@kent-tokyo/chematic 0.1.10 → 0.1.19

package/README.md

@@ -13,11 +13,23 @@ npm install @kent-tokyo/chematic
 ## Features
 
 - Parse SMILES strings into molecule handles
-- Molecular descriptors: MW, TPSA, LogP, Fsp3, QED, exact mass, rotatable bonds, HBD/HBA, aromatic ring count
-- Lipinski Rule-of-Five check
+- Molecular descriptors: MW, TPSA, LogP, Fsp3, QED, exact mass, rotatable bonds, HBD/HBA, aromatic ring count, Labute ASA
+- Drug-likeness filters: Lipinski, Veber, Egan, REOS, Ghose
+- EState indices (Hall & Kier 1991): per-atom values, sum/max/min
+- Gasteiger-Marsili PEOE partial charges: per-heavy-atom charges
+- VSA descriptors: SlogP_VSA (×12), SMR_VSA (×10), PEOE_VSA (×14)
+- SA score: synthetic accessibility estimate [1, 10]
+- Functional group identification (Ertl 2017 IFG)
 - Canonical SMILES generation
-- ECFP4, AtomPair, and Topological Torsion fingerprints with Tanimoto similarity
+- ECFP4/6, AtomPair, Torsion, and path fingerprints with Tanimoto similarity
 - BRICS fragment count
+- SDF/MOL block parsing
+- Topological descriptors: Wiener index, Hall-Kier κ, χ connectivity indices, Bertz CT
+- Shape descriptors (with 3D coordinates): PMI, NPR, radius of gyration, asphericity
+- 2D SVG depiction with CPK colors and atom/bond highlighting
+- SVG grid layout for multiple molecules
+- Reaction SMILES/SMIRKS parsing and transform
+- Add/remove explicit hydrogens
 
 ## Usage
 
@@ -28,6 +40,11 @@ import init, {
   tanimoto_atom_pair,
   tanimoto_torsion,
   brics_fragment_count,
+  gasteiger_charges_json,
+  slogp_vsa_json,
+  smr_vsa_json,
+  peoe_vsa_json,
+  identify_functional_groups,
 } from '@kent-tokyo/chematic';
 
 await init();
@@ -60,6 +77,25 @@ console.log(tanimoto_atom_pair(mol, caffeine)); // AtomPair Tanimoto
 console.log(tanimoto_torsion(mol, caffeine));   // Torsion Tanimoto
 ```
 
+```js
+// Sprint Q: New descriptors (v0.1.15)
+console.log(mol.sa_score());                     // synthetic accessibility [1,10]
+console.log(mol.labute_asa());                   // Labute approx. surface area (Ų)
+
+// Gasteiger partial charges (per heavy atom)
+const charges = JSON.parse(gasteiger_charges_json(mol));
+console.log(charges); // [-0.08, 0.12, -0.43, ...]
+
+// VSA descriptor bins
+const slogpVsa = JSON.parse(slogp_vsa_json(mol));
+const smrVsa   = JSON.parse(smr_vsa_json(mol));
+const peoeVsa  = JSON.parse(peoe_vsa_json(mol));
+
+// Functional group identification
+const ifg = JSON.parse(identify_functional_groups(mol));
+console.log(ifg); // [{"atoms":[1,2,3],"types":"OC=O"}, ...]
+```
+
 ## Building from source
 
 ```sh

package/chematic_wasm.d.ts

@@ -17,6 +17,12 @@ export class DepictOptions {
     free(): void;
     [Symbol.dispose](): void;
     constructor();
+    /**
+     * Set a per-atom color override (CSS color string).  Calling multiple times
+     * for the same `idx` uses the last value.  The atom is highlighted even if
+     * not in `set_highlight_atoms`.
+     */
+    set_atom_color(idx: number, color: string): void;
     set_atom_ids(v: boolean): void;
     set_background(bg: string): void;
     set_dark(dark: boolean): void;
@@ -168,6 +174,14 @@ export class MolHandle {
      * Crippen–Wildman octanol/water partition coefficient (LogP).
      */
     logp_crippen(): number;
+    /**
+     * Maximum EState index across all heavy atoms.
+     */
+    max_estate(): number;
+    /**
+     * Minimum EState index across all heavy atoms.
+     */
+    min_estate(): number;
     /**
      * Wildman–Crippen molar refractivity (MR).
      */
@@ -230,6 +244,10 @@ export class MolHandle {
      * Number of rotatable bonds.
      */
     rotatable_bond_count(): number;
+    /**
+     * Sum of EState indices over all heavy atoms.
+     */
+    sum_estate(): number;
     /**
      * Topological polar surface area (Ų).
      */
@@ -257,6 +275,14 @@ export function add_hydrogens(mol: MolHandle): MolHandle;
  */
 export function brics_fragment_count(mol: MolHandle): number;
 
+/**
+ * Render a reaction SMILES string (e.g. `"CC(=O)O.CCO>>CC(=O)OCC.O"`) as a
+ * single SVG showing reactants → products with `+` separators.
+ *
+ * Returns a self-contained SVG string.  Returns a JS error on invalid input.
+ */
+export function depict_reaction_svg(rxn_smiles: string): string;
+
 /**
  * Render a grid SVG from newline-separated SMILES (one per line).
  *
@@ -265,16 +291,110 @@ export function brics_fragment_count(mol: MolHandle): number;
  */
 export function depict_svg_grid(smiles_block: string, cols: number): string;
 
+/**
+ * Detect named functional groups in `mol`.
+ *
+ * Returns a JSON array of `{"name":"hydroxyl","atoms":[3]}` objects.
+ * Multiple matches of the same group (e.g. two hydroxyl groups) each appear
+ * as a separate entry.  Overlapping groups (carboxylic acid → "carboxyl" +
+ * "hydroxyl" + "carbonyl") are all returned.
+ */
+export function detect_functional_groups(mol: MolHandle): string;
+
 /**
  * Compute the ECFP4 fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
  */
 export function ecfp4_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * Per-atom EState values as a JSON array of f64.
+ *
+ * Indices match `mol.atoms()` order.  Hydrogen atoms get 0.0.
+ */
+export function estate_indices_json(mol: MolHandle): string;
+
+/**
+ * Gasteiger-Marsili PEOE partial charges as a JSON array of f64.
+ */
+export function gasteiger_charges_json(mol: MolHandle): string;
+
+/**
+ * Generate 3D coordinates for the molecule and return a PDB string.
+ *
+ * Coordinates are generated using distance-geometry placement with ring templates.
+ * Returns heavy-atom PDB (HETATM records, no explicit H).
+ */
+export function generate_3d_pdb(mol: MolHandle): string;
+
+/**
+ * Return information about a single atom as a JSON object.
+ *
+ * `idx` is the 0-based atom index (matching `atoms()` order).
+ * Returns `"null"` if `idx` is out of range.
+ *
+ * Fields: `element` (symbol), `hybridization` ("sp"/"sp2"/"sp3"),
+ * `charge` (formal charge integer), `isAromatic` (bool),
+ * `totalHydrogens` (explicit + implicit H count, integer).
+ * sp3d/sp3d2 (hypervalent P/S) are not distinguished from sp3/sp2.
+ */
+export function get_atom_info(mol: MolHandle, idx: number): string;
+
+/**
+ * Return bond information as a JSON object, looked up by the two bonded atom indices.
+ *
+ * Useful when you know the atom indices from SMARTS matching or `data-atom-idx` SVG
+ * attributes but not the bond index.  Returns `"null"` if no bond exists between them.
+ *
+ * Fields: same as `get_bond_info` plus `bondIdx` (u32).
+ */
+export function get_bond_between(mol: MolHandle, atom1: number, atom2: number): string;
+
+/**
+ * Return bond information as a JSON object, looked up by bond index.
+ *
+ * `idx` is the 0-based bond index (order matches `mol.bonds()` iteration).
+ * Returns `"null"` if `idx` is out of range.
+ *
+ * Fields: `bondOrder` (1.0/1.5/2.0/3.0), `isAromatic` (bool),
+ * `isInRing` (bool), `atomFrom` (u32), `atomTo` (u32).
+ */
+export function get_bond_info(mol: MolHandle, idx: number): string;
+
+/**
+ * Identify functional groups. Returns a JSON array of objects:
+ * `[{"atoms":[0,2,3],"type":"C,N,O"}, …]`
+ */
+export function identify_functional_groups(mol: MolHandle): string;
+
 /**
  * Returns `true` if the SMILES string can be parsed without error.
  */
 export function is_valid_smiles(s: string): boolean;
 
+/**
+ * Find all SMARTS matches in a molecule given only SMILES strings.
+ *
+ * Convenience wrapper around `smarts_match_atoms` that accepts raw SMILES
+ * instead of a `MolHandle`.  Returns the same JSON format: `[[0,1],[3,4]]`.
+ * Returns a JS error on SMILES or SMARTS parse failure.
+ */
+export function match_smarts_smiles(smiles: string, smarts: string): string;
+
+/**
+ * Serialize a SMILES string directly to a MOL V2000 block.
+ *
+ * Convenience wrapper; all atom coordinates are 0.0.
+ * Returns a JS error on SMILES parse failure.
+ */
+export function mol_block_from_smiles(smiles: string): string;
+
+/**
+ * Parse a MOL V2000 block and return a `MolHandle`.
+ *
+ * Returns a JS error string on parse failure.
+ */
+export function mol_from_sdf_block(block: string): MolHandle;
+
 /**
  * Parse a SMILES string into a `MolHandle`.
  *
@@ -282,6 +402,11 @@ export function is_valid_smiles(s: string): boolean;
  */
 export function parse_smiles(s: string): MolHandle;
 
+/**
+ * PEOE_VSA descriptors (14 bins) as a JSON array.
+ */
+export function peoe_vsa_json(mol: MolHandle): string;
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  */
@@ -296,6 +421,50 @@ export function remove_hydrogens(mol: MolHandle): MolHandle;
  */
 export function run_reactants(smirks: string, reactants_smiles: string): string;
 
+/**
+ * Synthetic Accessibility Score (1 = easy, 10 = hard).
+ */
+export function sa_score(mol: MolHandle): number;
+
+/**
+ * Parse an SDF string and return a JSON array of canonical SMILES strings.
+ *
+ * Invalid records are represented as `null` in the array.
+ */
+export function sdf_to_smiles_json(sdf: string): string;
+
+/**
+ * SlogP_VSA descriptors (12 bins) as a JSON array.
+ */
+export function slogp_vsa_json(mol: MolHandle): string;
+
+/**
+ * Find all substructure matches of a SMARTS pattern in `mol`.
+ *
+ * Returns JSON array of arrays of atom indices (sorted, 0-based).
+ * Example: `[[0,1,2],[3,4,5]]` — two matches.
+ * Returns `"[]"` if no match. Returns a JS error on invalid SMARTS.
+ */
+export function smarts_match_atoms(smarts: string, mol: MolHandle): string;
+
+/**
+ * Render a highlighted SVG from a SMILES string in one call.
+ *
+ * `atoms` — 0-based atom indices to highlight (Uint32Array in JS).
+ * `bonds` — 0-based bond indices to highlight (Uint32Array in JS).
+ * `color` — CSS color for highlights (e.g. `"#ef4444"`); empty string uses default yellow.
+ *
+ * Returns a JS error on SMILES parse failure.
+ */
+export function smiles_to_svg_highlighted(smiles: string, atoms: Uint32Array, bonds: Uint32Array, color: string): string;
+
+/**
+ * SMR_VSA descriptors (10 bins) as a JSON array.
+ */
+export function smr_vsa_json(mol: MolHandle): string;
+
+export function start(): void;
+
 /**
  * Tanimoto similarity between two molecules using AtomPair fingerprints.
  */
@@ -311,7 +480,164 @@ export function tanimoto_ecfp4(a: MolHandle, b: MolHandle): number;
  */
 export function tanimoto_fcfp4(a: MolHandle, b: MolHandle): number;
 
+/**
+ * Tanimoto similarity between two molecules given only SMILES strings (ECFP4).
+ *
+ * Returns a JS error on parse failure.
+ */
+export function tanimoto_smiles(smiles1: string, smiles2: string): number;
+
+/**
+ * Tanimoto similarity between two molecules using topological path fingerprints.
+ */
+export function tanimoto_topo_path(a: MolHandle, b: MolHandle): number;
+
 /**
  * Tanimoto similarity between two molecules using Topological Torsion fingerprints.
  */
 export function tanimoto_torsion(a: MolHandle, b: MolHandle): number;
+
+/**
+ * Serialize a molecule to a MOL V2000 block.
+ *
+ * All atom coordinates are written as 0.0 (the `Molecule` type has no 2D
+ * coordinate storage; real coordinates would require a separate layout pass).
+ */
+export function to_mol_block(mol: MolHandle): string;
+
+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_reaction_svg: (a: number, b: number) => [number, number, number, number];
+    readonly depict_svg_grid: (a: number, b: number, c: number) => [number, number];
+    readonly depictoptions_new: () => number;
+    readonly depictoptions_set_atom_color: (a: number, b: number, c: number, d: number) => void;
+    readonly depictoptions_set_atom_ids: (a: number, b: number) => void;
+    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_kekulize: (a: number, b: number) => void;
+    readonly depictoptions_set_padding: (a: number, b: number) => void;
+    readonly depictoptions_set_show_atom_indices: (a: number, b: number) => void;
+    readonly depictoptions_set_width: (a: number, b: number) => void;
+    readonly detect_functional_groups: (a: number) => [number, number];
+    readonly ecfp4_bitvec: (a: number) => [number, number];
+    readonly estate_indices_json: (a: number) => [number, number];
+    readonly gasteiger_charges_json: (a: number) => [number, number];
+    readonly generate_3d_pdb: (a: number) => [number, number];
+    readonly get_atom_info: (a: number, b: number) => [number, number];
+    readonly get_bond_between: (a: number, b: number, c: number) => [number, number];
+    readonly get_bond_info: (a: number, b: number) => [number, number];
+    readonly identify_functional_groups: (a: number) => [number, number];
+    readonly is_valid_smiles: (a: number, b: number) => number;
+    readonly match_smarts_smiles: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
+    readonly mol_from_sdf_block: (a: number, b: number) => [number, 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_max_estate: (a: number) => number;
+    readonly molhandle_min_estate: (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_sum_estate: (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 peoe_vsa_json: (a: 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 sa_score: (a: number) => number;
+    readonly sdf_to_smiles_json: (a: number, b: number) => [number, number];
+    readonly slogp_vsa_json: (a: number) => [number, number];
+    readonly smarts_match_atoms: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly smiles_to_svg_highlighted: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
+    readonly smr_vsa_json: (a: 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_smiles: (a: number, b: number, c: number, d: number) => [number, number, number];
+    readonly tanimoto_topo_path: (a: number, b: number) => number;
+    readonly tanimoto_torsion: (a: number, b: number) => number;
+    readonly to_mol_block: (a: number) => [number, number];
+    readonly start: () => void;
+    readonly __wbindgen_free: (a: number, b: number, c: number) => 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;
+    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>;