Class MoleculesDB

constructor

• new MoleculesDB(OCL, options?): MoleculesDB

• Parameters

  • OCL: __module

    openchemlib library

  • Optional options: {
        computeProperties: undefined | boolean;
    } = {}

    • computeProperties: undefined | boolean

  Returns MoleculesDB

OCL

computeProperties

db

searcher

statistics

appendCSV

• appendCSV(csv, options?): Promise<void>

• append to the current database a CSV file

  Parameters

  • csv: string | ArrayBuffer

    text file containing the comma separated value file

  • Optional options: {
        dynamicTyping: undefined | boolean;
        header: undefined | boolean;
        onStep: undefined | Function;
        skipEmptyLines: undefined | boolean;
    }

    • dynamicTyping: undefined | boolean

    • header: undefined | boolean

    • onStep: undefined | Function

      call back to execute after each molecule

    • skipEmptyLines: undefined | boolean

  Returns Promise<void>

appendColor

• appendColor(options): void

• Append the property data.color to each entry based on a data or property label {object} [options={}] {string} [options.dataLabel] name of the property from data to use {string} [options.propertyLabel] name of the property from properties to use {number} [options.colorLabel='color'] name of the property to add in data that will contain the color {number} [options.minValue] {number} [options.maxValue] {number} [options.minHue=0] {number} [options.maxHue=360] {number} [options.saturation=65] percent of color saturation {number} [options.lightness=65] percent of color lightness

  Parameters

  • options: any

  Returns void

appendEntries

• appendEntries(entries, options?): Promise<void>

• Append an array of entries to the current database. An entry is an object that by default should contain a 'ocl' property containing idCode and optionally index and coordinates

  Parameters

  • entries: object[]

  • Optional options: {
        coordinatesPath: undefined | string;
        idCodePath: undefined | string;
        indexPath: undefined | string;
        molfilePath: undefined | string;
        mwPath: undefined | string;
        onStep: undefined | Function;
        smilesPath: undefined | string;
    }

    • coordinatesPath: undefined | string

    • idCodePath: undefined | string

    • indexPath: undefined | string

    • molfilePath: undefined | string

    • mwPath: undefined | string

    • onStep: undefined | Function

      call back to execute after each molecule

    • smilesPath: undefined | string

  Returns Promise<void>

appendSDF

• appendSDF(sdf, options?): DB

• Append a SDF to the current database

  Parameters

  • sdf: string | ArrayBuffer

    text file containing the sdf

  • Optional options: {
        onStep: undefined | Function;
    }

    • onStep: undefined | Function

      call back to execute after each molecule

  Returns DB

appendSmilesList

• appendSmilesList(text, options?): DB

• Append a SDF to the current database

  Parameters

  • text: any

  • Optional options: {
        onStep: undefined | Function;
    }

    • onStep: undefined | Function

      call back to execute after each molecule

  Returns DB

getDB

• getDB(): any[]

• Returns an array with the current database

  Returns any[]

pushEntry

• pushEntry(molecule, data?, moleculeInfo?): void

• Add a molecule to the current database

  Parameters

  • molecule: Molecule

  • Optional data: object

  • Optional moleculeInfo: object

    may contain precalculated index and mw

  Returns void

pushMoleculeInfo

• pushMoleculeInfo(moleculeInfo, data?): void

• Add an entry in the database

  Parameters

  • moleculeInfo: object

    a molecule as a JSON that may contain the following properties: molfile, smiles, idCode, mf, index

  • Optional data: object

  Returns void

search

• search(query?, options?): any[]

• Search in a MoleculesDB Inside the database all the same molecules are group together

  Parameters

  • Optional query: any

    smiles, molfile, idlCode or instance of Molecule to look for

  • Optional options: {
        flattenResult: undefined | boolean;
        format: undefined | "smiles" | "molfile" | "smarts" | "idCode";
        keepMolecule: undefined | boolean;
        limit: undefined | number;
        mode: undefined | string;
    }

    • flattenResult: undefined | boolean

      The database group the data for the same product. This allows to flatten the result

    • format: undefined | "smiles" | "molfile" | "smarts" | "idCode"

      query format

    • keepMolecule: undefined | boolean

      keep the OCL.Molecule object in the result

    • limit: undefined | number

      maximal number of result

    • mode: undefined | string

      search by 'substructure', 'exact' or 'similarity'

  Returns any[]

  array of object of the type {(molecule), idCode, data, properties}

searchAsync

• searchAsync(query?, options?): Promise<any[]>

• Search in a MoleculesDB Inside the database all the same molecules are group together

  Parameters

  • Optional query: any

    smiles, molfile, idCode or instance of Molecule to look for

  • Optional options: {
        controler: undefined | AbortController;
        flattenResult: undefined | boolean;
        format: undefined | "smiles" | "molfile" | "smarts" | "idCode";
        interval: undefined | number;
        keepMolecule: undefined | boolean;
        limit: undefined | number;
        mode: undefined | string;
        onStep: undefined | Function;
    }

    • controler: undefined | AbortController

      callback to execute to check if the search should be aborted

    • flattenResult: undefined | boolean

      The database group the data for the same product. This allows to flatten the result

    • format: undefined | "smiles" | "molfile" | "smarts" | "idCode"

      query format

    • interval: undefined | number

      interval in ms to call the onStep callback

    • keepMolecule: undefined | boolean

      keep the OCL.Molecule object in the result

    • limit: undefined | number

      maximal number of result

    • mode: undefined | string

      search by 'substructure', 'exact' or 'similarity'

    • onStep: undefined | Function

      callback to execute after each interval

  Returns Promise<any[]>

  array of object of the type {(molecule), idCode, data, properties}