openchemlib 8.2.0 → 8.3.0

package/minimal.d.ts

@@ -8,6 +8,9 @@ export {
   IDepictorOptions,
   Reaction,
   SDFileParser,
+  ISmilesParserOptions,
+  ISmilesParserParseMoleculeOptions,
+  SmilesParser,
   SSSearcher,
   SSSearcherWithIndex,
   Util,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "openchemlib",
-  "version": "8.2.0",
+  "version": "8.3.0",
   "description": "Manipulate molecules",
   "keywords": [
     "chemistry",
@@ -27,9 +27,6 @@
     "test": "npm run build && npm run test-only && npm run eslint",
     "test-only": "jest"
   },
-  "jest": {
-    "testEnvironment": "node"
-  },
   "main": "./core.js",
   "files": [
     "dist",
@@ -56,14 +53,12 @@
   "homepage": "https://github.com/cheminfo/openchemlib-js",
   "devDependencies": {
     "benchmark": "^2.1.4",
-    "eslint": "^8.25.0",
-    "eslint-config-cheminfo": "^8.0.2",
-    "fs-extra": "^10.1.0",
+    "eslint": "^8.37.0",
+    "eslint-config-cheminfo": "^8.2.0",
     "gwt-api-exporter": "^2.0.0",
-    "jest": "^29.2.0",
-    "openchemlib-utils": "^2.1.3",
-    "prettier": "^2.7.1",
-    "rimraf": "^3.0.2",
-    "yargs": "^17.6.0"
+    "jest": "^29.5.0",
+    "openchemlib-utils": "^2.4.0",
+    "prettier": "^2.8.7",
+    "yargs": "^17.7.1"
   }
 }

package/types.d.ts

@@ -2,12 +2,14 @@
 
 export interface IMoleculeFromSmilesOptions {
   /**
-   * Disable extra coordinate computation. Default: false.
+   * Disable coordinate invention.
+   * @default `false`
    */
   noCoordinates?: boolean;
 
   /**
-   * Disable stereo features parsing. Default: false.
+   * Disable stereo features parsing.
+   * @default `false`
    */
   noStereo?: boolean;
 }
@@ -2573,6 +2575,77 @@ export declare class Molecule {
   setAssignParitiesToNitrogen(b: boolean): void;
 }
 
+export interface ISmilesParserOptions {
+  /**
+   * Enable SMARTS parsing with `'smarts'` or `'guess'`.
+   * @default `'smiles'`
+   */
+  smartsMode?: 'smiles' | 'smarts' | 'guess';
+
+  createSmartsWarnings?: boolean;
+
+  skipCoordinateTemplates?: boolean;
+
+  makeHydrogenExplicit?: boolean;
+
+  /**
+   * Disable parsing of CACTVS syntax.
+   */
+  noCactvs?: boolean;
+}
+
+export interface ISmilesParserParseMoleculeOptions {
+  /**
+   * Molecule to parse into.
+   */
+  molecule?: Molecule;
+
+  /**
+   * Disable coordinate invention.
+   * @default `false`
+   */
+  noCoordinates?: boolean;
+
+  /**
+   * Disable stereo features parsing.
+   * @default `false`
+   */
+  noStereo?: boolean;
+}
+
+export declare class SmilesParser {
+  /**
+   * Create a SMILES parser.
+   */
+  constructor(options?: ISmilesParserOptions);
+
+  /**
+   * Set the random seed used to invent coordinates.
+   * @param seed
+   */
+  setRandomSeed(seed: number): void;
+
+  /**
+   * Parse a SMILES string and return a molecule.
+   */
+  parseMolecule(
+    smiles: string,
+    options?: ISmilesParserParseMoleculeOptions,
+  ): Molecule;
+
+  /**
+   * Parse a SMILES string and return a reaction.
+   */
+  parseReaction(smiles: string): Reaction;
+
+  /**
+   * If createSmartsWarnings in the constructor was passed as true, then this method
+   * returns a list of all SMARTS features, which could not be interpreted in the most recently
+   * parsed SMILES/SMARTS pattern.
+   */
+  getSmartsWarning(): string;
+}
+
 export interface MolecularFormula {
   absoluteWeight: number;
 
@@ -3289,15 +3362,6 @@ export declare class ConformerGenerator {
    */
   getPotentialConformerCount(): number;
 
-  /**
-   * With best current knowledge about colliding torsion combinations
-   * and based on the individual frequencies of currently active torsions
-   * this method returns the conformers's overall contribution to the
-   * total set of non colliding conformers.
-   * @returns - This conformer's contribution to all conformers.
-   */
-  getPreviousConformerContribution(): number;
-
   /**
    * Returns an iterator of molecule conformers.
    */