 |
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).
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
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.
Elements
- 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
Options
- General Import options:
-
ImageSize Automatic specifies the overall size of the graphics to display Background White specifies what background color to use ViewPoint Automatic point 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
Examplesopen all
Basic Examples (2)
Show the Import elements available in a MOL file:
| In[1]:= |
| Out[1]= |  |
Import a 3D molecule model as a ball-and-stick model:
| In[2]:= |
| Out[2]= |  |
Show the bonds of the same molecule as a wireframe model:
| In[3]:= |
| Out[3]= |  |
Show the same molecule as space-filling atoms:
| In[4]:= |
| 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]:= |
| Out[1]= |  |
This gives the atom types and their 2D coordinates for the structure diagram:
| In[2]:= |
| Out[2]= |  |
This creates a molfile from the previous output:
| In[3]:= |
| Out[3]= |  |
New in 6 | Last modified in 7
