@kent-tokyo/chematic 1.1.0 → 1.1.1

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 1.1.0. The binding keeps bounded parsing,
+The current workspace line is 1.1.1. 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.
 
@@ -43,6 +43,11 @@ npm install @kent-tokyo/chematic
   `MolHandle.atom_pseudo_labels_json()` and immutable edits through
   `mol_with_atom_pseudo_label`; labels are bounded to `*`, `R`, and
   `R1..R9999`
+- Label-stable R-group decomposition through
+  `rgroup_decompose_columns_json(smilesJson, coreSmarts)`. The returned JSON
+  contains input-aligned `Core`, `R1`, `R2`, ... columns and uses `null` for
+  unmatched molecules or substituents absent from a matched row. The legacy
+  `rgroup_decompose_json` row API is unchanged.
 - 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
@@ -50,6 +55,8 @@ npm install @kent-tokyo/chematic
 - 2D SVG depiction with CPK colors and atom/bond highlighting
 - SVG grid layout for multiple molecules
 - Reaction SMILES/SMIRKS parsing and transform
+  (`run_reactants_checked` includes typed native and RDKit-profile rejection
+  diagnostics without returning rejected products as successes)
 - Add/remove explicit hydrogens
 - `embed_pipeline_v2_json`: torsion-knowledge-aware 3D embedding + stereo
   verification/repair + policy-gated force field, mirroring the Python

package/chematic_wasm.d.ts

@@ -925,12 +925,16 @@ export function conformer_ensemble_json(mol: MolHandle, n: number, rmsd_threshol
  *
  * This is the WASM counterpart of Python's `convert_format`. It supports
  * SMILES, MOL/SDF, MOL V3000, MOL2, CML, ChemicalJSON, MolJSON, and CDXML.
- * Coordinates and format-specific metadata are intentionally not carried
- * across this topology-only bridge; use the format-specific coordinate APIs
- * when those fields must be preserved.
+ * MOL2-to-MOL2 validates and retains the exact source. Other conversions use
+ * the topology-only bridge and do not carry format-specific metadata.
  */
 export function convert_common_format(text: string, input_format: string, output_format: string): string;
 
+/**
+ * Checked MOL2/CJSON conversion using the shared report schema.
+ */
+export function convert_with_report_json(text: string, input_format: string, output_format: string, policy: string): string;
+
 /**
  * Return the CPK color (CSS hex string) for the given element symbol.
  *
@@ -2219,6 +2223,11 @@ export function orca_output_to_json(text: string): string;
  */
 export function pains_matches_json(mol: MolHandle): string;
 
+/**
+ * Inspect strictly validated CJSON with exact source and opaque field paths.
+ */
+export function parse_cjson_record_json(text: string): string;
+
 /**
  * Parse CXSMARTS and return preserved metadata as JSON.
  * Returns error if atom count exceeds 10,000.
@@ -2235,6 +2244,11 @@ export function parse_cxsmarts_json(s: string): string;
  */
 export function parse_cxsmiles_json(s: string): string;
 
+/**
+ * Inspect partial charges, atom types and source retention for MOL2.
+ */
+export function parse_mol2_record_json(text: string): string;
+
 /**
  * Parse a SMILES string into a `MolHandle`.
  *
@@ -2565,6 +2579,18 @@ export function remove_hydrogens(mol: MolHandle): MolHandle;
  */
 export function retro_disconnect_json(mol: MolHandle, max_results: number, reaction_class: string): string;
 
+/**
+ * Label-stable R-group decomposition returned as RDKit-style table columns.
+ *
+ * `core_smarts` accepts the bounded mapped-core contract used by Rust and
+ * Python: terminal mapped wildcards such as `[*:2]`, or mapped core atoms.
+ * The returned JSON object contains `Core`, `R1`, `R2`, ... arrays parallel
+ * to the input rows. Unmatched rows and absent substituents are `null`.
+ * Output fragments retain their mapped attachment wildcard. The legacy
+ * [`super::rgroup_decompose_json`] function is unchanged.
+ */
+export function rgroup_decompose_columns_json(smiles_json: string, core_smarts: string): string;
+
 /**
  * Decompose a set of molecules against a core SMARTS, returning R-group SMILES.
  *
@@ -2594,6 +2620,16 @@ export function rgroup_decompose_json(smiles_json: string, core_smarts: string):
  */
 export function ring_families_json(mol: MolHandle): string;
 
+/**
+ * Validate the local CJSON profile and retain the exact UTF-8 source.
+ */
+export function roundtrip_cjson_record(text: string): string;
+
+/**
+ * Validate one MOL2 record and preserve its exact source, including metadata.
+ */
+export function roundtrip_mol2_record(text: string): string;
+
 /**
  * Parse and serialize a V3000 block while preserving V3000 metadata.
  *
@@ -3245,6 +3281,7 @@ export interface InitOutput {
     readonly conformerhandle_new: (a: number, b: number) => [number, number, number];
     readonly conformerhandle_remove_conformer: (a: number, b: number) => number;
     readonly convert_common_format: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
+    readonly convert_with_report_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
     readonly cpk_color: (a: number, b: number) => [number, number];
     readonly cube_grid_json: (a: number, b: number) => [number, number, number, number];
     readonly cube_shape_u32: (a: number, b: number) => [number, number, number];
@@ -3491,8 +3528,10 @@ export interface InitOutput {
     readonly orca_input_to_json: (a: number, b: number) => [number, number, number, number];
     readonly orca_output_to_json: (a: number, b: number) => [number, number, number, number];
     readonly pains_matches_json: (a: number) => [number, number];
+    readonly parse_cjson_record_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_cxsmarts_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_cxsmiles_json: (a: number, b: number) => [number, number, number, number];
+    readonly parse_mol2_record_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_smiles: (a: number, b: number) => [number, number, number];
     readonly pdb_coords_json: (a: number, b: number) => [number, number];
     readonly peoe_vsa_json: (a: number) => [number, number];
@@ -3539,8 +3578,11 @@ export interface InitOutput {
     readonly reaction_smarts_match: (a: number, b: number, c: number, d: number) => [number, number, number];
     readonly remove_hydrogens: (a: number) => number;
     readonly retro_disconnect_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly rgroup_decompose_columns_json: (a: number, b: number, c: number, d: number) => [number, number, 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];
+    readonly roundtrip_cjson_record: (a: number, b: number) => [number, number, number, number];
+    readonly roundtrip_mol2_record: (a: number, b: number) => [number, number, number, number];
     readonly roundtrip_mol_v3000_block: (a: number, b: number) => [number, number, number, number];
     readonly run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly run_reactants_checked: (a: number, b: number, c: number, d: number, e: number) => [number, number];

package/chematic_wasm.js

@@ -2550,9 +2550,8 @@ export function conformer_ensemble_json(mol, n, rmsd_threshold) {
  *
  * This is the WASM counterpart of Python's `convert_format`. It supports
  * SMILES, MOL/SDF, MOL V3000, MOL2, CML, ChemicalJSON, MolJSON, and CDXML.
- * Coordinates and format-specific metadata are intentionally not carried
- * across this topology-only bridge; use the format-specific coordinate APIs
- * when those fields must be preserved.
+ * MOL2-to-MOL2 validates and retains the exact source. Other conversions use
+ * the topology-only bridge and do not carry format-specific metadata.
  * @param {string} text
  * @param {string} input_format
  * @param {string} output_format
@@ -2583,6 +2582,41 @@ export function convert_common_format(text, input_format, output_format) {
     }
 }
 
+/**
+ * Checked MOL2/CJSON conversion using the shared report schema.
+ * @param {string} text
+ * @param {string} input_format
+ * @param {string} output_format
+ * @param {string} policy
+ * @returns {string}
+ */
+export function convert_with_report_json(text, input_format, output_format, policy) {
+    let deferred6_0;
+    let deferred6_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(input_format, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passStringToWasm0(output_format, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len2 = WASM_VECTOR_LEN;
+        const ptr3 = passStringToWasm0(policy, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len3 = WASM_VECTOR_LEN;
+        const ret = wasm.convert_with_report_json(ptr0, len0, ptr1, len1, ptr2, len2, ptr3, len3);
+        var ptr5 = ret[0];
+        var len5 = ret[1];
+        if (ret[3]) {
+            ptr5 = 0; len5 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred6_0 = ptr5;
+        deferred6_1 = len5;
+        return getStringFromWasm0(ptr5, len5);
+    } finally {
+        wasm.__wbindgen_free(deferred6_0, deferred6_1, 1);
+    }
+}
+
 /**
  * Return the CPK color (CSS hex string) for the given element symbol.
  *
@@ -5875,6 +5909,32 @@ export function pains_matches_json(mol) {
     }
 }
 
+/**
+ * Inspect strictly validated CJSON with exact source and opaque field paths.
+ * @param {string} text
+ * @returns {string}
+ */
+export function parse_cjson_record_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.parse_cjson_record_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);
+    }
+}
+
 /**
  * Parse CXSMARTS and return preserved metadata as JSON.
  * Returns error if atom count exceeds 10,000.
@@ -5933,6 +5993,32 @@ export function parse_cxsmiles_json(s) {
     }
 }
 
+/**
+ * Inspect partial charges, atom types and source retention for MOL2.
+ * @param {string} text
+ * @returns {string}
+ */
+export function parse_mol2_record_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.parse_mol2_record_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);
+    }
+}
+
 /**
  * Parse a SMILES string into a `MolHandle`.
  *
@@ -6833,6 +6919,42 @@ export function retro_disconnect_json(mol, max_results, reaction_class) {
     }
 }
 
+/**
+ * Label-stable R-group decomposition returned as RDKit-style table columns.
+ *
+ * `core_smarts` accepts the bounded mapped-core contract used by Rust and
+ * Python: terminal mapped wildcards such as `[*:2]`, or mapped core atoms.
+ * The returned JSON object contains `Core`, `R1`, `R2`, ... arrays parallel
+ * to the input rows. Unmatched rows and absent substituents are `null`.
+ * Output fragments retain their mapped attachment wildcard. The legacy
+ * [`super::rgroup_decompose_json`] function is unchanged.
+ * @param {string} smiles_json
+ * @param {string} core_smarts
+ * @returns {string}
+ */
+export function rgroup_decompose_columns_json(smiles_json, core_smarts) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(smiles_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(core_smarts, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.rgroup_decompose_columns_json(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);
+    }
+}
+
 /**
  * Decompose a set of molecules against a core SMARTS, returning R-group SMILES.
  *
@@ -6906,6 +7028,58 @@ export function ring_families_json(mol) {
     }
 }
 
+/**
+ * Validate the local CJSON profile and retain the exact UTF-8 source.
+ * @param {string} text
+ * @returns {string}
+ */
+export function roundtrip_cjson_record(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.roundtrip_cjson_record(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);
+    }
+}
+
+/**
+ * Validate one MOL2 record and preserve its exact source, including metadata.
+ * @param {string} text
+ * @returns {string}
+ */
+export function roundtrip_mol2_record(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.roundtrip_mol2_record(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);
+    }
+}
+
 /**
  * Parse and serialize a V3000 block while preserving V3000 metadata.
  *

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": "1.1.0",
+  "version": "1.1.1",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",