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.
-
property
all_molecules
¶ Returns all the frames of molecule associated with this XYZ.
-
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
¶ Returns molecule associated with this XYZ. In case multiple frame XYZ, returns the last frame.