openchemlib 8.21.0 → 9.0.0

package/README.md

@@ -27,50 +27,8 @@ npm install openchemlib
 
 ## Documentation
 
-This library is available in three different builds: `minimal`, `core` and `full`.
-Each larger build contains all functionalities from the smaller ones.
-
-The `core` build is the one that you get when you `require('openchemlib')`. It
-contains all functionalities that can be used in Node.js.
-
-The `minimal` (`require('openchemlib/minimal')`) build is a smaller one
-(~ half the size of `core`) that is meant to be used in a browser application
-if bundle size matters and prediction functionalities are not needed.
-
-The `full` build (`require('openchemlib/full')`) build is the largest build.
-It contains a structure viewer and a structure editor for browser applications.
-
 - [TypeDoc home page](https://cheminfo.github.io/openchemlib-js/index.html)
 
-### Modules present in minimal, core and full builds
-
-- [Molecule](https://cheminfo.github.io/openchemlib-js/classes/Molecule.html)
-- [Reaction](https://cheminfo.github.io/openchemlib-js/classes/Reaction.html)
-- [RingCollection](https://cheminfo.github.io/openchemlib-js/classes/RingCollection.html)
-- [SDFileParser](https://cheminfo.github.io/openchemlib-js/classes/SDFileParser.html)
-- [SSSearcher](https://cheminfo.github.io/openchemlib-js/classes/SSSearcher.html)
-- [SSSearcherWithIndex](https://cheminfo.github.io/openchemlib-js/classes/SSSearcherWithIndex.html)
-- [Util](https://cheminfo.github.io/openchemlib-js/modules/Util.html)
-
-### Modules present only in core and full builds
-
-- [CanonizerUtil](https://cheminfo.github.io/openchemlib-js/classes/CanonizerUtil.html)
-- [ConformerGenerator](https://cheminfo.github.io/openchemlib-js/classes/ConformerGenerator.html)
-- [DruglikenessPredictor](https://cheminfo.github.io/openchemlib-js/classes/DruglikenessPredictor.html)
-- [DrugScoreCalculator](https://cheminfo.github.io/openchemlib-js/modules/DrugScoreCalculator.html)
-- [ForceFieldMMFF94](https://cheminfo.github.io/openchemlib-js/classes/ForceFieldMMFF94.html)
-- [MoleculeProperties](https://cheminfo.github.io/openchemlib-js/classes/MoleculeProperties.html)
-- [ReactionEncoder](https://cheminfo.github.io/openchemlib-js/classes/ReactionEncoder.html)
-- [Reactor](https://cheminfo.github.io/openchemlib-js/classes/Reactor.html)
-- [ToxicityPredictor](https://cheminfo.github.io/openchemlib-js/classes/ToxicityPredictor.html)
-- [Transformer](https://cheminfo.github.io/openchemlib-js/classes/Transformer.html)
-
-### Modules present only in full build
-
-- [StructureEditor](https://cheminfo.github.io/openchemlib-js/classes/StructureEditor.html)
-- [StructureView](https://cheminfo.github.io/openchemlib-js/modules/StructureView.html)
-- [SVGRenderer](https://cheminfo.github.io/openchemlib-js/modules/SVGRenderer.html)
-
 ## Development
 
 To build this project, you need :
@@ -91,26 +49,18 @@ If you want to use a custom JDK installation, set the "jdk" key to be the path t
 ### npm scripts
 
 To run one of the scripts, use `npm run <scriptName>`.  
-To pass an options, use `npm run <scriptName> -- --option`.
+To pass additional options, use `npm run <scriptName> -- --option`.
 
-**Options**:
+**Options** :
 
 - -m [name]: only process module "name"
 - -v: verbose output
 
-#### compile:min / compile:pretty
-
-Execute the GWT compiler.
-
-#### export
-
-Transform the GWT compiled files to JavaScript modules.
-
-#### build:min / build:pretty
+#### build-java
 
-Compile and export.
+Compile and export the Java API.
 
-#### copy:openchemlib
+#### copy-openchemlib
 
 Copy the required java files from the openchemlib project.
 

package/{types.d.ts → dist/openchemlib.d.ts}

@@ -1,6 +1,28 @@
-// Minimal API
+export declare const Resources: {
+  /**
+   * Register the static resources.
+   * This is needed for some APIs.
+   * @param data - Object containing the resources or JSON string for such an object.
+   */
+  register(data: string | Record<string, string>): void;
+
+  /**
+   * Fetch and register the static resources asynchronously from a URL.
+   * @param url - URL to the resources.json file.
+   * If omitted, fetch will be done relative to the openchemlib.js module location.
+   */
+  registerFromUrl(url?: string): Promise<void>;
 
-export interface IMoleculeFromSmilesOptions {
+  /**
+   * Read and register the static resources synchronously.
+   * This is a convenience method for Node.js.
+   * @param path - Path to the resources.json file.
+   * If omitted, the file will be read relative to the openchemlib.js module location.
+   */
+  registerFromNodejs(path?: string): void;
+};
+
+export interface MoleculeFromSmilesOptions {
   /**
    * Disable coordinate invention.
    * @default false
@@ -65,7 +87,7 @@ export interface BondQueryFeatures {
   brigdeSpan: number;
 }
 
-export interface IMoleculeToSVGOptions extends IDepictorOptions {
+export interface MoleculeToSVGOptions extends DepictorOptions {
   /**
    * Factor used to compute the size of text nodes.
    * Default: 1.
@@ -75,12 +97,12 @@ export interface IMoleculeToSVGOptions extends IDepictorOptions {
   /**
    * font-weight attribute of atom labels.
    */
-  fontWeight?: string;
+  fontWeight?: number | string;
 
   /**
    * stroke-width styling property of bonds.
    */
-  strokeWidth?: string;
+  strokeWidth?: number | string;
 
   /**
    * Automatically crop the SVG to fit around the molecule.
@@ -96,7 +118,7 @@ export interface IMoleculeToSVGOptions extends IDepictorOptions {
   autoCropMargin?: number;
 }
 
-export interface IHoseCodesOptions {
+export interface HoseCodesOptions {
   /**
    * Maximum number of atoms from the center.
    * Default: 5.
@@ -112,7 +134,7 @@ export interface IHoseCodesOptions {
   type: 0 | 1;
 }
 
-export interface ISmilesGeneratorOptions {
+export interface SmilesGeneratorOptions {
   /**
    * Whether to create SMILES with SMARTS capabilities.
    * @default false
@@ -451,7 +473,7 @@ export declare class Molecule {
    */
   static fromSmiles(
     smiles: string,
-    options?: IMoleculeFromSmilesOptions,
+    options?: MoleculeFromSmilesOptions,
   ): Molecule;
 
   /**
@@ -518,7 +540,7 @@ export declare class Molecule {
 
   toSmarts(): string;
 
-  toIsomericSmiles(options?: ISmilesGeneratorOptions): string;
+  toIsomericSmiles(options?: SmilesGeneratorOptions): string;
 
   /**
    * Returns a MDL Molfile V2000 string.
@@ -542,7 +564,7 @@ export declare class Molecule {
     width: number,
     height: number,
     id?: string,
-    options?: IMoleculeToSVGOptions,
+    options?: MoleculeToSVGOptions,
   ): string;
 
   /**
@@ -597,7 +619,7 @@ export declare class Molecule {
    * Spherical Environments) codes represented as diastereotopic actelion IDs.
    * @param options
    */
-  getHoseCodes(options?: IHoseCodesOptions): string[][];
+  getHoseCodes(options?: HoseCodesOptions): string[][];
 
   getRingSet(): RingCollection;
 
@@ -1757,7 +1779,7 @@ export declare class Molecule {
     destMol: Molecule,
     includeAtom: boolean[],
     recognizeDelocalizedBonds: boolean,
-    atomMap: number[],
+    atomMap: number[] | null,
   ): void;
 
   /**
@@ -2678,7 +2700,7 @@ export declare class Molecule {
   setAssignParitiesToNitrogen(b: boolean): void;
 }
 
-export interface ISmilesParserOptions {
+export interface SmilesParserOptions {
   /**
    * Enable SMARTS parsing with `'smarts'` or `'guess'`.
    * @default 'smiles'
@@ -2702,7 +2724,7 @@ export interface ISmilesParserOptions {
   createSmartsWarnings?: boolean;
 }
 
-export interface ISmilesParserParseMoleculeOptions {
+export interface SmilesParserParseMoleculeOptions {
   /**
    * Molecule to parse into.
    */
@@ -2725,7 +2747,7 @@ export declare class SmilesParser {
   /**
    * Create a SMILES parser.
    */
-  constructor(options?: ISmilesParserOptions);
+  constructor(options?: SmilesParserOptions);
 
   /**
    * Set the random seed used to invent coordinates.
@@ -2738,7 +2760,7 @@ export declare class SmilesParser {
    */
   parseMolecule(
     smiles: string,
-    options?: ISmilesParserParseMoleculeOptions,
+    options?: SmilesParserParseMoleculeOptions,
   ): Molecule;
 
   /**
@@ -2772,12 +2794,6 @@ export declare class RingCollection {
 
   private constructor();
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   getAtomRingSize(atom: number): number;
 
   getBondRingSize(bond: number): number;
@@ -2853,7 +2869,7 @@ export declare class CanonizerUtil {
 /**
  * All depictor options default to `false`.
  */
-export interface IDepictorOptions {
+export interface DepictorOptions {
   inflateToMaxAVBL?: boolean;
   inflateToHighResAVBL?: boolean;
   chiralTextBelowMolecule?: boolean;
@@ -2909,12 +2925,6 @@ export declare class Reaction {
    */
   static fromRxn(rxn: string): Reaction;
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Serialize the `Reaction` to a reaction SMILES string.
    */
@@ -3201,12 +3211,6 @@ export declare class SDFileParser {
    */
   constructor(sdf: string, fields: string[]);
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Move to the next Molfile. Returns `true` if there is one, `false` otherwise.
    * @example
@@ -3258,12 +3262,6 @@ export declare class SSSearcher {
    */
   constructor();
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Set the `fragment` to search.
    * @param fragment - `Molecule` instance to set as fragment. It has to be
@@ -3299,12 +3297,6 @@ export declare class SSSearcherWithIndex {
    */
   constructor();
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Returns an array of the 512 idcodes that are used for computing indexes.
    */
@@ -3365,7 +3357,7 @@ export declare namespace Util {
    */
   export function getHoseCodesFromDiastereotopicID(
     diastereotopicID: string,
-    options?: IHoseCodesOptions,
+    options?: HoseCodesOptions,
   ): string[];
 }
 
@@ -3374,9 +3366,7 @@ export declare namespace Util {
  */
 export declare const version: string;
 
-// Core API
-
-export interface IParameterizedString {
+export interface ParameterizedString {
   type: number;
 
   value: string;
@@ -3391,15 +3381,15 @@ export declare class MoleculeProperties {
 
   logP: number;
 
-  logPString: IParameterizedString[];
+  logPString: ParameterizedString[];
 
   logS: number;
 
-  logSString: IParameterizedString[];
+  logSString: ParameterizedString[];
 
   polarSurfaceArea: number;
 
-  polarSurfaceAreaString: IParameterizedString[];
+  polarSurfaceAreaString: ParameterizedString[];
 
   rotatableBondCount: number;
 
@@ -3407,16 +3397,13 @@ export declare class MoleculeProperties {
 }
 
 export declare class DruglikenessPredictor {
+  /**
+   * Create a new predictor.
+   */
   constructor();
 
   static DRUGLIKENESS_UNKNOWN: number;
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Returns the calculated drug likeness as a double.
    * @param molecule
@@ -3428,7 +3415,7 @@ export declare class DruglikenessPredictor {
   /**
    * Returns detailed information about the previous drug likeness assessment.
    */
-  getDetail(): IParameterizedString[];
+  getDetail(): ParameterizedString[];
 }
 
 export declare namespace DrugScoreCalculator {
@@ -3437,7 +3424,7 @@ export declare namespace DrugScoreCalculator {
     mSolubility: number,
     mMolweight: number,
     mDruglikeness: number,
-    toxRisks: number[],
+    toxRisks: number[] | null,
   ): number;
 }
 
@@ -3456,12 +3443,6 @@ export declare class ToxicityPredictor {
 
   static RISK_NAMES: string[];
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Returns the calculated risk as an integer.
    * @param molecule
@@ -3475,23 +3456,23 @@ export declare class ToxicityPredictor {
    * @param molecule
    * @param riskType
    */
-  getDetail(molecule: Molecule, riskType: number): IParameterizedString[];
+  getDetail(molecule: Molecule, riskType: number): ParameterizedString[];
 }
 
-export interface IInitializeConformersOptions {
+export interface InitializeConformersOptions {
   /**
    * One of the ConformerGenerator.STRATEGY_ constants.
-   * Default: `ConformerGenerator.STRATEGY_LIKELY_RANDOM`.
+   * @default ConformerGenerator.STRATEGY_LIKELY_RANDOM
    */
   strategy?: number;
   /**
-   * Maximum number of distinct torsion sets the strategy will try.
-   * Default: `100000`.
+   * Maximum amount of distinct torsion sets the strategy will try.
+   * @efault 10_0000
    */
   maxTorsionSets?: number;
   /**
    * Use 60 degree steps for every rotatable bond instead of torsion DB.
-   * Default: `false`.
+   * @default false
    */
   use60degreeSteps?: boolean;
 }
@@ -3504,12 +3485,6 @@ export declare class ConformerGenerator {
 
   constructor(seed: number);
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Fills all free valences of mol with explicit hydrogens and tries to
    * create a reasonable conformer by starting with the most likely torsion set.
@@ -3536,7 +3511,7 @@ export declare class ConformerGenerator {
    */
   initializeConformers(
     mol: Molecule,
-    options?: IInitializeConformersOptions,
+    options?: InitializeConformersOptions,
   ): boolean;
 
   /**
@@ -3571,11 +3546,11 @@ export declare class ConformerGenerator {
 }
 
 // eslint-disable-next-line @typescript-eslint/no-empty-object-type
-export interface IForceFieldMMFF94Options {
+export interface ForceFieldMMFF94Options {
   // TODO
 }
 
-export interface IForceFieldMinimiseOptions {
+export interface ForceFieldMinimiseOptions {
   /**
    * The maximum number of iterations to run for.
    * Default: 4000.
@@ -3609,15 +3584,9 @@ export declare class ForceFieldMMFF94 {
   constructor(
     molecule: Molecule,
     tablename: 'MMFF94' | 'MMFF94s' | 'MMFF94s+',
-    options?: IForceFieldMMFF94Options,
+    options?: ForceFieldMMFF94Options,
   );
 
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
   /**
    * Returns the total number of atoms in this force field.
    */
@@ -3634,155 +3603,7 @@ export declare class ForceFieldMMFF94 {
    * @param options
    * @returns - Return code, 0 on success.
    */
-  minimise(options?: IForceFieldMinimiseOptions): number;
-}
-
-// Full API
-
-export declare namespace StructureView {
-  export function showStructures(cssClass: string): void;
-
-  export function renderStructure(id: string): void;
-
-  export function getIDCode(id: string): string;
-
-  export function drawStructure(
-    id: string,
-    idcode: string,
-    coordinates: string,
-    options?: IDepictorOptions,
-  ): void;
-
-  export function drawMolecule(
-    el: HTMLCanvasElement,
-    mol: Molecule,
-    options?: IDepictorOptions,
-  ): void;
-
-  export function drawStructureWithText(
-    id: string,
-    idcode: string,
-    coordinates: string,
-    options?: IDepictorOptions,
-    atomText?: string[],
-  ): void;
-}
-
-export declare class StructureEditor {
-  constructor(element: HTMLElement, useSVG?: boolean, scale?: number);
-
-  /**
-   * Create a new structure editor.
-   * @param id - Id of the DOM element
-   */
-  static createEditor(id: string): StructureEditor;
-
-  /**
-   * Create a new structure editor with an SVG toolbar.
-   * @param id  - Id of the DOM element
-   * @param scale
-   */
-  static createSVGEditor(id: string, scale: number): StructureEditor;
-
-  /**
-   * Returns the OCL object.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  getOCL(): any;
-
-  getMolecule(): Molecule;
-
-  /**
-   * Returns the current molecule as a string that contains its ID Code and
-   * coordinates separated by a space.
-   */
-  getIDCode(): string;
-
-  /**
-   * Sets the current molecule to the provided ID code. The string can optionally
-   * contain coordinates separated by a space.
-   * @param idCode
-   */
-  setIDCode(idCode: string): void;
-
-  /**
-   * Switches the current molecule in the editor in fragment mode or not.
-   * @param isFragment
-   */
-  setFragment(isFragment: boolean): void;
-
-  /**
-   * Returns whether the current molecule is a fragment.
-   */
-  isFragment(): boolean;
-
-  /**
-   * Returns the current molecule as a MDL Molfile V2000.
-   */
-  getMolFile(): string;
-
-  /**
-   * Sets the editor content to the molecule represented by this Molfile
-   * (V2000 or V3000)
-   * @param molfile
-   */
-  setMolFile(molfile: string): void;
-
-  /**
-   * Returns the current molecule as a MDL Molfile V3000.
-   */
-  getMolFileV3(): string;
-
-  /**
-   * Returns the current molecule as a SMILES string.
-   */
-  getSmiles(): string;
-
-  /**
-   * Sets the editor content to the molecule represented by this SMILES.
-   * @param smiles
-   */
-  setSmiles(smiles: string): void;
-
-  /**
-   * Sets a callback function which is called whenever an atom is hovered/unhovered
-   * by the mouse.
-   * @param callback
-   */
-  setAtomHightlightCallback(callback: AtomHighlightCallback): void;
-
-  /**
-   * Sets a callback function which is called whenever a bond is hovered/unhovered
-   * by the mouse.
-   * @param callback
-   */
-  setBondHightlightCallback(callback: BondHighlightCallback): void;
-
-  /**
-   * Sets a callback function which is called whenever the structure in the editor
-   * is changed.
-   * @param callback
-   */
-  setChangeListenerCallback(callback: ChangeListenerCallback): void;
-
-  hasFocus(): boolean;
-}
-
-export type AtomHighlightCallback = (atom: number, selected: boolean) => void;
-
-export type BondHighlightCallback = (bond: number, selected: boolean) => void;
-
-export type ChangeListenerCallback = (
-  idcode: string,
-  molecule: Molecule,
-) => void;
-
-export declare namespace SVGRenderer {
-  export function renderMolecule(
-    idCode: string,
-    width: number,
-    height: number,
-  ): string;
+  minimise(options?: ForceFieldMinimiseOptions): number;
 }
 
 export type OnChangeEventType =
@@ -3915,7 +3736,7 @@ interface CanvasEditorElementConstructor extends CustomElementConstructor {
  *
  * In Javascript:
  * ```js
- * import {registerCustomElement, Molecule, ReactionEncoder} from 'openchemlib/minimal';
+ * import {registerCustomElement, Molecule, ReactionEncoder} from 'openchemlib';
  *
  * // register CanvasEditorElement with `openchemlib-editor` tag name
  * const CanvasEditorElement = registerCustomElement();