pymatgen.io.xyz module

Module implementing an XYZ file object class.

class XYZ(mol: pymatgen.core.structure.Molecule, coord_precision: int = 6)

Bases: object

Basic class for importing and exporting Molecules or Structures in XYZ format.

Note

Exporting periodic structures in the XYZ format will lose information about the periodicity. Essentially, only Cartesian coordinates are written in this format and no information is retained about the lattice.

Parameters

• mol – Input molecule or list of molecules

• coord_precision – Precision to be used for coordinates.

property all_molecules

Returns all the frames of molecule associated with this XYZ.

as_dataframe()

Generates a coordinates data frame with columns: atom, x, y, and z In case of multiple frame XYZ, returns the last frame.

Returns

pandas.DataFrame

static from_file(filename)

Creates XYZ object from a file.

Parameters

filename – XYZ filename

Returns

XYZ object

static from_string(contents)

Creates XYZ object from a string.

Parameters

contents – String representing an XYZ file.

Returns

XYZ object

property molecule: pymatgen.core.structure.Molecule

Returns molecule associated with this XYZ. In case multiple frame XYZ, returns the last frame.

write_file(filename)

Writes XYZ to file.

Parameters

filename – File name of output file.