@kent-tokyo/chematic 0.4.19 → 0.4.28

package/chematic_wasm.d.ts

@@ -106,17 +106,6 @@ export class DepictOptions {
     set_width(w: number): void;
 }
 
-/**
- * MinHash LSH index: insert MHFP fingerprints and query by approximate similarity.
- *
- * ```js
- * const idx = new MhfpLshHandle(128);
- * const i0 = idx.add_smiles("c1ccccc1");    // benzene → index 0
- * const i1 = idx.add_smiles("Cc1ccccc1");   // toluene → index 1
- * const hits = JSON.parse(idx.query_json("c1ccccc1", 0.5));
- * // hits: [{index:0,similarity:1.0}, {index:1,similarity:0.xxx}]
- * ```
- */
 export class MhfpLshHandle {
     free(): void;
     [Symbol.dispose](): void;
@@ -514,6 +503,29 @@ export function autocorr_3d_json(mol: MolHandle): string;
  */
 export function balance_check_json(reaction_smiles: string): string;
 
+/**
+ * MinHash LSH index: insert MHFP fingerprints and query by approximate similarity.
+ *
+ * ```js
+ * const idx = new MhfpLshHandle(128);
+ * const i0 = idx.add_smiles("c1ccccc1");    // benzene → index 0
+ * const i1 = idx.add_smiles("Cc1ccccc1");   // toluene → index 1
+ * const hits = JSON.parse(idx.query_json("c1ccccc1", 0.5));
+ * // hits: [{index:0,similarity:1.0}, {index:1,similarity:0.xxx}]
+ * ```
+ * Generate a self-contained HTML report for a newline-separated list of SMILES.
+ *
+ * Empty lines and invalid SMILES are silently skipped.
+ * Returns the same card-grid HTML as Python's `chematic.report()`.
+ *
+ * ```js
+ * const html = mod.batch_report_html("CCO\nc1ccccc1\nCC(=O)O");
+ * const blob = new Blob([html], {type:'text/html'});
+ * const url  = URL.createObjectURL(blob);
+ * ```
+ */
+export function batch_report_html(smiles_lines: string): string;
+
 /**
  * Predict GI absorption and BBB penetration using the BOILED-Egg method
  * (Daina & Zoete 2016).
@@ -990,6 +1002,21 @@ export function get_dihedral_json(smiles: string, a: number, b: number, c: numbe
  */
 export function getaway_descriptors_json(mol: MolHandle): string;
 
+/**
+ * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
+ *
+ * Compute an HDF fingerprint and return it as a JSON array of float32 values.
+ *
+ * Returns a unit-norm vector of length `dim` as a JSON number array.
+ * Use cosine dot product for similarity: `a · b = sum(a[i]*b[i])`.
+ *
+ * ```js
+ * const fp = JSON.parse(hdf_json(mol));        // float[] of length 1024
+ * const sim = fp.reduce((s, v, i) => s + v * fp2[i], 0);  // cosine similarity
+ * ```
+ */
+export function hdf_json(mol: MolHandle, dim: number, radius: number, seed: bigint): string;
+
 /**
  * Identify functional groups. Returns a JSON array of objects:
  * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
@@ -1211,8 +1238,6 @@ export function mol_block_coords_json(mol_block: string): string;
 export function mol_block_from_smiles(smiles: string): string;
 
 /**
- * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
- *
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
  */
@@ -1225,6 +1250,14 @@ export function mol_from_cdxml(cdxml: string): MolHandle;
  */
 export function mol_from_cml(cml: string): MolHandle;
 
+/**
+ * Parse a MolJSON string into a `MolHandle`.
+ *
+ * MolJSON is a JSON-based molecular representation designed for LLM
+ * (large language model) compatibility.  Returns a JS error on invalid input.
+ */
+export function mol_from_moljson(json: string): MolHandle;
+
 /**
  * Parse a PDB file and return a `MolHandle` (topology only; coordinates are discarded).
  *
@@ -1750,6 +1783,14 @@ export function to_mol_block(mol: MolHandle): string;
  */
 export function to_mol_v3000_block(mol: MolHandle): string;
 
+/**
+ * Serialise a `MolHandle` to a MolJSON string (pretty-printed).
+ *
+ * Atom IDs are assigned as `"a1"`, `"a2"`, … in molecule atom order.
+ * The `hydrogens` field reflects computed implicit H count.
+ */
+export function to_moljson(mol: MolHandle): string;
+
 /**
  * Serialize a molecule to XYZ format.
  *
@@ -1823,6 +1864,7 @@ export interface InitOutput {
     readonly autocorr_2d_json: (a: number) => [number, number];
     readonly autocorr_3d_json: (a: number) => [number, number];
     readonly balance_check_json: (a: number, b: number) => [number, number];
+    readonly batch_report_html: (a: number, b: number) => [number, number];
     readonly boiled_egg_json: (a: number, b: number) => [number, number];
     readonly brics_fragment_count: (a: number) => number;
     readonly brics_fragments_json: (a: number) => [number, number];
@@ -1897,6 +1939,7 @@ export interface InitOutput {
     readonly get_descriptors_json: (a: number) => [number, number];
     readonly get_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number) => any;
     readonly getaway_descriptors_json: (a: number) => [number, number];
+    readonly hdf_json: (a: number, b: number, c: number, d: bigint) => [number, number];
     readonly identify_functional_groups: (a: number) => [number, number];
     readonly inchi_from_smiles: (a: number, b: number) => [number, number];
     readonly inchikey_from_smiles: (a: number, b: number) => [number, number];
@@ -1930,6 +1973,7 @@ export interface InitOutput {
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
     readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
     readonly mol_from_cml: (a: number, b: number) => [number, number, number];
+    readonly mol_from_moljson: (a: number, b: number) => [number, number, number];
     readonly mol_from_pdb: (a: number, b: number) => number;
     readonly mol_from_sdf_block: (a: number, b: number) => [number, number, number];
     readonly mol_from_v3000_block: (a: number, b: number) => [number, number, number];
@@ -1944,7 +1988,6 @@ export interface InitOutput {
     readonly molecule_report_json: (a: number, b: number) => [number, number, number, number];
     readonly molhandle_aromatic_ring_count: (a: number) => number;
     readonly molhandle_assign_cip_json: (a: number) => [number, number];
-    readonly molhandle_atom_count: (a: number) => number;
     readonly molhandle_bbb_passes: (a: number) => number;
     readonly molhandle_bbb_score: (a: number) => number;
     readonly molhandle_bertz_ct: (a: number) => number;
@@ -2054,7 +2097,6 @@ export interface InitOutput {
     readonly sssr_rings_json: (a: number) => [number, number];
     readonly standardize_smiles: (a: number, b: number) => [number, number];
     readonly standardize_smiles_report_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number];
-    readonly start: () => void;
     readonly tanimoto_atom_pair: (a: number, b: number) => number;
     readonly tanimoto_ecfp4: (a: number, b: number) => number;
     readonly tanimoto_ecfp6: (a: number, b: number) => number;
@@ -2069,6 +2111,7 @@ export interface InitOutput {
     readonly to_cml: (a: number) => [number, number];
     readonly to_mol_block: (a: number) => [number, number];
     readonly to_mol_v3000_block: (a: number) => [number, number];
+    readonly to_moljson: (a: number) => [number, number];
     readonly to_xyz: (a: number) => [number, number];
     readonly torsion_bitvec: (a: number) => [number, number];
     readonly virtual_screen_ecfp4_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
@@ -2077,6 +2120,8 @@ export interface InitOutput {
     readonly write_smiles: (a: number) => [number, number];
     readonly xlogp3_json: (a: number) => [number, number];
     readonly xlogp3_per_atom_json: (a: number) => [number, number];
+    readonly molhandle_atom_count: (a: number) => number;
+    readonly start: () => void;
     readonly __wbindgen_malloc: (a: number, b: number) => number;
     readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
     readonly __wbindgen_externrefs: WebAssembly.Table;

package/chematic_wasm.js

@@ -264,17 +264,6 @@ export class DepictOptions {
 }
 if (Symbol.dispose) DepictOptions.prototype[Symbol.dispose] = DepictOptions.prototype.free;
 
-/**
- * MinHash LSH index: insert MHFP fingerprints and query by approximate similarity.
- *
- * ```js
- * const idx = new MhfpLshHandle(128);
- * const i0 = idx.add_smiles("c1ccccc1");    // benzene → index 0
- * const i1 = idx.add_smiles("Cc1ccccc1");   // toluene → index 1
- * const hits = JSON.parse(idx.query_json("c1ccccc1", 0.5));
- * // hits: [{index:0,similarity:1.0}, {index:1,similarity:0.xxx}]
- * ```
- */
 export class MhfpLshHandle {
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
@@ -1203,6 +1192,44 @@ export function balance_check_json(reaction_smiles) {
     }
 }
 
+/**
+ * MinHash LSH index: insert MHFP fingerprints and query by approximate similarity.
+ *
+ * ```js
+ * const idx = new MhfpLshHandle(128);
+ * const i0 = idx.add_smiles("c1ccccc1");    // benzene → index 0
+ * const i1 = idx.add_smiles("Cc1ccccc1");   // toluene → index 1
+ * const hits = JSON.parse(idx.query_json("c1ccccc1", 0.5));
+ * // hits: [{index:0,similarity:1.0}, {index:1,similarity:0.xxx}]
+ * ```
+ * Generate a self-contained HTML report for a newline-separated list of SMILES.
+ *
+ * Empty lines and invalid SMILES are silently skipped.
+ * Returns the same card-grid HTML as Python's `chematic.report()`.
+ *
+ * ```js
+ * const html = mod.batch_report_html("CCO\nc1ccccc1\nCC(=O)O");
+ * const blob = new Blob([html], {type:'text/html'});
+ * const url  = URL.createObjectURL(blob);
+ * ```
+ * @param {string} smiles_lines
+ * @returns {string}
+ */
+export function batch_report_html(smiles_lines) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_lines, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.batch_report_html(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
 /**
  * Predict GI absorption and BBB penetration using the BOILED-Egg method
  * (Daina & Zoete 2016).
@@ -2403,6 +2430,38 @@ export function getaway_descriptors_json(mol) {
     }
 }
 
+/**
+ * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
+ *
+ * Compute an HDF fingerprint and return it as a JSON array of float32 values.
+ *
+ * Returns a unit-norm vector of length `dim` as a JSON number array.
+ * Use cosine dot product for similarity: `a · b = sum(a[i]*b[i])`.
+ *
+ * ```js
+ * const fp = JSON.parse(hdf_json(mol));        // float[] of length 1024
+ * const sim = fp.reduce((s, v, i) => s + v * fp2[i], 0);  // cosine similarity
+ * ```
+ * @param {MolHandle} mol
+ * @param {number} dim
+ * @param {number} radius
+ * @param {bigint} seed
+ * @returns {string}
+ */
+export function hdf_json(mol, dim, radius, seed) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.hdf_json(mol.__wbg_ptr, dim, radius, seed);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
 /**
  * Identify functional groups. Returns a JSON array of objects:
  * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
@@ -3028,8 +3087,6 @@ export function mol_block_from_smiles(smiles) {
 }
 
 /**
- * Parse a ChemDraw XML (CDXML) string into a `MolHandle`.
- *
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
  * @param {string} cdxml
@@ -3062,6 +3119,24 @@ export function mol_from_cml(cml) {
     return MolHandle.__wrap(ret[0]);
 }
 
+/**
+ * Parse a MolJSON string into a `MolHandle`.
+ *
+ * MolJSON is a JSON-based molecular representation designed for LLM
+ * (large language model) compatibility.  Returns a JS error on invalid input.
+ * @param {string} json
+ * @returns {MolHandle}
+ */
+export function mol_from_moljson(json) {
+    const ptr0 = passStringToWasm0(json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_moljson(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Parse a PDB file and return a `MolHandle` (topology only; coordinates are discarded).
  *
@@ -4540,6 +4615,28 @@ export function to_mol_v3000_block(mol) {
     }
 }
 
+/**
+ * Serialise a `MolHandle` to a MolJSON string (pretty-printed).
+ *
+ * Atom IDs are assigned as `"a1"`, `"a2"`, … in molecule atom order.
+ * The `hydrogens` field reflects computed implicit H count.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function to_moljson(mol) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.to_moljson(mol.__wbg_ptr);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
 /**
  * Serialize a molecule to XYZ format.
  *
@@ -4712,7 +4809,7 @@ export function xlogp3_per_atom_json(mol) {
 function __wbg_get_imports() {
     const import0 = {
         __proto__: null,
-        __wbg___wbindgen_string_get_71bb4348194e31f0: function(arg0, arg1) {
+        __wbg___wbindgen_string_get_b0ca35b86a603356: function(arg0, arg1) {
             const obj = arg1;
             const ret = typeof(obj) === 'string' ? obj : undefined;
             var ptr1 = isLikeNone(ret) ? 0 : passStringToWasm0(ret, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
@@ -4720,10 +4817,10 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_throw_ea4887a5f8f9a9db: function(arg0, arg1) {
+        __wbg___wbindgen_throw_344f42d3211c4765: function(arg0, arg1) {
             throw new Error(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_error_933f449d72fef598: function(arg0) {
+        __wbg_error_744744ff0c9861e6: function(arg0) {
             console.error(arg0);
         },
         __wbindgen_cast_0000000000000001: function(arg0) {

package/package.json

@@ -5,7 +5,7 @@
     "kent-tokyo <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "0.4.19",
+  "version": "0.4.28",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",