pymatgen.io.xyz module
Module implementing an XYZ file object class.
- class XYZ(mol: Molecule, coord_precision: int = 6)[source]
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.
- as_dataframe()[source]
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)[source]
Creates XYZ object from a file.
- Parameters:
filename – XYZ filename
- Returns:
XYZ object
- static from_string(contents)[source]
Creates XYZ object from a string.
- Parameters:
contents – String representing an XYZ file.
- Returns:
XYZ object