openchemlib 9.1.1 → 9.3.0

package/README.md

@@ -1,24 +1,21 @@
-# OpenChemLib JS
-
-JavaScript port of the [OpenChemLib](https://github.com/actelion/openchemlib) Java library.
-
 <h3 align="center">
-
   <a href="https://www.zakodium.com">
     <img src="https://www.zakodium.com/brand/zakodium-logo-white.svg" width="50" alt="Zakodium logo" />
   </a>
-
   <p>
     Maintained by <a href="https://www.zakodium.com">Zakodium</a>
   </p>
-  
-  [![NPM version][npm-image]][npm-url]
-  [![build status][ci-image]][ci-url]
-  [![npm download][download-image]][download-url]
-  [![DOI](https://www.zenodo.org/badge/23346814.svg)](https://www.zenodo.org/badge/latestdoi/23346814)
-
 </h3>
 
+# OpenChemLib JS
+
+[![NPM version][npm-image]][npm-url]
+[![npm download][download-image]][download-url]
+[![license][license-image]][license-url]
+[![DOI](https://www.zenodo.org/badge/23346814.svg)](https://www.zenodo.org/badge/latestdoi/23346814)
+
+JavaScript port of the [OpenChemLib](https://github.com/actelion/openchemlib) Java library.
+
 ## Installation
 
 ```console
@@ -27,11 +24,12 @@ npm install openchemlib
 
 ## Documentation
 
-- [TypeDoc home page](https://cheminfo.github.io/openchemlib-js/index.html)
+- [Generated API documentation](https://cheminfo.github.io/openchemlib-js/)
+- [Web examples](https://openchemlib-js.pages.dev)
 
 ## Development
 
-To build this project, you need :
+To build this project, you need:
 
 - Java JDK (Tested with version 21)
 - GWT (Tested with version 2.12.2, [Download build here](http://www.gwtproject.org/download.html))
@@ -39,7 +37,9 @@ To build this project, you need :
 
 ### Install dependencies
 
-`npm ci`
+```console
+npm ci
+```
 
 ### Configure directories
 
@@ -51,11 +51,6 @@ If you want to use a custom JDK installation, set the "jdk" key to be the path t
 To run one of the scripts, use `npm run <scriptName>`.  
 To pass additional options, use `npm run <scriptName> -- --option`.
 
-**Options** :
-
-- -m [name]: only process module "name"
-- -v: verbose output
-
 #### build-java
 
 Compile and export the Java API.
@@ -70,7 +65,7 @@ Copy the required java files from the openchemlib project.
 
 [npm-image]: https://img.shields.io/npm/v/openchemlib.svg
 [npm-url]: https://www.npmjs.com/package/openchemlib
-[ci-image]: https://github.com/cheminfo/openchemlib-js/workflows/Node.js%20CI/badge.svg?branch=main
-[ci-url]: https://github.com/cheminfo/openchemlib-js/actions?query=workflow%3A%22Node.js+CI%22
 [download-image]: https://img.shields.io/npm/dm/openchemlib.svg
 [download-url]: https://www.npmjs.com/package/openchemlib
+[license-image]: https://img.shields.io/npm/l/openchemlib.svg
+[license-url]: https://github.com/cheminfo/openchemlib-js/blob/main/LICENSE

package/dist/openchemlib.d.ts

@@ -2866,6 +2866,50 @@ export declare class CanonizerUtil {
   static getIDCode(mol: Molecule, type: number): string;
 }
 
+export interface CanonizerOptions {
+  createSymmetryRank?: boolean;
+  considerStereoheterotopicity?: boolean;
+  encodeAtomCustomLabels?: boolean;
+  encodeAtomSelection?: boolean;
+  assignParitiesToTetrahedralN?: boolean;
+  coordsAre3d?: boolean;
+  createPseudoStereoGroups?: boolean;
+  distinguishRacemicOrGroups?: boolean;
+  tieBreakFreeValenceAtoms?: boolean;
+  encodeAtomCustomLabelsWithoutRanking?: boolean;
+  neglectAnyStereoInformation?: boolean;
+}
+
+export declare class Canonizer {
+  constructor(mol: Molecule, options?: CanonizerOptions);
+
+  hasCIPParityDistinctionProblem(): boolean;
+
+  getCanMolecule(includeExplicitHydrogen: boolean): Molecule;
+
+  getIDCode(): string;
+
+  getFinalRank(): number[];
+
+  getSymmetryRank(atom: number): number;
+
+  getSymmetryRanks(): number[];
+
+  invalidateCoordinates(): void;
+
+  getEncodedCoordinates(keepPositionAndScale: boolean): string;
+
+  getEncodedMapping(): string;
+
+  normalizeEnantiomer(): boolean;
+
+  setParities(): void;
+
+  getGraphAtoms(): number[];
+
+  getGraphIndexes(): number[];
+}
+
 /**
  * All depictor options default to `false`.
  */