openchemlib 8.9.0 → 8.10.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "openchemlib",
-  "version": "8.9.0",
+  "version": "8.10.0",
   "description": "Manipulate molecules",
   "keywords": [
     "chemistry",
@@ -70,6 +70,7 @@
   },
   "homepage": "https://github.com/cheminfo/openchemlib-js",
   "devDependencies": {
+    "@types/jest": "^29.5.12",
     "benchmark": "^2.1.4",
     "eslint": "^8.56.0",
     "eslint-config-cheminfo": "^9.1.1",

package/types.d.ts

@@ -61,6 +61,24 @@ export interface IHoseCodesOptions {
   type: 0 | 1;
 }
 
+export interface ISmilesGeneratorOptions {
+  /**
+   * Whether to create SMILES with SMARTS capabilities.
+   * @default `false`
+   */
+  createSmarts?: boolean;
+  /**
+   * Whether to include mapping information (atomMapNo) in the SMILES.
+   * @default `false`
+   */
+  includeMapping?: boolean;
+  /**
+   * Should localisation of double bonds be attempted?
+   * @default `false`
+   */
+  kekulizedOutput?: boolean;
+}
+
 export interface Rectangle {
   /**
    * X-coordinate of the top-left corner.
@@ -93,6 +111,8 @@ export declare class Molecule {
 
   // based on JSMolecule.java you can do a regexp ".*static.* (int|long|double)(.*) = .*;" and replace with "$2: number;"
 
+  // bonds to represent aromaticity
+
   static CANONIZER_CREATE_SYMMETRY_RANK: number;
   static CANONIZER_CONSIDER_DIASTEREOTOPICITY: number;
   static CANONIZER_CONSIDER_ENANTIOTOPICITY: number;
@@ -437,7 +457,9 @@ export declare class Molecule {
 
   toSmiles(): string;
 
-  toIsomericSmiles(): string;
+  toSmarts(): string;
+
+  toIsomericSmiles(options?: ISmilesGeneratorOptions): string;
 
   /**
    * Returns a MDL Molfile V2000 string.
@@ -1302,7 +1324,7 @@ export declare class Molecule {
    * @param mapNo
    * @param autoMapped
    */
-  setAtomMapNo(atom: number, mapNo: number, autoMapped: boolean): void;
+  setAtomMapNo(atom: number, mapNo: number, autoMapped?: boolean): void;
 
   /**
    * Set atom to specific isotop or to have a natural isotop distribution
@@ -2592,8 +2614,6 @@ export interface ISmilesParserOptions {
    */
   smartsMode?: 'smiles' | 'smarts' | 'guess';
 
-  createSmartsWarnings?: boolean;
-
   skipCoordinateTemplates?: boolean;
 
   makeHydrogenExplicit?: boolean;
@@ -2602,6 +2622,13 @@ export interface ISmilesParserOptions {
    * Disable parsing of CACTVS syntax.
    */
   noCactvs?: boolean;
+
+  /**
+   * Consider single dots '.' (rather than '..') as molecule separator when parsing reactions.
+   */
+  singleDotSeparator?: boolean;
+
+  createSmartsWarnings?: boolean;
 }
 
 export interface ISmilesParserParseMoleculeOptions {