Mathematica Import/Export Format

XYZ (.xyz)

MIME type: chemical/x-xyz
XMOL 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 and meta-information.
Does not store chemical bond information.
Developed in 1990 at the Minnesota Supercomputer Center.

Import and Export fully support the XYZ format.

IMPORT AND EXPORT

Import["file.xyz"] reads an XYZ molecule model and gives a visual representation of it.

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

Import["file.xyz"] returns a Graphics3D object.

Import["file.xyz", elem] imports the specified element from an XYZ file.

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

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

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

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

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

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

Export["file.xyz", {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 XYZ 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 element:

"Graphics3D"

XYZ file rendered as a Graphics3D object

Import uses the "Graphics3D" element by default for the XYZ format.

Data representation elements:

	"VertexCoordinates"	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.xyz", {vert, coord}, {{"VertexTypes", "VertexCoordinates"}}] creates an XYZ model from a specification of atom types and their 3D coordinates.

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 model.

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