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 reads Versions 2.0 and 3.0 of the MOL format.

Export creates Version 2.0 molfiles.

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, sub_a, sub_b, ...}] 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 expr_i as specifying the corresponding elem_i.

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 "Graphics3D" element for 3D molfiles and "StructureDiagram" for 2D molfiles.

Data representation elements:

	"EdgeRules"	connectivity data, given as a list of rules
	"EdgeTypes"	bond types, as a list of strings
	"FormalCharges"	charges of the atoms given by "VertexTypes"
	"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 "Rendering" are:

	"BallAndStick"	displays atoms and bonds as a ball-and-stick model
	"Spacefilling"	atoms shown as overlapping spheres
	"Wireframe"	bonds rendered as lines