@kent-tokyo/chematic 0.5.0 → 0.8.0

package/chematic_wasm.d.ts

@@ -1283,6 +1283,17 @@ export function mol_block_coords_json(mol_block: string): string;
  */
 export function mol_block_from_smiles(smiles: string): string;
 
+/**
+ * Rejected wedge/hash stereocenters for a MOL V2000 block, as JSON.
+ *
+ * Companion to [`mol_from_sdf_block`]/[`mol_block_coords_json`] -- returns
+ * `[{"atom_idx":N,"reason":"..."}]`, empty unless a wedge/hash bond was
+ * present at some center and got rejected. See
+ * `crates/chematic-py/src/formats.rs`'s `from_mol_block_with_diagnostics`
+ * for the reason vocabulary (kept identical across bindings).
+ */
+export function mol_block_stereo_diagnostics_json(mol_block: string): string;
+
 /**
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
@@ -1341,6 +1352,12 @@ export function mol_from_xyz(xyz: string): MolHandle;
  */
 export function mol_next_atom_idx(mol: MolHandle): number;
 
+/**
+ * Rejected wedge/hash stereocenters for a MOL V3000 block, as JSON. Same
+ * shape as [`mol_block_stereo_diagnostics_json`] but for V3000 input.
+ */
+export function mol_v3000_stereo_diagnostics_json(block: string): string;
+
 /**
  * Return a new `MolHandle` with one atom appended.
  *
@@ -1542,6 +1559,54 @@ export function predict_pka_json(smiles: string): string;
  */
 export function random_smiles_json(smiles: string, count: number, seed: bigint): string;
 
+/**
+ * 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).
+ *
+ * Bit-for-bit identical to
+ * `rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048).GetFingerprint(mol)`
+ * for every input this preprocessing handles. **Not** the same bits as `ecfp4_bitvec`
+ * (that path uses chematic's own FNV-1a hash and is not RDKit-bit-compatible by
+ * design -- the two are never silently interchanged).
+ *
+ * Returns a JS error (its string carrying `RdkitMorganError`'s `Display` text, e.g.
+ * `"rdkit-exact ecfp4: aromaticity: ..."`) if RDKit-parity aromaticity preprocessing
+ * fails, never a silent fallback to `ecfp4_bitvec`'s Hückel-based engine -- the two
+ * engines are not bit-compatible, so a silent substitution would look successful
+ * while actually returning the wrong hash. See `docs/ecfp4_bitexact_api_rfc.md`.
+ */
+export function rdkit_ecfp4_bitvec(mol: MolHandle): Uint8Array;
+
+/**
+ * Same fingerprint as `rdkit_ecfp4_bitvec`, plus the raw (unfolded) data behind it, as
+ * JSON: `{"fingerprint":[u8,...],"sparseCounts":{"rawId":count,...},
+ * "rawBitInfo":{"rawId":[[atomIdx,radius],...],...},
+ * "foldedBitInfo":{"bit":[[atomIdx,radius],...],...}}`.
+ *
+ * Returns a JS error on the same preprocessing failures as `rdkit_ecfp4_bitvec`.
+ */
+export function rdkit_ecfp4_detail_json(mol: MolHandle): string;
+
+/**
+ * RDKit-bit-exact Morgan/ECFP fingerprint at a caller-chosen radius/bit-width, as a
+ * bit-packed byte vector (`nbits / 8` bytes, LSB-first).
+ *
+ * `radius` must be 0, 1, 2 (`rdkit_ecfp4_bitvec`'s ECFP4), or 3. `nbits` must be one
+ * of 128, 256, 512, 1024, or 2048. Each of these 20 combinations is independently
+ * re-verified against a live RDKit oracle (not assumed to generalize from
+ * radius=2/2048 bits alone) -- see `validation/ecfp4_rdkit_stable_api_fixtures.json`.
+ * An unsupported value returns a JS error rather than being silently coerced to the
+ * nearest supported one.
+ */
+export function rdkit_ecfp_config_bitvec(mol: MolHandle, radius: number, nbits: number): Uint8Array;
+
+/**
+ * Same fingerprint as `rdkit_ecfp_config_bitvec`, plus the raw (unfolded) data -- see
+ * `rdkit_ecfp4_detail_json` for the JSON shape (identical, generalized to this
+ * function's `radius`/`nbits`).
+ */
+export function rdkit_ecfp_config_detail_json(mol: MolHandle, radius: number, nbits: number): string;
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  */
@@ -1630,11 +1695,15 @@ export function sdf_from_records_json(smiles_json: string, names_json: string, p
  *
  * Each record has the shape:
  * ```json
- * {"smiles":"CC(=O)O","name":"aspirin","properties":{"MW":"180.2","Activity":"high"}}
+ * {"smiles":"CC(=O)O","name":"aspirin","properties":{"MW":"180.2","Activity":"high"},"stereo_diagnostics":[]}
  * ```
  *
  * Invalid records are represented as `null`.  SD data fields are included in
- * `properties`; multi-line values are joined with `\n`.
+ * `properties`; multi-line values are joined with `\n`. `stereo_diagnostics`
+ * is a list of `{"atom_idx":N,"reason":"..."}` objects, one per rejected
+ * wedge/hash center (see [`mol_block_stereo_diagnostics_json`] for the
+ * reason vocabulary) -- empty unless a wedge/hash bond was present at some
+ * center and got rejected.
  */
 export function sdf_to_records_json(sdf: string): string;
 
@@ -2036,6 +2105,7 @@ export interface InitOutput {
     readonly mol2_to_smiles: (a: number, b: number) => [number, number];
     readonly mol_block_coords_json: (a: number, b: number) => [number, number, number, number];
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
+    readonly mol_block_stereo_diagnostics_json: (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];
@@ -2044,6 +2114,7 @@ export interface InitOutput {
     readonly mol_from_v3000_block: (a: number, b: number) => [number, number, number];
     readonly mol_from_xyz: (a: number, b: number) => [number, number, number];
     readonly mol_next_atom_idx: (a: number) => number;
+    readonly mol_v3000_stereo_diagnostics_json: (a: number, b: number) => [number, number, number, number];
     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];
@@ -2141,6 +2212,10 @@ export interface InitOutput {
     readonly pharmacophore_fp_3d_summary: (a: number) => [number, number];
     readonly predict_pka_json: (a: number, b: number) => [number, number];
     readonly random_smiles_json: (a: number, b: number, c: number, d: bigint) => [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];
+    readonly rdkit_ecfp_config_detail_json: (a: number, b: number, c: number) => [number, number, number, number];
     readonly remove_hydrogens: (a: number) => number;
     readonly rgroup_decompose_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly ring_families_json: (a: number) => [number, number, number, number];

package/chematic_wasm.js

@@ -3177,6 +3177,38 @@ export function mol_block_from_smiles(smiles) {
     }
 }
 
+/**
+ * Rejected wedge/hash stereocenters for a MOL V2000 block, as JSON.
+ *
+ * Companion to [`mol_from_sdf_block`]/[`mol_block_coords_json`] -- returns
+ * `[{"atom_idx":N,"reason":"..."}]`, empty unless a wedge/hash bond was
+ * present at some center and got rejected. See
+ * `crates/chematic-py/src/formats.rs`'s `from_mol_block_with_diagnostics`
+ * for the reason vocabulary (kept identical across bindings).
+ * @param {string} mol_block
+ * @returns {string}
+ */
+export function mol_block_stereo_diagnostics_json(mol_block) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(mol_block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mol_block_stereo_diagnostics_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);
+    }
+}
+
 /**
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
@@ -3308,6 +3340,33 @@ export function mol_next_atom_idx(mol) {
     return ret >>> 0;
 }
 
+/**
+ * Rejected wedge/hash stereocenters for a MOL V3000 block, as JSON. Same
+ * shape as [`mol_block_stereo_diagnostics_json`] but for V3000 input.
+ * @param {string} block
+ * @returns {string}
+ */
+export function mol_v3000_stereo_diagnostics_json(block) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(block, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mol_v3000_stereo_diagnostics_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);
+    }
+}
+
 /**
  * Return a new `MolHandle` with one atom appended.
  *
@@ -3874,6 +3933,120 @@ export function random_smiles_json(smiles, count, seed) {
     }
 }
 
+/**
+ * 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).
+ *
+ * Bit-for-bit identical to
+ * `rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048).GetFingerprint(mol)`
+ * for every input this preprocessing handles. **Not** the same bits as `ecfp4_bitvec`
+ * (that path uses chematic's own FNV-1a hash and is not RDKit-bit-compatible by
+ * design -- the two are never silently interchanged).
+ *
+ * Returns a JS error (its string carrying `RdkitMorganError`'s `Display` text, e.g.
+ * `"rdkit-exact ecfp4: aromaticity: ..."`) if RDKit-parity aromaticity preprocessing
+ * fails, never a silent fallback to `ecfp4_bitvec`'s Hückel-based engine -- the two
+ * engines are not bit-compatible, so a silent substitution would look successful
+ * while actually returning the wrong hash. See `docs/ecfp4_bitexact_api_rfc.md`.
+ * @param {MolHandle} mol
+ * @returns {Uint8Array}
+ */
+export function rdkit_ecfp4_bitvec(mol) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.rdkit_ecfp4_bitvec(mol.__wbg_ptr);
+    if (ret[3]) {
+        throw takeFromExternrefTable0(ret[2]);
+    }
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Same fingerprint as `rdkit_ecfp4_bitvec`, plus the raw (unfolded) data behind it, as
+ * JSON: `{"fingerprint":[u8,...],"sparseCounts":{"rawId":count,...},
+ * "rawBitInfo":{"rawId":[[atomIdx,radius],...],...},
+ * "foldedBitInfo":{"bit":[[atomIdx,radius],...],...}}`.
+ *
+ * Returns a JS error on the same preprocessing failures as `rdkit_ecfp4_bitvec`.
+ * @param {MolHandle} mol
+ * @returns {string}
+ */
+export function rdkit_ecfp4_detail_json(mol) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.rdkit_ecfp4_detail_json(mol.__wbg_ptr);
+        var ptr1 = ret[0];
+        var len1 = ret[1];
+        if (ret[3]) {
+            ptr1 = 0; len1 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred2_0 = ptr1;
+        deferred2_1 = len1;
+        return getStringFromWasm0(ptr1, len1);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
+/**
+ * RDKit-bit-exact Morgan/ECFP fingerprint at a caller-chosen radius/bit-width, as a
+ * bit-packed byte vector (`nbits / 8` bytes, LSB-first).
+ *
+ * `radius` must be 0, 1, 2 (`rdkit_ecfp4_bitvec`'s ECFP4), or 3. `nbits` must be one
+ * of 128, 256, 512, 1024, or 2048. Each of these 20 combinations is independently
+ * re-verified against a live RDKit oracle (not assumed to generalize from
+ * radius=2/2048 bits alone) -- see `validation/ecfp4_rdkit_stable_api_fixtures.json`.
+ * An unsupported value returns a JS error rather than being silently coerced to the
+ * nearest supported one.
+ * @param {MolHandle} mol
+ * @param {number} radius
+ * @param {number} nbits
+ * @returns {Uint8Array}
+ */
+export function rdkit_ecfp_config_bitvec(mol, radius, nbits) {
+    _assertClass(mol, MolHandle);
+    const ret = wasm.rdkit_ecfp_config_bitvec(mol.__wbg_ptr, radius, nbits);
+    if (ret[3]) {
+        throw takeFromExternrefTable0(ret[2]);
+    }
+    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
+    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+    return v1;
+}
+
+/**
+ * Same fingerprint as `rdkit_ecfp_config_bitvec`, plus the raw (unfolded) data -- see
+ * `rdkit_ecfp4_detail_json` for the JSON shape (identical, generalized to this
+ * function's `radius`/`nbits`).
+ * @param {MolHandle} mol
+ * @param {number} radius
+ * @param {number} nbits
+ * @returns {string}
+ */
+export function rdkit_ecfp_config_detail_json(mol, radius, nbits) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ret = wasm.rdkit_ecfp_config_detail_json(mol.__wbg_ptr, radius, nbits);
+        var ptr1 = ret[0];
+        var len1 = ret[1];
+        if (ret[3]) {
+            ptr1 = 0; len1 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred2_0 = ptr1;
+        deferred2_1 = len1;
+        return getStringFromWasm0(ptr1, len1);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
 /**
  * Return a copy of the molecule with all explicit hydrogen atoms removed.
  * @param {MolHandle} mol
@@ -4087,11 +4260,15 @@ export function sdf_from_records_json(smiles_json, names_json, props_json) {
  *
  * Each record has the shape:
  * ```json
- * {"smiles":"CC(=O)O","name":"aspirin","properties":{"MW":"180.2","Activity":"high"}}
+ * {"smiles":"CC(=O)O","name":"aspirin","properties":{"MW":"180.2","Activity":"high"},"stereo_diagnostics":[]}
  * ```
  *
  * Invalid records are represented as `null`.  SD data fields are included in
- * `properties`; multi-line values are joined with `\n`.
+ * `properties`; multi-line values are joined with `\n`. `stereo_diagnostics`
+ * is a list of `{"atom_idx":N,"reason":"..."}` objects, one per rejected
+ * wedge/hash center (see [`mol_block_stereo_diagnostics_json`] for the
+ * reason vocabulary) -- empty unless a wedge/hash bond was present at some
+ * center and got rejected.
  * @param {string} sdf
  * @returns {string}
  */

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": "0.5.0",
+  "version": "0.8.0",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",