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Mathematica > Data Manipulation > Importing & Exporting >
Mathematica Import/Export Format

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 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.
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, 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 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
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 "Rendering" are:
"BallAndStick"displays atoms and bonds as a ball-and-stick model
"Spacefilling"atoms shown as overlapping spheres
"Wireframe"bonds rendered as lines
EXAMPLESCLOSE ALL
Basic Examples
Show the Import elements available in a MOL file:
Import a 3D molecule model as a ball-and-stick model:
Show the bonds of the same molecule as a wireframe model:
Show the same molecule as space-filling atoms:
When importing a molfile that contains a 2D representation of a molecule, Mathematica automatically renders it as a chemical structure diagram:
This gives the atom types and their 2D coordinates for the structure diagram:
This creates a molfile from the previous output:
Show the Import elements available in a MOL file:
In[1]:=
Click for copyable input
Out[1]=
Import a 3D molecule model as a ball-and-stick model:
In[2]:=
Click for copyable input
Out[2]=
Show the bonds of the same molecule as a wireframe model:
In[3]:=
Click for copyable input
Out[3]=
Show the same molecule as space-filling atoms:
In[4]:=
Click for copyable input
Out[4]=
 
When importing a molfile that contains a 2D representation of a molecule, Mathematica automatically renders it as a chemical structure diagram:
In[1]:=
Click for copyable input
Out[1]=
This gives the atom types and their 2D coordinates for the structure diagram:
In[2]:=
Click for copyable input
Out[2]=
This creates a molfile from the previous output:
In[3]:=
Click for copyable input
Out[3]=
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