@kent-tokyo/chematic 1.0.3 → 1.0.5

package/README.md

@@ -160,29 +160,9 @@ portable across native and `wasm32-unknown-unknown`
 precision across every JS engine, only that the value is finite, non-negative,
 and enforced correctly on all of them.
 
-## Version History
-
-**v0.1.94** (2026-06-12):
-- SA Score corpus expanded: 188 FDA molecules (1415 unique fragments)
-- Enhanced fingerprints: True MHFP, True ERG, path FP with bond types
-- Full multi-sphere CIP stereochemistry for R/S assignment
-- InChI stereo layer round-trip support (tetrahedral and E/Z)
-
-**v0.1.93** (2026-06-12):
-- Full multi-sphere CIP priority rules
-- Correct stereochemistry assignment for complex chiral centers
-
-**v0.1.92** (2026-06-12):
-- InChI stereo layer parsing (tetrahedral `/t` and E/Z `/b`)
-- Path fingerprint with bond type interleaving
-
-**v0.1.91** (2026-06-12):
-- True MHFP (structural fragment hashing)
-- True ERG (Ertl 2017 functional group detection)
-
 ## Bundle Size
 
-~500 KB gzip / ~1.3 MB raw (reduced from ~819 KB gzip in v0.4.17, -38.5%).
+The optimized v1.0.2-candidate artifact was measured at **3.30 MB raw / 1.21 MB gzip**. Bundle size depends on features and toolchain; see [`benchmarks/2026-09-04-wasm-size.md`](../../benchmarks/2026-09-04-wasm-size.md) for exact tools, digest, and reproduction steps.
 
 PNG rasterization (`tiny_skia`) is excluded from the WASM build — use SVG output instead. All SVG depiction APIs remain fully available.
 

package/chematic_wasm.d.ts

@@ -856,6 +856,13 @@ export function ecfp6_bitvec_with_chirality(mol: MolHandle, use_chirality: boole
  */
 export function ecfp_bitvec_custom(mol: MolHandle, radius: number, nbits: number, use_chirality: boolean): Uint8Array;
 
+/**
+ * Apply a loss-preserving page/presentation edit to a CDXML document.
+ * `edit_json` is a `CdxmlEdit` command object; unknown presentation XML is
+ * retained and the result is reparsed before it is returned.
+ */
+export function edit_cdxml_document_json(cdxml: string, edit_json: string): string;
+
 /**
  * Run `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
  * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
@@ -2152,6 +2159,18 @@ export function ring_families_json(mol: MolHandle): string;
  */
 export function run_reactants(smirks: string, reactants_smiles: string): string;
 
+/**
+ * Parse an MDL RXN V2000 file into the typed reaction-document JSON
+ * contract shared with the Rust and Python bindings.
+ */
+export function rxn_document_from_rxn(text: string): string;
+
+/**
+ * Write typed reaction-document JSON as MDL RXN V2000. Unsupported rich
+ * fields return an error instead of being silently discarded.
+ */
+export function rxn_document_to_rxn(document_json: string): string;
+
 /**
  * Synthetic Accessibility Score (1 = easy, 10 = hard).
  */
@@ -2218,6 +2237,22 @@ export function sdf_to_records_json(sdf: string): string;
  */
 export function sdf_to_smiles_json(sdf: string): string;
 
+/**
+ * Apply an explicit Markush selection command to a semantic model JSON.
+ */
+export function semantic_apply_json_command(model_json: string, command_json: string): string;
+
+/**
+ * Expand a validated semantic model against a base SMILES and return the
+ * expanded graph plus source-to-expanded atom mapping.
+ */
+export function semantic_expand_json(base_smiles: string, model_json: string): string;
+
+/**
+ * Validate and normalize a typed Markush/polymer semantic model JSON.
+ */
+export function semantic_model_json(model_json: string): string;
+
 /**
  * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
  * Rotates the D-side subtree around the B—C bond.
@@ -2681,6 +2716,7 @@ export interface InitOutput {
     readonly ecfp6_bitvec: (a: number) => [number, number];
     readonly ecfp6_bitvec_with_chirality: (a: number, b: number) => [number, number];
     readonly ecfp_bitvec_custom: (a: number, b: number, c: number, d: number) => [number, number];
+    readonly edit_cdxml_document_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly embed_ensemble_v2_json: (a: number, b: number, c: number) => [number, number];
     readonly embed_pipeline_v2_json: (a: number, b: number, c: number) => [number, number];
     readonly enumerate_library_2way: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
@@ -2890,11 +2926,16 @@ export interface InitOutput {
     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 run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly rxn_document_from_rxn: (a: number, b: number) => [number, number, number, number];
+    readonly rxn_document_to_rxn: (a: number, b: number) => [number, number, number, number];
     readonly sa_score: (a: number) => number;
     readonly screen_smiles_json: (a: number, b: number, c: number, d: number) => [number, number];
     readonly sdf_from_records_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
     readonly sdf_to_records_json: (a: number, b: number) => [number, number];
     readonly sdf_to_smiles_json: (a: number, b: number) => [number, number];
+    readonly semantic_apply_json_command: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly semantic_expand_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly semantic_model_json: (a: number, b: number) => [number, number, number, number];
     readonly set_dihedral_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number) => [number, number, number, number];
     readonly shape_descriptors_json: (a: number) => [number, number];
     readonly slogp_vsa_json: (a: number) => [number, number];

package/chematic_wasm.js

@@ -2067,6 +2067,37 @@ export function ecfp_bitvec_custom(mol, radius, nbits, use_chirality) {
     return v1;
 }
 
+/**
+ * Apply a loss-preserving page/presentation edit to a CDXML document.
+ * `edit_json` is a `CdxmlEdit` command object; unknown presentation XML is
+ * retained and the result is reparsed before it is returned.
+ * @param {string} cdxml
+ * @param {string} edit_json
+ * @returns {string}
+ */
+export function edit_cdxml_document_json(cdxml, edit_json) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(cdxml, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(edit_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.edit_cdxml_document_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);
+    }
+}
+
 /**
  * Run `embed_ensemble_v2` on `mol`'s own atom order (never canonicalizes/
  * reparses, same convention as `embed_pipeline_v2_json`). See the module doc
@@ -5401,6 +5432,60 @@ export function run_reactants(smirks, reactants_smiles) {
     }
 }
 
+/**
+ * Parse an MDL RXN V2000 file into the typed reaction-document JSON
+ * contract shared with the Rust and Python bindings.
+ * @param {string} text
+ * @returns {string}
+ */
+export function rxn_document_from_rxn(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.rxn_document_from_rxn(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);
+    }
+}
+
+/**
+ * Write typed reaction-document JSON as MDL RXN V2000. Unsupported rich
+ * fields return an error instead of being silently discarded.
+ * @param {string} document_json
+ * @returns {string}
+ */
+export function rxn_document_to_rxn(document_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 ret = wasm.rxn_document_to_rxn(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);
+    }
+}
+
 /**
  * Synthetic Accessibility Score (1 = easy, 10 = hard).
  * @param {MolHandle} mol
@@ -5548,6 +5633,91 @@ export function sdf_to_smiles_json(sdf) {
     }
 }
 
+/**
+ * Apply an explicit Markush selection command to a semantic model JSON.
+ * @param {string} model_json
+ * @param {string} command_json
+ * @returns {string}
+ */
+export function semantic_apply_json_command(model_json, command_json) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(model_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.semantic_apply_json_command(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);
+    }
+}
+
+/**
+ * Expand a validated semantic model against a base SMILES and return the
+ * expanded graph plus source-to-expanded atom mapping.
+ * @param {string} base_smiles
+ * @param {string} model_json
+ * @returns {string}
+ */
+export function semantic_expand_json(base_smiles, model_json) {
+    let deferred4_0;
+    let deferred4_1;
+    try {
+        const ptr0 = passStringToWasm0(base_smiles, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passStringToWasm0(model_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len1 = WASM_VECTOR_LEN;
+        const ret = wasm.semantic_expand_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);
+    }
+}
+
+/**
+ * Validate and normalize a typed Markush/polymer semantic model JSON.
+ * @param {string} model_json
+ * @returns {string}
+ */
+export function semantic_model_json(model_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(model_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.semantic_model_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);
+    }
+}
+
 /**
  * Set dihedral angle A—B—C—D and return PDB block with modified coordinates.
  * Rotates the D-side subtree around the B—C bond.

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": "1.0.3",
+  "version": "1.0.5",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",