@ export class XYZReader {
     read(step: number): Frame | undefined;
 }
 
+/**
+ * Covalent radius (in angstrom) for an element symbol.
+ *
+ * Case-insensitive lookup against the built-in periodic table. Returns
+ * `null` (`undefined` in JS) for an unrecognised symbol. This is the
+ * single source of truth for covalent radii — downstream code (e.g. bond
+ * perception) should call this rather than carrying its own table.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * covalentRadius("C");  // 0.76
+ * covalentRadius("h");  // 0.31 (case-insensitive)
+ * covalentRadius("Xx"); // undefined
+ * ```
+ */
+export function covalentRadius(symbol: string): number | undefined;
+
 /**
  * Generate 3D coordinates for a molecular [`Frame`].
  *

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, CHGCARReader, CIFReader, CenterOfMass, CenterOfMassResult, Cluster, ClusterCenters, ClusterResult, CubeReader, DCDReader, Frame, FrameIndexEntry, GyrationTensor, InertiaTensor, LAMMPSReader, LAMMPSTrajReader, LinkedCell, MSD, MSDResult, MolRecReader, NeighborList, PDBReader, RDF, RDFResult, RadiusOfGyration, SDFReader, SmilesIR, Topology, TopologyRingInfo, WasmArray, WasmKMeans, WasmLammpsDataStream, WasmLammpsDumpStream, WasmPca2, WasmPcaResult, WasmPdbStream, WasmSdfStream, WasmXyzStream, XYZReader, generate3D, parseSMILES, start, wasmMemory, writeFrame
+    Block, Box, CHGCARReader, CIFReader, CenterOfMass, CenterOfMassResult, Cluster, ClusterCenters, ClusterResult, CubeReader, DCDReader, Frame, FrameIndexEntry, GyrationTensor, InertiaTensor, LAMMPSReader, LAMMPSTrajReader, LinkedCell, MSD, MSDResult, MolRecReader, NeighborList, PDBReader, RDF, RDFResult, RadiusOfGyration, SDFReader, SmilesIR, Topology, TopologyRingInfo, WasmArray, WasmKMeans, WasmLammpsDataStream, WasmLammpsDumpStream, WasmPca2, WasmPcaResult, WasmPdbStream, WasmSdfStream, WasmXyzStream, XYZReader, covalentRadius, generate3D, parseSMILES, start, wasmMemory, writeFrame
 } from "./molrs_bg.js";

package/molrs_bg.js

@@ -3111,7 +3111,7 @@ export class MSD {
         wasm.msd_reset(this.__wbg_ptr);
     }
     /**
-     * Run the stateless [`molrs_compute::MSD`] over every fed frame and
+     * Run the stateless [`molrs::compute::MSD`] over every fed frame and
      * return the per-frame time series.
      *
      * The first frame is always the reference, so `results()[0].mean ≈ 0`.
@@ -3561,7 +3561,7 @@ export class RDF {
      *
      * Use this for non-periodic systems or to override the box volume.
      * Internally wraps the supplied volume as a cubic SimBox since the
-     * underlying [`molrs_compute::RDF`] pulls its normalization volume from
+     * underlying [`molrs::compute::RDF`] pulls its normalization volume from
      * `frame.simbox`.
      *
      * # Arguments
@@ -4531,7 +4531,7 @@ export class WasmArray {
 if (Symbol.dispose) WasmArray.prototype[Symbol.dispose] = WasmArray.prototype.free;
 
 /**
- * Wrapper for [`molrs_compute::kmeans::KMeans`].
+ * Wrapper for [`molrs::compute::kmeans::KMeans`].
  *
  * # Example (JavaScript)
  *
@@ -5211,7 +5211,7 @@ export class WasmLammpsDumpStream {
 if (Symbol.dispose) WasmLammpsDumpStream.prototype[Symbol.dispose] = WasmLammpsDumpStream.prototype.free;
 
 /**
- * Stateless wrapper for [`molrs_compute::pca::Pca2`].
+ * Stateless wrapper for [`molrs::compute::pca::Pca2`].
  *
  * All configuration lives on [`fitTransform`](Self::fit_transform).
  *
@@ -6357,6 +6357,31 @@ export class XYZReader {
 }
 if (Symbol.dispose) XYZReader.prototype[Symbol.dispose] = XYZReader.prototype.free;
 
+/**
+ * Covalent radius (in angstrom) for an element symbol.
+ *
+ * Case-insensitive lookup against the built-in periodic table. Returns
+ * `null` (`undefined` in JS) for an unrecognised symbol. This is the
+ * single source of truth for covalent radii — downstream code (e.g. bond
+ * perception) should call this rather than carrying its own table.
+ *
+ * # Example (JavaScript)
+ *
+ * ```js
+ * covalentRadius("C");  // 0.76
+ * covalentRadius("h");  // 0.31 (case-insensitive)
+ * covalentRadius("Xx"); // undefined
+ * ```
+ * @param {string} symbol
+ * @returns {number | undefined}
+ */
+export function covalentRadius(symbol) {
+    const ptr0 = passStringToWasm0(symbol, wasm.__wbindgen_malloc_command_export, wasm.__wbindgen_realloc_command_export);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.covalentRadius(ptr0, len0);
+    return ret[0] === 0 ? undefined : ret[1];
+}
+
 /**
  * Generate 3D coordinates for a molecular [`Frame`].
  *
@@ -6549,18 +6574,18 @@ export function writeFrame(frame, format) {
         wasm.__wbindgen_free_command_export(deferred3_0, deferred3_1, 1);
     }
 }
-export function __wbg___wbindgen_debug_string_0accd80f45e5faa2(arg0, arg1) {
+export function __wbg___wbindgen_debug_string_8a447059637473e2(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_fbc4c3e30b409f08() {
+export function __wbg___wbindgen_memory_9751d9a3017e7c25() {
     const ret = wasm.memory;
     return ret;
 }
-export function __wbg___wbindgen_string_get_72bdf95d3ae505b1(arg0, arg1) {
+export function __wbg___wbindgen_string_get_71bb4348194e31f0(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);
@@ -6568,10 +6593,10 @@ export function __wbg___wbindgen_string_get_72bdf95d3ae505b1(arg0, arg1) {
     getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
     getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
 }
-export function __wbg___wbindgen_throw_1506f2235d1bdba0(arg0, arg1) {
+export function __wbg___wbindgen_throw_ea4887a5f8f9a9db(arg0, arg1) {
     throw new Error(getStringFromWasm0(arg0, arg1));
 }
-export function __wbg_done_60cf307fcc680536(arg0) {
+export function __wbg_done_b62d4a7d2286852a(arg0) {
     const ret = arg0.done;
     return ret;
 }
@@ -6590,38 +6615,38 @@ export function __wbg_frameindexentry_new(arg0) {
     const ret = FrameIndexEntry.__wrap(arg0);
     return ret;
 }
-export function __wbg_getRandomValues_3f44b700395062e5() { return handleError(function (arg0, arg1) {
+export function __wbg_getRandomValues_76dfc69825c9c552() { return handleError(function (arg0, arg1) {
     globalThis.crypto.getRandomValues(getArrayU8FromWasm0(arg0, arg1));
 }, arguments); }
-export function __wbg_get_0429a91975f37e2e(arg0, arg1) {
+export function __wbg_get_f6f94ffcaf26eed1(arg0, arg1) {
     const ret = arg0.get(arg1);
     return ret;
 }
-export function __wbg_get_unchecked_33f6e5c9e2f2d6b2(arg0, arg1) {
+export function __wbg_get_unchecked_54a4374c38e08460(arg0, arg1) {
     const ret = arg0[arg1 >>> 0];
     return ret;
 }
-export function __wbg_keys_75e37d4b5a2a8470(arg0) {
+export function __wbg_keys_8c9f7da46ee76e8d(arg0) {
     const ret = arg0.keys();
     return ret;
 }
-export function __wbg_length_27cfc5149a8eb2e7(arg0) {
+export function __wbg_length_4875795b8939c6b6(arg0) {
     const ret = arg0.length;
     return ret;
 }
-export function __wbg_length_280688879ee7deb5(arg0) {
+export function __wbg_length_589238bdcf171f0e(arg0) {
     const ret = arg0.length;
     return ret;
 }
-export function __wbg_length_33096ac1966bb961(arg0) {
+export function __wbg_length_750ab89c52b42479(arg0) {
     const ret = arg0.length;
     return ret;
 }
-export function __wbg_length_4a591ecaa01354d9(arg0) {
+export function __wbg_length_bf9e65fd7019a3f2(arg0) {
     const ret = arg0.length;
     return ret;
 }
-export function __wbg_length_66f1a4b2e9026940(arg0) {
+export function __wbg_length_c6054974c0a6cdb9(arg0) {
     const ret = arg0.length;
     return ret;
 }
@@ -6633,74 +6658,74 @@ export function __wbg_new_227d7c05414eb861() {
     const ret = new Error();
     return ret;
 }
-export function __wbg_new_578aeef4b6b94378(arg0) {
+export function __wbg_new_36e147a8ced3c6e0() {
+    const ret = new Array();
+    return ret;
+}
+export function __wbg_new_81880fb5002cb255(arg0) {
     const ret = new Uint8Array(arg0);
     return ret;
 }
-export function __wbg_new_d90091b82fdf5b91() {
-    const ret = new Array();
+export function __wbg_new_from_slice_3f5658f83d8d0725(arg0, arg1) {
+    const ret = new Uint32Array(getArrayU32FromWasm0(arg0, arg1));
     return ret;
 }
-export function __wbg_new_from_slice_1b23616ada25abcb(arg0, arg1) {
+export function __wbg_new_from_slice_7b8c5f56d6f4bffc(arg0, arg1) {
     const ret = new Int32Array(getArrayI32FromWasm0(arg0, arg1));
     return ret;
 }
-export function __wbg_new_from_slice_3c93d0bc613de8f0(arg0, arg1) {
+export function __wbg_new_from_slice_98e57cb2fe2e6a5d(arg0, arg1) {
     const ret = new Float64Array(getArrayF64FromWasm0(arg0, arg1));
     return ret;
 }
-export function __wbg_new_from_slice_47be4219028de35d(arg0, arg1) {
-    const ret = new Uint32Array(getArrayU32FromWasm0(arg0, arg1));
+export function __wbg_new_with_length_3f188e379a8c6a4d(arg0) {
+    const ret = new Float64Array(arg0 >>> 0);
     return ret;
 }
-export function __wbg_new_with_length_1eb3643ef8ff666a(arg0) {
+export function __wbg_new_with_length_793583df958b3ae2(arg0) {
     const ret = new Int32Array(arg0 >>> 0);
     return ret;
 }
-export function __wbg_new_with_length_21806dff02ad1c3e(arg0) {
-    const ret = new Uint32Array(arg0 >>> 0);
-    return ret;
-}
-export function __wbg_new_with_length_36a4998e27b014c5(arg0) {
+export function __wbg_new_with_length_9b650f44b5c44a4e(arg0) {
     const ret = new Uint8Array(arg0 >>> 0);
     return ret;
 }
-export function __wbg_new_with_length_b4a87ccced374381(arg0) {
-    const ret = new Float64Array(arg0 >>> 0);
+export function __wbg_new_with_length_ecf42de9ee25651c(arg0) {
+    const ret = new Uint32Array(arg0 >>> 0);
     return ret;
 }
-export function __wbg_next_eb8ca7351fa27906() { return handleError(function (arg0) {
+export function __wbg_next_0c4066e251d2eff9() { return handleError(function (arg0) {
     const ret = arg0.next();
     return ret;
 }, arguments); }
-export function __wbg_prototypesetcall_3249fc62a0fafa30(arg0, arg1, arg2) {
-    Uint8Array.prototype.set.call(getArrayU8FromWasm0(arg0, arg1), arg2);
-}
-export function __wbg_prototypesetcall_3560ffd2e7034ba8(arg0, arg1, arg2) {
+export function __wbg_prototypesetcall_1f31756936f35af0(arg0, arg1, arg2) {
     Int32Array.prototype.set.call(getArrayI32FromWasm0(arg0, arg1), arg2);
 }
-export function __wbg_prototypesetcall_59640349d2c6d881(arg0, arg1, arg2) {
+export function __wbg_prototypesetcall_26a86dd8c73de125(arg0, arg1, arg2) {
     Uint32Array.prototype.set.call(getArrayU32FromWasm0(arg0, arg1), arg2);
 }
-export function __wbg_prototypesetcall_d1ae8885a2e9d458(arg0, arg1, arg2) {
+export function __wbg_prototypesetcall_83f8c8d8e36faf9f(arg0, arg1, arg2) {
     Float64Array.prototype.set.call(getArrayF64FromWasm0(arg0, arg1), arg2);
 }
-export function __wbg_push_a6822215aa43e71c(arg0, arg1) {
+export function __wbg_prototypesetcall_d721637c7ca66eb8(arg0, arg1, arg2) {
+    Uint8Array.prototype.set.call(getArrayU8FromWasm0(arg0, arg1), arg2);
+}
+export function __wbg_push_f724b5db8acf89d2(arg0, arg1) {
     const ret = arg0.push(arg1);
     return ret;
 }
-export function __wbg_set_63b87f7c2d096ec3(arg0, arg1, arg2) {
+export function __wbg_set_404b02690d27a687(arg0, arg1, arg2) {
     arg0.set(getArrayF64FromWasm0(arg1, arg2));
 }
-export function __wbg_set_ad3bde048c79fe2b(arg0, arg1, arg2) {
+export function __wbg_set_699bda357d38bc49(arg0, arg1, arg2) {
     arg0.set(getArrayI32FromWasm0(arg1, arg2));
 }
-export function __wbg_set_index_73ced2e1b4a2a37e(arg0, arg1, arg2) {
-    arg0[arg1 >>> 0] = arg2;
-}
-export function __wbg_set_index_88b4ef962117fc1b(arg0, arg1, arg2) {
+export function __wbg_set_index_4cab6f2df9ae8120(arg0, arg1, arg2) {
     arg0[arg1 >>> 0] = arg2 >>> 0;
 }
+export function __wbg_set_index_dd52456a7aef02bf(arg0, arg1, arg2) {
+    arg0[arg1 >>> 0] = arg2;
+}
 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);
@@ -6708,7 +6733,7 @@ export function __wbg_stack_3b0d974bbf31e44f(arg0, arg1) {
     getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
     getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
 }
-export function __wbg_value_f3625092ee4b37f4(arg0) {
+export function __wbg_value_49f783bb59765962(arg0) {
     const ret = arg0.value;
     return ret;
 }

package/package.json

@@ -5,7 +5,7 @@
     "MolCrafts"
   ],
   "description": "WASM bindings for molrs",
-  "version": "0.0.17",
+  "version": "0.1.1",
   "license": "BSD-3-Clause",
   "repository": {
     "type": "git",