@kent-tokyo/chematic 0.14.0 → 0.15.0

package/chematic_wasm.d.ts

@@ -597,7 +597,7 @@ export function cdxml_to_smiles_json(cdxml: string): string;
  * CIP stereo assignments via the accurate hierarchical-digraph engine, as a JSON
  * array of `{atomIdx, cipCode}` objects -- same shape as [`cip_assignments_json`],
  * but merges the accurate engine's tetrahedral R/S (~99.6% oracle-stable agreement,
- * see `docs/cip_accurate_rfc.md`) with legacy's E/Z and allene answers (the accurate
+ * see `docs/rfcs/cip_accurate_rfc.md`) with legacy's E/Z and allene answers (the accurate
  * engine computes neither). Atoms it can't resolve are omitted here -- see
  * [`cip_unresolved_json`] -- never a silently-guessed label. Returns `"null"` on an
  * internal engine error (budget-independent computations should not normally hit this).
@@ -861,6 +861,23 @@ export function erg_vec_json(mol: MolHandle): string;
  */
 export function estate_indices_json(mol: MolHandle): string;
 
+/**
+ * Extract an extxyz frame's coordinates, cell, per-atom properties and
+ * frame metadata as JSON, in the SAME atom order [`mol_from_extxyz`]
+ * returns topology for (both read the identical frame via
+ * `chematic_mol::parse_extxyz`, so atom-index correspondence between the
+ * two calls is structural, not just conventional).
+ *
+ * Returns JSON `{"coords":[[x,y,z],...],
+ * "lattice":[9 numbers]|null,
+ * "properties":{"name":[[...atom values...], ...], ...},
+ * "info":{"key":"value", ...}}`.
+ *
+ * Returns a JS error on parse failure or if the frame exceeds the WASM
+ * atom-count limit.
+ */
+export function extxyz_frame_json(text: string): string;
+
 /**
  * FCFP4 (pharmacophore, radius-2) fingerprint as a bit-packed byte vector (256 bytes).
  */
@@ -1331,6 +1348,19 @@ export function mol_from_cdxml(cdxml: string): MolHandle;
  */
 export function mol_from_cml(cml: string): MolHandle;
 
+/**
+ * Parse an Extended XYZ (extxyz) frame and return a `MolHandle` (topology +
+ * element/position only; use [`extxyz_frame_json`] to recover coordinates,
+ * cell, per-atom properties and frame metadata in the SAME atom order).
+ *
+ * A plain XYZ file (free-form comment, no `Lattice=`/`Properties=`) parses
+ * too. Only the first frame of a multi-frame file is read.
+ *
+ * Returns a JS error on parse failure or if the frame exceeds the WASM
+ * atom-count limit.
+ */
+export function mol_from_extxyz(text: string): MolHandle;
+
 /**
  * Parse a MolJSON string into a `MolHandle`.
  *
@@ -1597,7 +1627,7 @@ export function random_smiles_json(smiles: string, count: number, seed: bigint):
  * `"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`.
+ * while actually returning the wrong hash. See `docs/rfcs/ecfp4_bitexact_api_rfc.md`.
  */
 export function rdkit_ecfp4_bitvec(mol: MolHandle): Uint8Array;
 
@@ -1951,6 +1981,26 @@ export function tanimoto_torsion(a: MolHandle, b: MolHandle): number;
  */
 export function to_cml(mol: MolHandle): string;
 
+/**
+ * Write a molecule + coordinates as an Extended XYZ (extxyz) frame.
+ *
+ * `coords_json`: `[[x,y,z],...]` (Å), same order and length as `mol`'s
+ * atoms.
+ *
+ * `options_json`: an optional JSON object,
+ * `{"lattice":[9 numbers]|null,"properties":{"name":[[...]],...},"info":{"key":"value",...}}`
+ * -- pass `"{}"` for a plain (non-extended) frame. Only real-valued
+ * per-atom `properties` columns are supported from this binding (matches
+ * the Python `to_extxyz` binding's scope); build a
+ * `chematic_mol::XyzProperty` directly from Rust for integer/string/logical
+ * columns.
+ *
+ * Returns a JS error if `coords_json`/`options_json` are malformed, if
+ * `coords_json`'s length doesn't match `mol`'s atom count, or if a
+ * `properties` column's row count doesn't match it.
+ */
+export function to_extxyz_json(mol: MolHandle, coords_json: string, options_json: string): string;
+
 /**
  * Serialize a molecule to a MOL V2000 block with 2D coordinates.
  *
@@ -2103,6 +2153,7 @@ 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 extxyz_frame_json: (a: number, b: number) => [number, number, number, number];
     readonly fcfp4_bitvec: (a: number) => [number, number];
     readonly fcfp6_bitvec: (a: number) => [number, number];
     readonly find_reaction_center_json: (a: number, b: number) => [number, number];
@@ -2159,6 +2210,7 @@ export interface InitOutput {
     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_extxyz: (a: number, b: number) => [number, number, number];
     readonly mol_from_moljson: (a: number, b: number) => [number, number, number];
     readonly mol_from_pdb: (a: number, b: number) => number;
     readonly mol_from_sdf_block: (a: number, b: number) => [number, number, number];
@@ -2302,6 +2354,7 @@ export interface InitOutput {
     readonly tanimoto_topo_path: (a: number, b: number) => number;
     readonly tanimoto_torsion: (a: number, b: number) => number;
     readonly to_cml: (a: number) => [number, number];
+    readonly to_extxyz_json: (a: number, b: number, c: number, d: number, e: number) => [number, number, number, number];
     readonly to_mol_block: (a: number) => [number, number];
     readonly to_mol_v3000_block: (a: number) => [number, number];
     readonly to_moljson: (a: number) => [number, number];

package/chematic_wasm.js

@@ -1402,7 +1402,7 @@ export function cdxml_to_smiles_json(cdxml) {
  * CIP stereo assignments via the accurate hierarchical-digraph engine, as a JSON
  * array of `{atomIdx, cipCode}` objects -- same shape as [`cip_assignments_json`],
  * but merges the accurate engine's tetrahedral R/S (~99.6% oracle-stable agreement,
- * see `docs/cip_accurate_rfc.md`) with legacy's E/Z and allene answers (the accurate
+ * see `docs/rfcs/cip_accurate_rfc.md`) with legacy's E/Z and allene answers (the accurate
  * engine computes neither). Atoms it can't resolve are omitted here -- see
  * [`cip_unresolved_json`] -- never a silently-guessed label. Returns `"null"` on an
  * internal engine error (budget-independent computations should not normally hit this).
@@ -2063,6 +2063,44 @@ export function estate_indices_json(mol) {
     }
 }
 
+/**
+ * Extract an extxyz frame's coordinates, cell, per-atom properties and
+ * frame metadata as JSON, in the SAME atom order [`mol_from_extxyz`]
+ * returns topology for (both read the identical frame via
+ * `chematic_mol::parse_extxyz`, so atom-index correspondence between the
+ * two calls is structural, not just conventional).
+ *
+ * Returns JSON `{"coords":[[x,y,z],...],
+ * "lattice":[9 numbers]|null,
+ * "properties":{"name":[[...atom values...], ...], ...},
+ * "info":{"key":"value", ...}}`.
+ *
+ * Returns a JS error on parse failure or if the frame exceeds the WASM
+ * atom-count limit.
+ * @param {string} text
+ * @returns {string}
+ */
+export function extxyz_frame_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.extxyz_frame_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);
+    }
+}
+
 /**
  * FCFP4 (pharmacophore, radius-2) fingerprint as a bit-packed byte vector (256 bytes).
  * @param {MolHandle} mol
@@ -3283,6 +3321,29 @@ export function mol_from_cml(cml) {
     return MolHandle.__wrap(ret[0]);
 }
 
+/**
+ * Parse an Extended XYZ (extxyz) frame and return a `MolHandle` (topology +
+ * element/position only; use [`extxyz_frame_json`] to recover coordinates,
+ * cell, per-atom properties and frame metadata in the SAME atom order).
+ *
+ * A plain XYZ file (free-form comment, no `Lattice=`/`Properties=`) parses
+ * too. Only the first frame of a multi-frame file is read.
+ *
+ * Returns a JS error on parse failure or if the frame exceeds the WASM
+ * atom-count limit.
+ * @param {string} text
+ * @returns {MolHandle}
+ */
+export function mol_from_extxyz(text) {
+    const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_extxyz(ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Parse a MolJSON string into a `MolHandle`.
  *
@@ -3988,7 +4049,7 @@ export function random_smiles_json(smiles, count, seed) {
  * `"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`.
+ * while actually returning the wrong hash. See `docs/rfcs/ecfp4_bitexact_api_rfc.md`.
  * @param {MolHandle} mol
  * @returns {Uint8Array}
  */
@@ -4964,6 +5025,52 @@ export function to_cml(mol) {
     }
 }
 
+/**
+ * Write a molecule + coordinates as an Extended XYZ (extxyz) frame.
+ *
+ * `coords_json`: `[[x,y,z],...]` (Å), same order and length as `mol`'s
+ * atoms.
+ *
+ * `options_json`: an optional JSON object,
+ * `{"lattice":[9 numbers]|null,"properties":{"name":[[...]],...},"info":{"key":"value",...}}`
+ * -- pass `"{}"` for a plain (non-extended) frame. Only real-valued
+ * per-atom `properties` columns are supported from this binding (matches
+ * the Python `to_extxyz` binding's scope); build a
+ * `chematic_mol::XyzProperty` directly from Rust for integer/string/logical
+ * columns.
+ *
+ * Returns a JS error if `coords_json`/`options_json` are malformed, if
+ * `coords_json`'s length doesn't match `mol`'s atom count, or if a
+ * `properties` column's row count doesn't match it.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {string} options_json
+ * @returns {string}
+ */
+export function to_extxyz_json(mol, coords_json, options_json) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(options_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.to_extxyz_json(mol.__wbg_ptr, ptr0, len0, 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);
+    }
+}
+
 /**
  * Serialize a molecule to a MOL V2000 block with 2D coordinates.
  *

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": "0.14.0",
+  "version": "0.15.0",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",