@kent-tokyo/chematic 1.1.3 → 1.1.4

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 1.1.3. The binding keeps bounded parsing,
+The current workspace line is 1.1.4. 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.
 

package/chematic_wasm.d.ts

@@ -454,6 +454,18 @@ export class MolHandle {
      * weights use zero-based molecule atom order.
      */
     rdkit_align_json(probe_coords_json: string, reference_coords_json: string, atom_map_json: string | null | undefined, weights_json: string | null | undefined, reflect: boolean, max_iterations: number): string;
+    /**
+     * RDKit `GetAllConformerBestRMS` as a JSON number array in
+     * `(1,0), (2,0), (2,1), ...` order. Atom mappings are computed once for
+     * the entire batch.
+     */
+    rdkit_all_conformer_best_rms_json(conformers_json: string, max_matches: number, symmetrize: boolean, weights_json?: string | null): string;
+    /**
+     * RDKit 2026.09.1 `GetAllConformerBestRMSToRef` as a JSON number array
+     * in reference-major order. Atom mappings are computed once for the
+     * entire Cartesian product.
+     */
+    rdkit_all_conformer_best_rms_to_reference_json(reference: MolHandle, probe_conformers_json: string, reference_conformers_json: string, max_matches: number, symmetrize: boolean, weights_json?: string | null): string;
     /**
      * RDKit `GetBestAlignmentTransform` as JSON, bounded by `max_matches`.
      */
@@ -1261,6 +1273,18 @@ export function erg_vec_json(mol: MolHandle): string;
  */
 export function estate_indices_json(mol: MolHandle): string;
 
+/**
+ * Decode an RDKit atom code as stable JSON.
+ *
+ * Returns `{"symbol":"C","branchCount":3,"piElectronCount":1}`.
+ */
+export function explain_rdkit_atom_code_json(code: number): string;
+
+/**
+ * Decode a decimal legacy RDKit torsion code as stable JSON.
+ */
+export function explain_rdkit_topological_torsion_code_json(code_decimal: string, size: number): string;
+
 /**
  * Extract an extxyz frame's coordinates, cell, per-atom properties and
  * frame metadata as JSON, in the SAME atom order [`mol_from_extxyz`]
@@ -2444,6 +2468,17 @@ export function preflight_smiles_json(smiles: string, width: number, height: num
  */
 export function prepare_rdkit_ecfp4(mol: MolHandle): PreparedRdkitEcfp4Handle;
 
+/**
+ * Amino-acid-only mmCIF projection in the same schema as
+ * [`protein_from_pdb_json`].
+ */
+export function protein_from_mmcif_json(text: string): string;
+
+/**
+ * Amino-acid-only PDB projection as stable JSON.
+ */
+export function protein_from_pdb_json(text: string): string;
+
 /**
  * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
  * `qcschema_molecule` document, in the SAME atom order
@@ -2490,6 +2525,14 @@ export function qcschema_validate_atomic_result(json: string): string;
  */
 export function random_smiles_json(smiles: string, count: number, seed: bigint): string;
 
+/**
+ * RDKit atom-pair atom code for one atom.
+ *
+ * `branch_subtract` is normally 0 for atom-pair diagnostics, 1 for a
+ * torsion endpoint, and 2 for an interior torsion atom.
+ */
+export function rdkit_atom_code(mol: MolHandle, atom_index: number, branch_subtract: number): number;
+
 /**
  * RDKit-bit-exact ECFP4 (radius=2, 2048 bits, `useChirality=false`, `useBondTypes=true`,
  * RDKit's default atom invariant) as a bit-packed byte vector (256 bytes = 2048 bits).
@@ -2590,6 +2633,21 @@ export function rdkit_path_bitvec(mol: MolHandle): Uint8Array;
  */
 export function rdkit_rdk_bitvec(mol: MolHandle): Uint8Array;
 
+/**
+ * RDKit 2026.09.1 RDKFingerprint with `ignoreAtoms`: every branched path
+ * containing one of `ignored_atoms` is excluded. Invalid indices return a JS
+ * error; an empty list is bit-identical to [`rdkit_rdk_bitvec`].
+ */
+export function rdkit_rdk_bitvec_ignoring_atoms(mol: MolHandle, ignored_atoms: Uint32Array): Uint8Array;
+
+/**
+ * Pack a JSON array of atom indices into RDKit's legacy torsion code.
+ *
+ * The decimal string return type avoids losing precision in JavaScript's
+ * `number` type for codes above 2^53.
+ */
+export function rdkit_topological_torsion_path_code_decimal(mol: MolHandle, path_json: string): string;
+
 /**
  * Compute the opt-in RDKit-compatible hashed topological-torsion fingerprint
  * as a bit-packed byte vector (256 bytes = 2048 bits). This remains separate
@@ -3427,6 +3485,8 @@ export interface InitOutput {
     readonly enumerate_tautomers_json: (a: number) => [number, number];
     readonly erg_vec_json: (a: number) => [number, number];
     readonly estate_indices_json: (a: number) => [number, number];
+    readonly explain_rdkit_atom_code_json: (a: number) => [number, number];
+    readonly explain_rdkit_topological_torsion_code_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly extxyz_frame_json: (a: number, b: number) => [number, number, number, number];
     readonly extxyz_frames_batch_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly fcfp4_bitvec: (a: number) => [number, number];
@@ -3597,6 +3657,8 @@ export interface InitOutput {
     readonly molhandle_qed: (a: number) => number;
     readonly molhandle_randic_index: (a: number) => number;
     readonly molhandle_rdkit_align_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number, j: number, k: number) => [number, number, number, number];
+    readonly molhandle_rdkit_all_conformer_best_rms_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number, number];
+    readonly molhandle_rdkit_all_conformer_best_rms_to_reference_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number, j: number) => [number, number, number, number];
     readonly molhandle_rdkit_best_alignment_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number) => [number, number, number, number];
     readonly molhandle_rdkit_best_rms: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number) => [number, number, number];
     readonly molhandle_rdkit_bounds_matrix_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
@@ -3657,10 +3719,13 @@ export interface InitOutput {
     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 protein_from_mmcif_json: (a: number, b: number) => [number, number, number, number];
+    readonly protein_from_pdb_json: (a: number, b: number) => [number, 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];
     readonly random_smiles_json: (a: number, b: number, c: number, d: bigint) => [number, number, number, number];
+    readonly rdkit_atom_code: (a: number, b: number, c: number) => [number, number, number];
     readonly rdkit_ecfp4_bitvec: (a: number) => [number, number, number, number];
     readonly rdkit_ecfp4_detail_json: (a: number) => [number, number, number, number];
     readonly rdkit_ecfp_config_bitvec: (a: number, b: number, c: number) => [number, number, number, number];
@@ -3673,6 +3738,8 @@ export interface InitOutput {
     readonly rdkit_nearest_neighbors_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly rdkit_path_bitvec: (a: number) => [number, number];
     readonly rdkit_rdk_bitvec: (a: number) => [number, number];
+    readonly rdkit_rdk_bitvec_ignoring_atoms: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly rdkit_topological_torsion_path_code_decimal: (a: number, b: number, c: number) => [number, number, number, number];
     readonly rdkit_torsion_bitvec: (a: number) => [number, number];
     readonly rdkitreadresult_coords_json: (a: number) => [number, number, number, number];
     readonly rdkitreadresult_molecule: (a: number) => number;

package/chematic_wasm.js

@@ -1092,6 +1092,75 @@ export class MolHandle {
             wasm.__wbindgen_free(deferred6_0, deferred6_1, 1);
         }
     }
+    /**
+     * RDKit `GetAllConformerBestRMS` as a JSON number array in
+     * `(1,0), (2,0), (2,1), ...` order. Atom mappings are computed once for
+     * the entire batch.
+     * @param {string} conformers_json
+     * @param {number} max_matches
+     * @param {boolean} symmetrize
+     * @param {string | null} [weights_json]
+     * @returns {string}
+     */
+    rdkit_all_conformer_best_rms_json(conformers_json, max_matches, symmetrize, weights_json) {
+        let deferred4_0;
+        let deferred4_1;
+        try {
+            const ptr0 = passStringToWasm0(conformers_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len0 = WASM_VECTOR_LEN;
+            var ptr1 = isLikeNone(weights_json) ? 0 : passStringToWasm0(weights_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            var len1 = WASM_VECTOR_LEN;
+            const ret = wasm.molhandle_rdkit_all_conformer_best_rms_json(this.__wbg_ptr, ptr0, len0, max_matches, symmetrize, ptr1, len1);
+            var ptr3 = ret[0];
+            var len3 = ret[1];
+            if (ret[3]) {
+                ptr3 = 0; len3 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred4_0 = ptr3;
+            deferred4_1 = len3;
+            return getStringFromWasm0(ptr3, len3);
+        } finally {
+            wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+        }
+    }
+    /**
+     * RDKit 2026.09.1 `GetAllConformerBestRMSToRef` as a JSON number array
+     * in reference-major order. Atom mappings are computed once for the
+     * entire Cartesian product.
+     * @param {MolHandle} reference
+     * @param {string} probe_conformers_json
+     * @param {string} reference_conformers_json
+     * @param {number} max_matches
+     * @param {boolean} symmetrize
+     * @param {string | null} [weights_json]
+     * @returns {string}
+     */
+    rdkit_all_conformer_best_rms_to_reference_json(reference, probe_conformers_json, reference_conformers_json, max_matches, symmetrize, weights_json) {
+        let deferred5_0;
+        let deferred5_1;
+        try {
+            _assertClass(reference, MolHandle);
+            const ptr0 = passStringToWasm0(probe_conformers_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len0 = WASM_VECTOR_LEN;
+            const ptr1 = passStringToWasm0(reference_conformers_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len1 = WASM_VECTOR_LEN;
+            var ptr2 = isLikeNone(weights_json) ? 0 : passStringToWasm0(weights_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            var len2 = WASM_VECTOR_LEN;
+            const ret = wasm.molhandle_rdkit_all_conformer_best_rms_to_reference_json(this.__wbg_ptr, reference.__wbg_ptr, ptr0, len0, ptr1, len1, max_matches, symmetrize, ptr2, len2);
+            var ptr4 = ret[0];
+            var len4 = ret[1];
+            if (ret[3]) {
+                ptr4 = 0; len4 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred5_0 = ptr4;
+            deferred5_1 = len4;
+            return getStringFromWasm0(ptr4, len4);
+        } finally {
+            wasm.__wbindgen_free(deferred5_0, deferred5_1, 1);
+        }
+    }
     /**
      * RDKit `GetBestAlignmentTransform` as JSON, bounded by `max_matches`.
      * @param {string} probe_coords_json
@@ -3496,6 +3565,53 @@ export function estate_indices_json(mol) {
     }
 }
 
+/**
+ * Decode an RDKit atom code as stable JSON.
+ *
+ * Returns `{"symbol":"C","branchCount":3,"piElectronCount":1}`.
+ * @param {number} code
+ * @returns {string}
+ */
+export function explain_rdkit_atom_code_json(code) {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        const ret = wasm.explain_rdkit_atom_code_json(code);
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Decode a decimal legacy RDKit torsion code as stable JSON.
+ * @param {string} code_decimal
+ * @param {number} size
+ * @returns {string}
+ */
+export function explain_rdkit_topological_torsion_code_json(code_decimal, size) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(code_decimal, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.explain_rdkit_topological_torsion_code_json(ptr0, len0, size);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Extract an extxyz frame's coordinates, cell, per-atom properties and
  * frame metadata as JSON, in the SAME atom order [`mol_from_extxyz`]
@@ -6609,6 +6725,59 @@ export function prepare_rdkit_ecfp4(mol) {
     return PreparedRdkitEcfp4Handle.__wrap(ret[0]);
 }
 
+/**
+ * Amino-acid-only mmCIF projection in the same schema as
+ * [`protein_from_pdb_json`].
+ * @param {string} text
+ * @returns {string}
+ */
+export function protein_from_mmcif_json(text) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.protein_from_mmcif_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Amino-acid-only PDB projection as stable JSON.
+ * @param {string} text
+ * @returns {string}
+ */
+export function protein_from_pdb_json(text) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.protein_from_pdb_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
  * `qcschema_molecule` document, in the SAME atom order
@@ -6741,6 +6910,25 @@ export function random_smiles_json(smiles, count, seed) {
     }
 }
 
+/**
+ * RDKit atom-pair atom code for one atom.
+ *
+ * `branch_subtract` is normally 0 for atom-pair diagnostics, 1 for a
+ * torsion endpoint, and 2 for an interior torsion atom.
+ * @param {MolHandle} mol
+ * @param {number} atom_index
+ * @param {number} branch_subtract
+ * @returns {number}
+ */
+export function rdkit_atom_code(mol, atom_index, branch_subtract) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.rdkit_atom_code(mol.__wbg_ptr, atom_index, branch_subtract);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return ret[0] >>> 0;
+}
+
 /**
  * RDKit-bit-exact ECFP4 (radius=2, 2048 bits, `useChirality=false`, `useBondTypes=true`,
  * RDKit's default atom invariant) as a bit-packed byte vector (256 bytes = 2048 bits).
@@ -7014,6 +7202,58 @@ export function rdkit_rdk_bitvec(mol) {
     return v1;
 }
 
+/**
+ * RDKit 2026.09.1 RDKFingerprint with `ignoreAtoms`: every branched path
+ * containing one of `ignored_atoms` is excluded. Invalid indices return a JS
+ * error; an empty list is bit-identical to [`rdkit_rdk_bitvec`].
+ * @param {MolHandle} mol
+ * @param {Uint32Array} ignored_atoms
+ * @returns {Uint8Array}
+ */
+export function rdkit_rdk_bitvec_ignoring_atoms(mol, ignored_atoms) {
+    _assertClass(mol, MolHandle);
+    const ptr0 = passArray32ToWasm0(ignored_atoms, wasm.__wbindgen_malloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.rdkit_rdk_bitvec_ignoring_atoms(mol.__wbg_ptr, ptr0, len0);
+    if (ret[3]) {
+        throw takeFromExternrefTable0(ret[2]);
+    }
+    var v2 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v2;
+}
+
+/**
+ * Pack a JSON array of atom indices into RDKit's legacy torsion code.
+ *
+ * The decimal string return type avoids losing precision in JavaScript's
+ * `number` type for codes above 2^53.
+ * @param {MolHandle} mol
+ * @param {string} path_json
+ * @returns {string}
+ */
+export function rdkit_topological_torsion_path_code_decimal(mol, path_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(path_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.rdkit_topological_torsion_path_code_decimal(mol.__wbg_ptr, ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Compute the opt-in RDKit-compatible hashed topological-torsion fingerprint
  * as a bit-packed byte vector (256 bytes = 2048 bits). This remains separate

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": "1.1.3",
+  "version": "1.1.4",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",