@kent-tokyo/chematic 0.1.4 → 0.1.9

package/README.md

@@ -2,38 +2,66 @@
 
 WebAssembly bindings for [chematic](https://github.com/kent-tokyo/chematic), a pure-Rust cheminformatics library.
 
-This crate exposes `#[wasm_bindgen]` bindings so that chematic can be used directly from JavaScript and TypeScript in the browser or Node.js.
+Published to npm as [`@kent-tokyo/chematic`](https://www.npmjs.com/package/@kent-tokyo/chematic).
+
+## Installation
+
+```sh
+npm install @kent-tokyo/chematic
+```
 
 ## Features
 
 - Parse SMILES strings into molecule handles
-- Compute molecular descriptors: molecular weight, TPSA, formula, heavy atom count, H-bond donors/acceptors
+- Molecular descriptors: MW, TPSA, LogP, Fsp3, QED, exact mass, rotatable bonds, HBD/HBA, aromatic ring count
 - Lipinski Rule-of-Five check
 - Canonical SMILES generation
-- ECFP4 fingerprints and Tanimoto similarity
+- ECFP4, AtomPair, and Topological Torsion fingerprints with Tanimoto similarity
+- BRICS fragment count
 
 ## Usage
 
-Build with [wasm-pack](https://rustwasm.github.io/wasm-pack/):
+```js
+import init, {
+  parse_smiles,
+  tanimoto_ecfp4,
+  tanimoto_atom_pair,
+  tanimoto_torsion,
+  brics_fragment_count,
+} from '@kent-tokyo/chematic';
 
-```sh
-wasm-pack build --target web
-```
+await init();
 
-Then in JavaScript/TypeScript:
+const mol = parse_smiles('CC(=O)Oc1ccccc1C(=O)O'); // aspirin
 
-```js
-import init, { parse_smiles, tanimoto_ecfp4 } from './pkg/chematic_wasm.js';
+// Descriptors
+console.log(mol.atom_count());          // 13
+console.log(mol.molecular_weight());    // ~180.16
+console.log(mol.formula());             // "C9H8O4"
+console.log(mol.tpsa());               // ~63.6
+console.log(mol.logp_crippen());        // ~1.2
+console.log(mol.fsp3());               // ~0.111
+console.log(mol.qed());                // drug-likeness score [0, 1]
+console.log(mol.exact_mass());         // ~180.042
+console.log(mol.hbd_count());          // 1
+console.log(mol.hba_count());          // 4
+console.log(mol.rotatable_bond_count()); // 3
+console.log(mol.aromatic_ring_count()); // 1
+console.log(mol.lipinski_passes());     // true
+console.log(mol.canonical_smiles());    // canonical SMILES string
 
-await init();
+// BRICS fragmentation
+console.log(brics_fragment_count(mol)); // ≥ 2
 
-const mol = parse_smiles('c1ccccc1');
-console.log(mol.atom_count());       // 6
-console.log(mol.molecular_weight()); // ~78.11
-console.log(mol.formula());          // "C6H6"
-console.log(mol.lipinski_passes());  // true
+// Fingerprint similarity
+const caffeine = parse_smiles('Cn1cnc2c1c(=O)n(c(=O)n2C)C');
+console.log(tanimoto_ecfp4(mol, caffeine));    // ECFP4 Tanimoto
+console.log(tanimoto_atom_pair(mol, caffeine)); // AtomPair Tanimoto
+console.log(tanimoto_torsion(mol, caffeine));   // Torsion Tanimoto
+```
+
+## Building from source
 
-const aspirin = parse_smiles('CC(=O)Oc1ccccc1C(=O)O');
-const sim = tanimoto_ecfp4(mol, aspirin);
-console.log(sim); // < 1.0
+```sh
+wasm-pack build --target bundler --release
 ```

package/chematic_wasm.d.ts

@@ -1,6 +1,32 @@
 /* tslint:disable */
 /* eslint-disable */
 
+/**
+ * Style options for [`MolHandle::depict_svg_opts`].
+ *
+ * Construct with `new DepictOptions()`, then call setters:
+ * ```js
+ * const opts = new DepictOptions();
+ * opts.set_background("transparent");
+ * opts.set_dark(true);
+ * opts.set_width(240);
+ * opts.set_height(240);
+ * ```
+ */
+export class DepictOptions {
+    free(): void;
+    [Symbol.dispose](): void;
+    constructor();
+    set_background(bg: string): void;
+    set_dark(dark: boolean): void;
+    set_height(h: number): void;
+    set_highlight_atoms(atoms: Uint32Array): void;
+    set_highlight_bonds(bonds: Uint32Array): void;
+    set_highlight_color(color: string): void;
+    set_padding(p: number): void;
+    set_width(w: number): void;
+}
+
 /**
  * A handle to a parsed molecule.  Owns the molecule behind an `Rc` so that
  * it can be cheaply cloned on the JS side without copying atom/bond data.
@@ -17,6 +43,10 @@ export class MolHandle {
      * Number of heavy atoms (explicit atoms in the graph; does not count implicit H).
      */
     atom_count(): number;
+    /**
+     * Bertz complexity index (BertzCT).
+     */
+    bertz_ct(): number;
     /**
      * Number of bonds.
      */
@@ -25,10 +55,67 @@ export class MolHandle {
      * Canonical SMILES string.
      */
     canonical_smiles(): string;
+    /**
+     * Kier–Hall χ0 molecular connectivity index.
+     */
+    chi0(): number;
+    /**
+     * Kier–Hall χ0v valence-weighted connectivity index.
+     */
+    chi0v(): number;
+    /**
+     * Kier–Hall χ1 molecular connectivity index.
+     */
+    chi1(): number;
+    /**
+     * Kier–Hall χ1v valence-weighted connectivity index.
+     */
+    chi1v(): number;
+    /**
+     * Kier–Hall χ2 molecular connectivity index.
+     */
+    chi2(): number;
+    /**
+     * Kier–Hall χ2v valence-weighted connectivity index.
+     */
+    chi2v(): number;
+    /**
+     * Kier–Hall χ3 molecular connectivity index.
+     */
+    chi3(): number;
+    /**
+     * Kier–Hall χ3v valence-weighted connectivity index.
+     */
+    chi3v(): number;
+    /**
+     * Kier–Hall χ4 molecular connectivity index.
+     */
+    chi4(): number;
+    /**
+     * Kier–Hall χ4v valence-weighted connectivity index.
+     */
+    chi4v(): number;
+    /**
+     * 2D SVG depiction of the molecule (CPK coloring).
+     */
+    depict_svg(): string;
+    /**
+     * 2D SVG depiction with style options.
+     */
+    depict_svg_opts(opts: DepictOptions): string;
+    /**
+     * Returns `true` if the molecule passes Egan's absorption criteria
+     * (TPSA ≤ 131.6 Ų and LogP ≤ 5.88).
+     */
+    egan_passes(): boolean;
     /**
      * Monoisotopic (exact) mass.
      */
     exact_mass(): number;
+    /**
+     * Sum of formal charges.
+     */
+    formal_charge_sum(): number;
     /**
      * Molecular formula string (Hill notation: C first, H second, then alphabetical).
      */
@@ -37,6 +124,11 @@ export class MolHandle {
      * Fraction of sp3 carbons (Fsp3).
      */
     fsp3(): number;
+    /**
+     * Returns `true` if the molecule passes Ghose's drug-likeness filter
+     * (MW 160–480, LogP −0.4–5.6, HeavyAtoms 20–70, MR 40–130).
+     */
+    ghose_passes(): boolean;
     /**
      * Number of hydrogen bond acceptors (Lipinski: all N and O atoms).
      */
@@ -49,6 +141,22 @@ export class MolHandle {
      * Number of non-hydrogen heavy atoms.
      */
     heavy_atom_count(): number;
+    /**
+     * Hall–Kier κ1 shape index.
+     */
+    kappa1(): number;
+    /**
+     * Hall–Kier κ2 shape index.
+     */
+    kappa2(): number;
+    /**
+     * Hall–Kier κ3 shape index.
+     */
+    kappa3(): number;
+    /**
+     * Labute approximate surface area (Ų).
+     */
+    labute_asa(): number;
     /**
      * Returns `true` if the molecule satisfies Lipinski's Rule of Five.
      */
@@ -57,14 +165,64 @@ export class MolHandle {
      * Crippen–Wildman octanol/water partition coefficient (LogP).
      */
     logp_crippen(): number;
+    /**
+     * Wildman–Crippen molar refractivity (MR).
+     */
+    molar_refractivity(): number;
     /**
      * Average molecular weight (Da).
      */
     molecular_weight(): number;
+    /**
+     * Morgan count fingerprint as a JSON object string (`{"<hash>": count, …}`).
+     *
+     * `radius` controls the ECFP radius (2 = ECFP4-equivalent).
+     */
+    morgan_fp_counts_json(radius: number): string;
+    /**
+     * Number of non-aromatic rings containing at least one heteroatom.
+     */
+    num_aliphatic_heterocycles(): number;
+    /**
+     * Number of aromatic rings containing at least one heteroatom (N, O, S, …).
+     */
+    num_aromatic_heterocycles(): number;
+    /**
+     * Number of bridgehead atoms (shared by ≥2 rings with ≥3 ring bonds).
+     */
+    num_bridgehead_atoms(): number;
+    /**
+     * Number of heteroatoms (non-C, non-H heavy atoms).
+     */
+    num_heteroatoms(): number;
+    /**
+     * Number of fully saturated rings containing at least one heteroatom.
+     */
+    num_saturated_heterocycles(): number;
+    /**
+     * Number of spiro atoms (sole shared atom between exactly 2 rings).
+     */
+    num_spiro_atoms(): number;
+    /**
+     * Number of assigned stereocenters (R/S).
+     */
+    num_stereocenters(): number;
+    /**
+     * Returns `true` if the molecule has no PAINS structural alerts.
+     */
+    pains_passes(): boolean;
     /**
      * Quantitative Estimate of Drug-likeness (QED); range [0, 1].
      */
     qed(): number;
+    /**
+     * Returns `true` if the molecule passes the REOS (Rapid Elimination Of Swill) filter.
+     */
+    reos_passes(): boolean;
+    /**
+     * Total number of rings (SSSR count).
+     */
+    ring_count(): number;
     /**
      * Number of rotatable bonds.
      */
@@ -73,8 +231,22 @@ export class MolHandle {
      * Topological polar surface area (Ų).
      */
     tpsa(): number;
+    /**
+     * Returns `true` if the molecule passes Veber's oral bioavailability criteria
+     * (TPSA ≤ 140 Ų and rotatable bonds ≤ 10).
+     */
+    veber_passes(): boolean;
+    /**
+     * Wiener topological index (sum of all pairwise shortest-path distances).
+     */
+    wiener_index(): number;
 }
 
+/**
+ * Return a copy of the molecule with all implicit hydrogens converted to explicit H atoms.
+ */
+export function add_hydrogens(mol: MolHandle): MolHandle;
+
 /**
  * Number of BRICS fragments produced by fragmenting the molecule.
  *
@@ -82,11 +254,24 @@ export class MolHandle {
  */
 export function brics_fragment_count(mol: MolHandle): number;
 
+/**
+ * Render a grid SVG from newline-separated SMILES (one per line).
+ *
+ * Lines that fail to parse are silently skipped.
+ * `cols` controls the number of columns (each cell is 200×200 px).
+ */
+export function depict_svg_grid(smiles_block: string, cols: number): string;
+
 /**
  * Compute the ECFP4 fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  */
 export function ecfp4_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * Returns `true` if the SMILES string can be parsed without error.
+ */
+export function is_valid_smiles(s: string): boolean;
+
 /**
  * Parse a SMILES string into a `MolHandle`.
  *
@@ -94,6 +279,20 @@ export function ecfp4_bitvec(mol: MolHandle): Uint8Array;
  */
 export function parse_smiles(s: string): MolHandle;
 
+/**
+ * Return a copy of the molecule with all explicit hydrogen atoms removed.
+ */
+export function remove_hydrogens(mol: MolHandle): MolHandle;
+
+/**
+ * Apply a SMIRKS reaction template and return product SMILES as a JSON string.
+ *
+ * `reactants_smiles`: pipe-separated SMILES, one per reactant slot in the SMIRKS.
+ * Returns a JSON array of arrays: `[["product_smi", …], …]`.
+ * Returns a JS error on parse failure or arity mismatch.
+ */
+export function run_reactants(smirks: string, reactants_smiles: string): string;
+
 /**
  * Tanimoto similarity between two molecules using AtomPair fingerprints.
  */
@@ -104,7 +303,119 @@ export function tanimoto_atom_pair(a: MolHandle, b: MolHandle): number;
  */
 export function tanimoto_ecfp4(a: MolHandle, b: MolHandle): number;
 
+/**
+ * Tanimoto similarity between two molecules using FCFP4 fingerprints (pharmacophore-based).
+ */
+export function tanimoto_fcfp4(a: MolHandle, b: MolHandle): number;
+
 /**
  * Tanimoto similarity between two molecules using Topological Torsion fingerprints.
  */
 export function tanimoto_torsion(a: MolHandle, b: MolHandle): number;
+
+export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembly.Module;
+
+export interface InitOutput {
+    readonly memory: WebAssembly.Memory;
+    readonly __wbg_depictoptions_free: (a: number, b: number) => void;
+    readonly __wbg_molhandle_free: (a: number, b: number) => void;
+    readonly add_hydrogens: (a: number) => number;
+    readonly brics_fragment_count: (a: number) => number;
+    readonly depict_svg_grid: (a: number, b: number, c: number) => [number, number];
+    readonly depictoptions_new: () => number;
+    readonly depictoptions_set_background: (a: number, b: number, c: number) => void;
+    readonly depictoptions_set_dark: (a: number, b: number) => void;
+    readonly depictoptions_set_height: (a: number, b: number) => void;
+    readonly depictoptions_set_highlight_atoms: (a: number, b: number, c: number) => void;
+    readonly depictoptions_set_highlight_bonds: (a: number, b: number, c: number) => void;
+    readonly depictoptions_set_highlight_color: (a: number, b: number, c: number) => void;
+    readonly depictoptions_set_padding: (a: number, b: number) => void;
+    readonly depictoptions_set_width: (a: number, b: number) => void;
+    readonly ecfp4_bitvec: (a: number) => [number, number];
+    readonly is_valid_smiles: (a: number, b: number) => number;
+    readonly molhandle_aromatic_ring_count: (a: number) => number;
+    readonly molhandle_atom_count: (a: number) => number;
+    readonly molhandle_bertz_ct: (a: number) => number;
+    readonly molhandle_bond_count: (a: number) => number;
+    readonly molhandle_canonical_smiles: (a: number) => [number, number];
+    readonly molhandle_chi0: (a: number) => number;
+    readonly molhandle_chi0v: (a: number) => number;
+    readonly molhandle_chi1: (a: number) => number;
+    readonly molhandle_chi1v: (a: number) => number;
+    readonly molhandle_chi2: (a: number) => number;
+    readonly molhandle_chi2v: (a: number) => number;
+    readonly molhandle_chi3: (a: number) => number;
+    readonly molhandle_chi3v: (a: number) => number;
+    readonly molhandle_chi4: (a: number) => number;
+    readonly molhandle_chi4v: (a: number) => number;
+    readonly molhandle_depict_svg: (a: number) => [number, number];
+    readonly molhandle_depict_svg_opts: (a: number, b: number) => [number, number];
+    readonly molhandle_egan_passes: (a: number) => number;
+    readonly molhandle_exact_mass: (a: number) => number;
+    readonly molhandle_formal_charge_sum: (a: number) => number;
+    readonly molhandle_formula: (a: number) => [number, number];
+    readonly molhandle_fsp3: (a: number) => number;
+    readonly molhandle_ghose_passes: (a: number) => number;
+    readonly molhandle_hba_count: (a: number) => number;
+    readonly molhandle_hbd_count: (a: number) => number;
+    readonly molhandle_heavy_atom_count: (a: number) => number;
+    readonly molhandle_kappa1: (a: number) => number;
+    readonly molhandle_kappa2: (a: number) => number;
+    readonly molhandle_kappa3: (a: number) => number;
+    readonly molhandle_labute_asa: (a: number) => number;
+    readonly molhandle_lipinski_passes: (a: number) => number;
+    readonly molhandle_logp_crippen: (a: number) => number;
+    readonly molhandle_molar_refractivity: (a: number) => number;
+    readonly molhandle_molecular_weight: (a: number) => number;
+    readonly molhandle_morgan_fp_counts_json: (a: number, b: number) => [number, number];
+    readonly molhandle_num_aliphatic_heterocycles: (a: number) => number;
+    readonly molhandle_num_aromatic_heterocycles: (a: number) => number;
+    readonly molhandle_num_bridgehead_atoms: (a: number) => number;
+    readonly molhandle_num_heteroatoms: (a: number) => number;
+    readonly molhandle_num_saturated_heterocycles: (a: number) => number;
+    readonly molhandle_num_spiro_atoms: (a: number) => number;
+    readonly molhandle_num_stereocenters: (a: number) => number;
+    readonly molhandle_pains_passes: (a: number) => number;
+    readonly molhandle_qed: (a: number) => number;
+    readonly molhandle_reos_passes: (a: number) => number;
+    readonly molhandle_ring_count: (a: number) => number;
+    readonly molhandle_rotatable_bond_count: (a: number) => number;
+    readonly molhandle_tpsa: (a: number) => number;
+    readonly molhandle_veber_passes: (a: number) => number;
+    readonly molhandle_wiener_index: (a: number) => number;
+    readonly parse_smiles: (a: number, b: number) => [number, number, number];
+    readonly remove_hydrogens: (a: number) => number;
+    readonly run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly tanimoto_atom_pair: (a: number, b: number) => number;
+    readonly tanimoto_ecfp4: (a: number, b: number) => number;
+    readonly tanimoto_fcfp4: (a: number, b: number) => number;
+    readonly tanimoto_torsion: (a: number, b: number) => number;
+    readonly __wbindgen_externrefs: WebAssembly.Table;
+    readonly __wbindgen_malloc: (a: number, b: number) => number;
+    readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
+    readonly __wbindgen_free: (a: number, b: number, c: number) => void;
+    readonly __externref_table_dealloc: (a: 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>;