The SI format#

The Digichem coordinate format is written in YAML, and contains six properties:

$ digichem convert Benzene.xyz -o si
version: 2.1.0
name: null
charge: 0
multiplicity: 1
atoms:
- {atom: C, x: 1.38314, y: -0.22144, z: 0.00537}
- {atom: C, x: 0.50694, y: -1.30651, z: -0.00792}
- {atom: C, x: -0.87093, y: -1.09053, z: -0.0147}
- {atom: C, x: -1.3729, y: 0.21095, z: -0.00441}
- {atom: C, x: -0.4967, y: 1.29607, z: 0.0106}
- {atom: C, x: 0.88118, y: 1.07996, z: 0.01366}
- {atom: H, x: 2.4568, y: -0.38978, z: 0.00923}
- {atom: H, x: 0.89795, y: -2.32061, z: -0.01321}
- {atom: H, x: -1.55354, y: -1.93593, z: -0.02737}
- {atom: H, x: -2.44648, y: 0.37928, z: -0.00825}
- {atom: H, x: -0.88777, y: 2.31003, z: 0.01974}
- {atom: H, x: 1.56378, y: 1.92549, z: 0.02297}
history: null
version

The version string of the input file, used by the digichem parser for backwards compatibility.

name

An optional string describing the name of the molecule. The name is only used for descriptive purposes, and can be omitted. If it is omitted, the name of the file itself is used as the name of the molecule.

charge

Integer charge of the molecule.

multiplicity

Integer multiplicity of the molecule.

atoms

A list of dictionaries describing the geometry of the molecule. Each dictionary contains four key:value pairs:

  • atom: The atom type as its standard element symbol.

  • x: The x coordinate, in angstrom.

  • y: The y coordinate, in angstrom.

  • z: The z coordinate, in angstrom.

history

An optional unique identifier describing the calculation that generated the geometry in this file.

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