MOL (.mol)

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 ExportImport 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 as specifying the corresponding .
  • 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.

ElementsElements

  • 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 element for molfiles that contain 3D molecule models, and 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

OptionsOptions

  • 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, Mathematica 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 are:
  • "BallAndStick"displays atoms and bonds as a ball-and-stick model
    "Spacefilling"atoms shown as overlapping spheres
    "Wireframe"bonds rendered as lines

ExamplesExamplesopen allclose all

Basic Examples (2)Basic Examples (2)

Show the Import elements available in a MOL file:

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

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

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Show the same molecule as space-filling atoms:

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

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

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This creates a molfile from the previous output:

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