XYZ (.xyz)

BackgroundBackground

    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 ExportImport 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,suba,subb,}] 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 as specifying the corresponding .
  • 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.

ElementsElements

  • 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
  • "Graphics3D"XYZ file rendered as a Graphics3D object
  • Import uses the 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.

OptionsOptions

  • General Import 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, the Wolfram Language 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 are:
  • "BallAndStick"displays atoms and bonds as a ball-and-stick model
    "Spacefilling"atoms shown as overlapping spheres
    "Wireframe"bonds rendered as lines

ExamplesExamplesopen allclose all

Basic Examples  (1)Basic Examples  (1)

Import an XYZ example file, rendering it as a ball-and-stick model:

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Show the same molecule as space-filling atoms:

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Read the atom types and atom coordinates:

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Export this data to XYZ:

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Introduced in 2007
(6.0)