Mathematica Import/Export Format

SDF (.sdf)

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

Import and Export support version 2 of the SDF format.

IMPORT AND EXPORT

Import["file.sdf"] imports a molecule model or a structure diagram from an SDF file.

Export["file.sdf", expr] exports elements of a molecule model to an SDF file.

Import["file.sdf"]gives a Graphics3D object when reading a 3D molecule model and vector graphics when importing a planar representation of a molecule.

Import["file.sdf", elem] imports the specified element from an SDF file.

Import["file.sdf", {elem, sub_a, sub_b, ...}] imports a subelement.

Import["file.sdf", {{elem₁, elem₂, ...}}] imports multiple elements.

The import format can be specified with Import["file", "SDF"] or Import["file", {"SDF", elem, ...}].

Export["file.sdf", expr, elem] creates an SDF file by treating expr as specifying element elem.

Export["file.sdf", {expr₁, expr₂, ...}, {{elem₁, elem₂, ...}}] treats each expr_i as specifying the corresponding elem_i.

Export["file.sdf", expr, opt₁->val₁, ...] exports expr with the specified option elements taken to have the specified values.

Export["file.sdf", {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 SDF 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 renderings of all molecule models stored in the file
	"Graphics3D",n	3D rendering of the n molecule
	"StructureDiagram"	2D structure formulas of all molecules

Import by default uses the "Graphics3D" element for SDF files that contain 3D molecule models, and "StructureDiagram" for structure formulas.

Data representation elements:

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

Import["file.sdf", "EdgeRules"] gives the connectivity data for all chemical compounds stored in the file as a list of lists of rules.

Export["file.sdf", {vertlist, coordlist}, {{"VertexTypes", "VertexCoordinates"}}] creates an SDF file from a specification of atom types and their 2D or 3D coordinates.

Meta-information element:

"Header"

header information for each molecule stored in the file, given as a list of strings

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