pymatgen.io.xyz module
Module implementing an XYZ file object class.
- class XYZ(mol: pymatgen.core.structure.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
- property molecule: pymatgen.core.structure.Molecule[source]
Returns molecule associated with this XYZ. In case multiple frame XYZ, returns the last frame.