Class MoleculesDB

constructor

• new MoleculesDB(
      OCL: __module,
      options?: { computeProperties?: boolean; keepEmptyMolecules?: boolean },
  ): MoleculesDB

  Creates an instance of MoleculesDB.

  Parameters

  • OCL: __module

    openchemlib library
  • Optionaloptions: { computeProperties?: boolean; keepEmptyMolecules?: boolean } = {}

    Options.

  Returns MoleculesDB

calculatedStatistics

computeProperties

dataStatistics

db

keepEmptyMolecules

OCL

searcher

nbData

• get nbData(): number

  Returns number

nbMolecules

• get nbMolecules(): number

  Returns number

statistics

• get statistics(): { calculated: never[]; data: never[] }

  Returns { calculated: never[]; data: never[] }

appendColor

• appendColor(options: any): 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

appendCSV

• appendCSV(
      csv: string | ArrayBuffer,
      options?: {
          dynamicTyping?: boolean;
          header?: boolean;
          onStep?: Function;
          skipEmptyLines?: boolean;
      },
  ): Promise<void>

  append to the current database a CSV file

  Parameters

  • csv: string | ArrayBuffer

    text file containing the comma separated value file
  • Optionaloptions: {
        dynamicTyping?: boolean;
        header?: boolean;
        onStep?: Function;
        skipEmptyLines?: boolean;
    }

    options.

    • OptionaldynamicTyping?: boolean

      dynamically type the data (convert values to number of boolean if possible)

    • Optionalheader?: boolean

      if the first line of the file is a header

    • OptionalonStep?: Function

      call back to execute after each molecule

    • OptionalskipEmptyLines?: boolean

      skip empty lines

  Returns Promise<void>

appendEntries

• appendEntries(
      entries: object[],
      options?: {
          coordinatesPath?: string;
          idCodePath?: string;
          indexPath?: string;
          molfilePath?: string;
          mwPath?: string;
          onStep?: Function;
          smilesPath?: string;
      },
  ): 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[]
  • Optionaloptions: {
        coordinatesPath?: string;
        idCodePath?: string;
        indexPath?: string;
        molfilePath?: string;
        mwPath?: string;
        onStep?: Function;
        smilesPath?: string;
    }

    • OptionalcoordinatesPath?: string

    • OptionalidCodePath?: string

    • OptionalindexPath?: string

    • OptionalmolfilePath?: string

    • OptionalmwPath?: string

    • OptionalonStep?: Function

      call back to execute after each molecule

    • OptionalsmilesPath?: string

  Returns Promise<void>

appendSDF

• appendSDF(
      sdf: string | ArrayBuffer,
      options?: {
          dynamicTyping?: boolean;
          eol?: string;
          mixedEOL?: boolean;
          onStep?: Function;
      },
  ): Promise<void>

  Append a SDF to the current database

  Parameters

  • sdf: string | ArrayBuffer

    text file containing the sdf
  • Optionaloptions: { dynamicTyping?: boolean; eol?: string; mixedEOL?: boolean; onStep?: Function }

    options

    • OptionaldynamicTyping?: boolean

      Dynamically type the data

    • Optionaleol?: string

      Specify the end of line character. Default will be the one found in the file

    • OptionalmixedEOL?: boolean

      Set to true if you know there is a mixture between \r\n and \n

    • OptionalonStep?: Function

      callback to execute after each molecule

  Returns Promise<void>

appendSmilesList

• appendSmilesList(
      smiles: string | ArrayBuffer,
      options?: { onStep?: Function },
  ): Promise<void>

  Append a list of SMILES to the current database.

  Parameters

  • smiles: string | ArrayBuffer

    text file containing a list of smiles
  • Optionaloptions: { onStep?: Function }

    Options

    • OptionalonStep?: Function

      call back to execute after each molecule

  Returns Promise<void>

clear

• clear(): void

  Returns void

getDB

• getDB(): any[]

  Returns an array with the current database

  Returns any[]

pushEntry

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

  Add a molecule to the current database.

  Parameters

  • molecule: Molecule

    The molecule to append.
  • Optionaldata: object

    Options.
  • OptionalmoleculeInfo: object

    May contain precalculated index and mw.

  Returns void

pushMoleculeInfo

• pushMoleculeInfo(moleculeInfo: object, data?: object): 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
  • Optionaldata: object

  Returns void

search

• search(
      query?: string | Molecule,
      options?: {
          flattenResult?: boolean;
          format?: "smiles" | "molfile" | "smarts" | "idCode";
          keepMolecule?: boolean;
          limit?: number;
          mode?:
              | "exact"
              | "substructure"
              | "substructureOR"
              | "similarity"
              | "exactNoStereo";
      },
  ): any[]

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

  Parameters

  • Optionalquery: string | Molecule

    smiles, molfile, idlCode or instance of Molecule to look for
  • Optionaloptions: {
        flattenResult?: boolean;
        format?: "smiles" | "molfile" | "smarts" | "idCode";
        keepMolecule?: boolean;
        limit?: number;
        mode?:
            | "exact"
            | "substructure"
            | "substructureOR"
            | "similarity"
            | "exactNoStereo";
    }

    Options

    • OptionalflattenResult?: boolean

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

    • Optionalformat?: "smiles" | "molfile" | "smarts" | "idCode"

      query format

    • OptionalkeepMolecule?: boolean

      keep the OCL.Molecule object in the result

    • Optionallimit?: number

      maximal number of result

    • Optionalmode?: "exact" | "substructure" | "substructureOR" | "similarity" | "exactNoStereo"

      search algorithm

  Returns any[]

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

searchAsync

• searchAsync(
      query?: string | Molecule,
      options?: {
          controler?: AbortController;
          flattenResult?: boolean;
          format?: "smiles" | "molfile" | "smarts" | "idCode";
          interval?: number;
          keepMolecule?: boolean;
          limit?: number;
          mode?:
              | "exact"
              | "substructure"
              | "substructureOR"
              | "similarity"
              | "exactNoStereo";
          onStep?: Function;
      },
  ): Promise<any[]>

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

  Parameters

  • Optionalquery: string | Molecule

    smiles, molfile, idCode or instance of Molecule to look for
  • Optionaloptions: {
        controler?: AbortController;
        flattenResult?: boolean;
        format?: "smiles" | "molfile" | "smarts" | "idCode";
        interval?: number;
        keepMolecule?: boolean;
        limit?: number;
        mode?:
            | "exact"
            | "substructure"
            | "substructureOR"
            | "similarity"
            | "exactNoStereo";
        onStep?: Function;
    }

    Options.

    • Optionalcontroler?: AbortController

      callback to execute to check if the search should be aborted

    • OptionalflattenResult?: boolean

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

    • Optionalformat?: "smiles" | "molfile" | "smarts" | "idCode"

      query format

    • Optionalinterval?: number

      interval in ms to call the onStep callback

    • OptionalkeepMolecule?: boolean

      keep the OCL.Molecule object in the result

    • Optionallimit?: number

      maximal number of result

    • Optionalmode?: "exact" | "substructure" | "substructureOR" | "similarity" | "exactNoStereo"

      search algorithm

    • OptionalonStep?: Function

      callback to execute after each interval

  Returns Promise<any[]>

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