@kent-tokyo/chematic 1.0.35 → 1.0.37

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 1.0.35. The binding keeps bounded parsing,
+The current workspace line is 1.0.37. 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

@@ -754,10 +754,16 @@ export function chematic_version(): 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/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).
+ * see `docs/rfcs/cip_accurate_rfc.md`), E/Z ranked by the same engine and legacy's
+ * allene answers. Atoms it can't resolve are omitted here -- see
+ * [`cip_unresolved_json`] -- never a silently-guessed label. A phosphorus on an
+ * unsaturated ring (cyclophosphazene) gets RDKit's CIPLabeler label, which flips
+ * with the ring's Kekulé spelling; its object carries `"kekuleDependent": true`.
+ * A ring centre with three single bonds and a lone pair (bridgehead amine)
+ * gets RDKit's label for the parsed SMILES spelling and carries
+ * `"spellingDependent": true`.
+ * Returns `"null"` on an internal engine error (budget-independent computations
+ * should not normally hit this).
  */
 export function cip_assignments_accurate_json(mol: MolHandle): string;
 
@@ -1672,6 +1678,14 @@ export function mmff94_charges_typed_json(mol: MolHandle): string;
  */
 export function mmff94_energy_breakdown_from_coords_json(mol: MolHandle, coords_json: string): string;
 
+/**
+ * [`mmff94_energy_breakdown_from_coords_json`] with
+ * `ignore_interfrag_interactions`: `true` leaves out van der Waals and
+ * electrostatic pairs between disconnected fragments, as RDKit's
+ * `MMFFGetMoleculeForceField` does by default.
+ */
+export function mmff94_energy_breakdown_from_coords_json_with_options(mol: MolHandle, coords_json: string, ignore_interfrag_interactions: boolean): string;
+
 /**
  * Computes energy on an internally generated conformer.
  * `MolHandle` stores topology only; coordinates previously read from PDB/XYZ
@@ -2021,6 +2035,20 @@ export function normalize_cxsmiles(s: string): string;
  */
 export function normalize_reaction_smiles(rxn_smiles: string): string;
 
+/**
+ * Apply one bounded metadata edit without changing atom ownership or linkage
+ * topology. Returns the same tagged envelope as validation.
+ */
+export function nucleic_acid_apply_json_command(document_json: string, command_json: string): string;
+
+/**
+ * Validate and normalize a bounded `chematic.nucleic-acid.v1` document.
+ *
+ * Returns a stable JSON envelope with either `ok: true` and the normalized
+ * document or `ok: false` and a typed error category.
+ */
+export function nucleic_acid_validate_json(document_json: string): string;
+
 /**
  * Parse an OpenDX (APBS scalar-field subset) file and return its full
  * [`chematic_mol::VolumetricGrid`] as JSON (same shape as
@@ -3193,6 +3221,7 @@ export interface InitOutput {
     readonly mmff94_charges_json: (a: number) => [number, number];
     readonly mmff94_charges_typed_json: (a: number) => [number, number];
     readonly mmff94_energy_breakdown_from_coords_json: (a: number, b: number, c: number) => [number, number];
+    readonly mmff94_energy_breakdown_from_coords_json_with_options: (a: number, b: number, c: number, d: number) => [number, number];
     readonly mmff94_energy_breakdown_json: (a: number) => [number, number];
     readonly mmff94_partial_charges_json: (a: number) => [number, number];
     readonly mmp_pairs_json: (a: number, b: number) => [number, number, number, number];
@@ -3309,6 +3338,8 @@ export interface InitOutput {
     readonly neutralize_charges: (a: number) => number;
     readonly normalize_cxsmiles: (a: number, b: number) => [number, number, number, number];
     readonly normalize_reaction_smiles: (a: number, b: number) => [number, number, number, number];
+    readonly nucleic_acid_apply_json_command: (a: number, b: number, c: number, d: number) => [number, number];
+    readonly nucleic_acid_validate_json: (a: number, b: number) => [number, number];
     readonly opendx_grid_json: (a: number, b: number) => [number, number, number, number];
     readonly opendx_shape_u32: (a: number, b: number) => [number, number, number];
     readonly opendx_values_f64: (a: number, b: number) => [number, number, number];

package/chematic_wasm.js

@@ -1889,10 +1889,16 @@ export function chematic_version() {
  * 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/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).
+ * see `docs/rfcs/cip_accurate_rfc.md`), E/Z ranked by the same engine and legacy's
+ * allene answers. Atoms it can't resolve are omitted here -- see
+ * [`cip_unresolved_json`] -- never a silently-guessed label. A phosphorus on an
+ * unsaturated ring (cyclophosphazene) gets RDKit's CIPLabeler label, which flips
+ * with the ring's Kekulé spelling; its object carries `"kekuleDependent": true`.
+ * A ring centre with three single bonds and a lone pair (bridgehead amine)
+ * gets RDKit's label for the parsed SMILES spelling and carries
+ * `"spellingDependent": true`.
+ * Returns `"null"` on an internal engine error (budget-independent computations
+ * should not normally hit this).
  * @param {MolHandle} mol
  * @returns {string}
  */
@@ -4223,6 +4229,32 @@ export function mmff94_energy_breakdown_from_coords_json(mol, coords_json) {
     }
 }
 
+/**
+ * [`mmff94_energy_breakdown_from_coords_json`] with
+ * `ignore_interfrag_interactions`: `true` leaves out van der Waals and
+ * electrostatic pairs between disconnected fragments, as RDKit's
+ * `MMFFGetMoleculeForceField` does by default.
+ * @param {MolHandle} mol
+ * @param {string} coords_json
+ * @param {boolean} ignore_interfrag_interactions
+ * @returns {string}
+ */
+export function mmff94_energy_breakdown_from_coords_json_with_options(mol, coords_json, ignore_interfrag_interactions) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        _assertClass(mol, MolHandle);
+        const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.mmff94_energy_breakdown_from_coords_json_with_options(mol.__wbg_ptr, ptr0, len0, ignore_interfrag_interactions);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
 /**
  * Computes energy on an internally generated conformer.
  * `MolHandle` stores topology only; coordinates previously read from PDB/XYZ
@@ -5110,6 +5142,53 @@ export function normalize_reaction_smiles(rxn_smiles) {
     }
 }
 
+/**
+ * Apply one bounded metadata edit without changing atom ownership or linkage
+ * topology. Returns the same tagged envelope as validation.
+ * @param {string} document_json
+ * @param {string} command_json
+ * @returns {string}
+ */
+export function nucleic_acid_apply_json_command(document_json, command_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(command_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.nucleic_acid_apply_json_command(ptr0, len0, ptr1, len1);
+        deferred3_0 = ret[0];
+        deferred3_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * Validate and normalize a bounded `chematic.nucleic-acid.v1` document.
+ *
+ * Returns a stable JSON envelope with either `ok: true` and the normalized
+ * document or `ok: false` and a typed error category.
+ * @param {string} document_json
+ * @returns {string}
+ */
+export function nucleic_acid_validate_json(document_json) {
+    let deferred2_0;
+    let deferred2_1;
+    try {
+        const ptr0 = passStringToWasm0(document_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.nucleic_acid_validate_json(ptr0, len0);
+        deferred2_0 = ret[0];
+        deferred2_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
+    }
+}
+
 /**
  * Parse an OpenDX (APBS scalar-field subset) file and return its full
  * [`chematic_mol::VolumetricGrid`] as JSON (same shape as

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": "1.0.35",
+  "version": "1.0.37",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",