@kent-tokyo/chematic 1.0.18 → 1.0.20

package/README.md

@@ -4,7 +4,7 @@ WebAssembly bindings for [chematic](https://github.com/kent-tokyo/chematic), a p
 
 Published to npm as [`@kent-tokyo/chematic`](https://www.npmjs.com/package/@kent-tokyo/chematic).
 
-The current workspace line is 1.0.15. The binding keeps bounded parsing,
+The current workspace line is 1.0.20. The binding keeps bounded parsing,
 typed failures, and opt-in `embed_pipeline_v2_json`; 3D/MMFF94 behavior remains
 Experimental and is not a claim of full RDKit parity.
 
@@ -36,6 +36,10 @@ npm install @kent-tokyo/chematic
 - Bounded topology parsing for CML (`mol_from_cml_strict` provides the opt-in
   non-empty, balanced, single-root boundary), ChemicalJSON (`mol_from_cjson`), MolJSON,
   CDXML, MOL2, and PDB/mmCIF
+- Index-aligned wildcard/R-group inspection with
+  `MolHandle.atom_pseudo_labels_json()` and immutable edits through
+  `mol_with_atom_pseudo_label`; labels are bounded to `*`, `R`, and
+  `R1..R9999`
 - PDBx/mmCIF, PQR, QCSchema JSON, ORCA input/output, Gaussian Cube, OpenDX,
   and LAMMPS data/dump I/O (JSON-based bindings; see `format_io.rs`)
 - Topological descriptors: Wiener index, Hall-Kier κ, χ connectivity indices, Bertz CT

package/chematic_wasm.d.ts

@@ -158,6 +158,13 @@ export class MolHandle {
      * Number of heavy atoms (explicit atoms in the graph; does not count implicit H).
      */
     atom_count(): number;
+    /**
+     * Index-aligned pseudoatom labels as stable JSON.
+     *
+     * Real atoms are `null`; wildcard entries are objects with `kind`,
+     * `label`, and nullable `r_group_number` fields.
+     */
+    atom_pseudo_labels_json(): string;
     /**
      * Returns true when TPSA < 90 Ų, MW < 400, HBD ≤ 3.
      */
@@ -466,6 +473,22 @@ export class MolHandle {
     zagreb_index_m1(): number;
 }
 
+/**
+ * Immutable RDKit-compatible ECFP4 preprocessing cache.
+ *
+ * Create it with [`prepare_rdkit_ecfp4`], then call [`bitvec`](Self::bitvec)
+ * repeatedly without repeating aromaticity and ring perception.
+ */
+export class PreparedRdkitEcfp4Handle {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Compute the cached radius-2, 2048-bit fingerprint as 256 packed bytes.
+     */
+    bitvec(): Uint8Array;
+}
+
 /**
  * Reusable prepared index for the RDKit-compatible Morgan profile.
  *
@@ -1331,9 +1354,10 @@ export function inchi_from_smiles(smiles: string): string;
 export function inchikey_from_smiles(smiles: string): string;
 
 /**
- * Invert the stereochemistry of a tetrahedral stereocenter (U/D wedge bonds).
+ * Invert a tetrahedral stereocenter and synchronize incident U/D wedge bonds.
  *
- * If the atom has no wedge/dash bonds, returns an unchanged copy.
+ * Recorded chirality is inverted even without a wedge; when a wedge/hash is
+ * present its depiction marker is inverted too.
  * Returns error if atom_idx is invalid.
  */
 export function invert_stereocenter_at(mol: MolHandle, atom_idx: number): MolHandle;
@@ -1901,6 +1925,11 @@ export function mol_with_atom_charge(mol: MolHandle, idx: number, charge: number
  */
 export function mol_with_atom_element(mol: MolHandle, idx: number, element_symbol: string): MolHandle;
 
+/**
+ * Return a molecule with atom `idx` changed to `*`, `R`, or `R<n>`.
+ */
+export function mol_with_atom_pseudo_label(mol: MolHandle, idx: number, label: string): MolHandle;
+
 /**
  * Return a new `MolHandle` with atom `idx` and all its bonds removed.
  *
@@ -2173,6 +2202,15 @@ export function predict_pka_json(smiles: string): string;
  */
 export function preflight_smiles_json(smiles: string, width: number, height: number): string;
 
+/**
+ * Perform RDKit-compatible aromaticity/ring preprocessing once.
+ *
+ * This is the prepared-molecule counterpart to RDKit's sanitized molecule
+ * object. Preparation errors remain typed JS errors and are never replaced by
+ * a non-compatible fallback fingerprint.
+ */
+export function prepare_rdkit_ecfp4(mol: MolHandle): PreparedRdkitEcfp4Handle;
+
 /**
  * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
  * `qcschema_molecule` document, in the SAME atom order
@@ -2963,6 +3001,7 @@ export interface InitOutput {
     readonly __wbg_depictoptions_free: (a: number, b: number) => void;
     readonly __wbg_mhfplshhandle_free: (a: number, b: number) => void;
     readonly __wbg_molhandle_free: (a: number, b: number) => void;
+    readonly __wbg_preparedrdkitecfp4handle_free: (a: number, b: number) => void;
     readonly __wbg_rdkitsearchindex_free: (a: number, b: number) => void;
     readonly __wbg_smilesbatchstreamhandle_free: (a: number, b: number) => void;
     readonly add_hydrogens: (a: number) => number;
@@ -3134,12 +3173,14 @@ export interface InitOutput {
     readonly mol_with_atom_added: (a: number, b: number, c: number) => [number, number, number];
     readonly mol_with_atom_charge: (a: number, b: number, c: number) => [number, number, number];
     readonly mol_with_atom_element: (a: number, b: number, c: number, d: number) => [number, number, number];
+    readonly mol_with_atom_pseudo_label: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly mol_with_atom_removed: (a: number, b: number) => [number, number, number];
     readonly mol_with_bond_added: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly mol_with_bond_removed: (a: number, b: number) => [number, number, number];
     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_pseudo_labels_json: (a: number) => [number, number];
     readonly molhandle_bbb_passes: (a: number) => number;
     readonly molhandle_bbb_score: (a: number) => number;
     readonly molhandle_bertz_ct: (a: number) => number;
@@ -3240,6 +3281,8 @@ export interface InitOutput {
     readonly pqr_to_json: (a: number, b: number) => [number, number, number, number];
     readonly predict_pka_json: (a: number, b: number) => [number, number];
     readonly preflight_smiles_json: (a: number, b: number, c: number, d: number) => [number, number];
+    readonly prepare_rdkit_ecfp4: (a: number) => [number, number, number];
+    readonly preparedrdkitecfp4handle_bitvec: (a: number) => [number, number];
     readonly qcschema_molecule_coords_json: (a: number, b: number) => [number, number, number, number];
     readonly qcschema_validate_atomic_input: (a: number, b: number) => [number, number, number, number];
     readonly qcschema_validate_atomic_result: (a: number, b: number) => [number, number, number, number];

package/chematic_wasm.js

@@ -404,6 +404,25 @@ export class MolHandle {
         const ret = wasm.molhandle_atom_count(this.__wbg_ptr);
         return ret >>> 0;
     }
+    /**
+     * Index-aligned pseudoatom labels as stable JSON.
+     *
+     * Real atoms are `null`; wildcard entries are objects with `kind`,
+     * `label`, and nullable `r_group_number` fields.
+     * @returns {string}
+     */
+    atom_pseudo_labels_json() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.molhandle_atom_pseudo_labels_json(this.__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);
+        }
+    }
     /**
      * Returns true when TPSA < 90 Ų, MW < 400, HBD ≤ 3.
      * @returns {boolean}
@@ -1089,6 +1108,42 @@ export class MolHandle {
 }
 if (Symbol.dispose) MolHandle.prototype[Symbol.dispose] = MolHandle.prototype.free;
 
+/**
+ * Immutable RDKit-compatible ECFP4 preprocessing cache.
+ *
+ * Create it with [`prepare_rdkit_ecfp4`], then call [`bitvec`](Self::bitvec)
+ * repeatedly without repeating aromaticity and ring perception.
+ */
+export class PreparedRdkitEcfp4Handle {
+    static __wrap(ptr) {
+        const obj = Object.create(PreparedRdkitEcfp4Handle.prototype);
+        obj.__wbg_ptr = ptr;
+        PreparedRdkitEcfp4HandleFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        PreparedRdkitEcfp4HandleFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_preparedrdkitecfp4handle_free(ptr, 0);
+    }
+    /**
+     * Compute the cached radius-2, 2048-bit fingerprint as 256 packed bytes.
+     * @returns {Uint8Array}
+     */
+    bitvec() {
+        const ret = wasm.preparedrdkitecfp4handle_bitvec(this.__wbg_ptr);
+        var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+        return v1;
+    }
+}
+if (Symbol.dispose) PreparedRdkitEcfp4Handle.prototype[Symbol.dispose] = PreparedRdkitEcfp4Handle.prototype.free;
+
 /**
  * Reusable prepared index for the RDKit-compatible Morgan profile.
  *
@@ -3392,9 +3447,10 @@ export function inchikey_from_smiles(smiles) {
 }
 
 /**
- * Invert the stereochemistry of a tetrahedral stereocenter (U/D wedge bonds).
+ * Invert a tetrahedral stereocenter and synchronize incident U/D wedge bonds.
  *
- * If the atom has no wedge/dash bonds, returns an unchanged copy.
+ * Recorded chirality is inverted even without a wedge; when a wedge/hash is
+ * present its depiction marker is inverted too.
  * Returns error if atom_idx is invalid.
  * @param {MolHandle} mol
  * @param {number} atom_idx
@@ -4777,6 +4833,24 @@ export function mol_with_atom_element(mol, idx, element_symbol) {
     return MolHandle.__wrap(ret[0]);
 }
 
+/**
+ * Return a molecule with atom `idx` changed to `*`, `R`, or `R<n>`.
+ * @param {MolHandle} mol
+ * @param {number} idx
+ * @param {string} label
+ * @returns {MolHandle}
+ */
+export function mol_with_atom_pseudo_label(mol, idx, label) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passStringToWasm0(label, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_with_atom_pseudo_label(mol.__wbg_ptr, idx, ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Return a new `MolHandle` with atom `idx` and all its bonds removed.
  *
@@ -5572,6 +5646,24 @@ export function preflight_smiles_json(smiles, width, height) {
     }
 }
 
+/**
+ * Perform RDKit-compatible aromaticity/ring preprocessing once.
+ *
+ * This is the prepared-molecule counterpart to RDKit's sanitized molecule
+ * object. Preparation errors remain typed JS errors and are never replaced by
+ * a non-compatible fallback fingerprint.
+ * @param {MolHandle} mol
+ * @returns {PreparedRdkitEcfp4Handle}
+ */
+export function prepare_rdkit_ecfp4(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.prepare_rdkit_ecfp4(mol.__wbg_ptr);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return PreparedRdkitEcfp4Handle.__wrap(ret[0]);
+}
+
 /**
  * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
  * `qcschema_molecule` document, in the SAME atom order
@@ -8021,6 +8113,9 @@ const MhfpLshHandleFinalization = (typeof FinalizationRegistry === 'undefined')
 const MolHandleFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_molhandle_free(ptr, 1));
+const PreparedRdkitEcfp4HandleFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_preparedrdkitecfp4handle_free(ptr, 1));
 const RdkitSearchIndexFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_rdkitsearchindex_free(ptr, 1));

package/package.json

@@ -5,7 +5,7 @@
     "Kentaro Tanabe (kent-tokyo) <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "1.0.18",
+  "version": "1.0.20",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",