MOL (.mol)

  • Import and Export support Version 2 of the MOL format.
  • Background

      MIME type: chemical/x-mdl-molfile
      MDL molecule model files.
      Used in cheminformatics applications and on the web for storing and exchanging 3D molecule models.
      Plain text tabular format.
      Represents a single chemical compound.
      Stores atomic coordinates, chemical bond information, and metadata.
      Maintained by Elsevier Molecular Design Limited (MDL).

    Import and Export

    • Import["file.mol"] imports a molecule model or a structure diagram from a molfile.
    • Export["file.mol",expr] exports elements of a molecule model to a molfile.
    • Import["file.mol"] gives a Graphics3D object when reading a 3D molecule model and vector graphics when importing a planar representation of a molecule.
    • Import["file.mol",elem] imports the specified element from a molfile.
    • Import["file.mol",{elem,suba,subb,}] imports a subelement.
    • Import["file.mol",{{elem1,elem2,}}] imports multiple elements.
    • The import format can be specified with Import["file","MOL"] or Import["file",{"MOL",elem,}].
    • Export["file.mol",expr,elem] creates a molfile by treating expr as specifying element elem.
    • Export["file.mol",{expr1,expr2,},{{elem1,elem2,}}] treats each expri as specifying the corresponding elemi.
    • Export["file.mol",expr,opt1->val1,] exports expr with the specified option elements taken to have the specified values.
    • Export["file.mol",{elem1->expr1,elem2->expr2,},"Rules"] uses rules to specify the elements to be exported.
    • See the reference pages for full general information on Import and Export.
    • ImportString and ExportString support the MOL format.


    • General Import elements:
    • "Elements"list of elements and options available in this file
      "Rules"full list of rules for each element and option
      "Options"list of rules for options, properties, and settings
    • Graphics elements:
    • "Graphics3D"3D rendering of the molecule model
      "StructureDiagram"2D structure formula
    • Import by default uses the "Graphics3D" element for molfiles that contain 3D molecule models and "StructureDiagram" for structure formulas.
    • Data representation elements:
    • "EdgeRules"connectivity data, given as a list of rules
      "EdgeTypes"bond types, given as a list of strings
      "FormalCharges"electric charges of the atoms, given as a list of integers
      "MassNumbers"isotope mass numbers
      "VertexCoordinates"2D or 3D atomic coordinates, typically given in picometers
      "VertexTypes"all atoms or groups constituting the molecule, typically given as a list of chemical element abbreviations
    • Export["file.mol",{vert,coord},{{"VertexTypes","VertexCoordinates"}}] creates a molfile from a specification of atom types and their 2D or 3D coordinates.
    • Meta-information element:
    • "Header"header information from the file


    • General Import options:
    • ImageSizeAutomaticspecifies the overall size of the graphics to display
      BackgroundWhitespecifies what background color to use
      ViewPointAutomaticpoint in space from which the 3D model is to be viewed
    • With the default setting "ViewPoint"->Automatic, the Wolfram Language automatically calculates the optimal viewing angle for the imported molecule geometry.
    • Selecting a 3D rendering style:
    • "Rendering""BallAndStick"specifies the visualization method
    • Possible settings for "Rendering" are:
    • "BallAndStick"displays atoms and bonds as a ball-and-stick model
      "Spacefilling"atoms shown as overlapping spheres
      "Wireframe"bonds rendered as lines


    Basic Examples  (2)

    Show the Import elements available in a MOL file:

    Click for copyable input

    Import a 3D molecule model as a ball-and-stick model:

    Click for copyable input

    Show the bonds of the same molecule as a wireframe model:

    Click for copyable input

    Show the same molecule as space-filling atoms:

    Click for copyable input

    When importing a molfile that contains a 2D representation of a molecule, the Wolfram Language automatically renders it as a chemical structure diagram:

    Click for copyable input

    This gives the atom types and their 2D coordinates for the structure diagram:

    Click for copyable input

    This creates a molfile from the previous output:

    Click for copyable input

    See Also

    "FASTA"  "FASTQ"  "PDB"  "SDF"  "XYZ"  "HIN"  "JCAMP-DX"  "SFF"  "FCS"

    Introduced in 2007
    | Updated in 2008