XYZData

class sknano.io.XYZData(fpath=None, **kwargs)

Bases: sknano.io.xyz.XYZReader

Class for reading and writing StructureData in xyz format.

Parameters:fpath (str, optional) –

Attributes

atoms	Structure Atoms.
basis	Structure BasisAtoms.
comment_line	Comment line.
crystal_cell	Structure CrystalCell.
fmtstr	Format string.
lattice	Structure Crystal3DLattice.
lattice_shift	Lattice displacement vector.
scaling_matrix	CrystalCell.scaling_matrix.
structure	An alias to self.
unit_cell	Structure UnitCell.

Methods

clear()	Clear list of StructureMixin.atoms.
make_supercell(scaling_matrix[, wrap_coords])	Make supercell.
read()	Read xyz file.
read_data(*args, **kwargs)	Read LAMMPS Data file.
read_dump(*args, **kwargs)	Read LAMMPS Dump file.
read_pdb(*args, **kwargs)	Read PDB file.
read_xyz(*args, **kwargs)	Read XYZ file.
rotate(**kwargs)	Rotate crystal cell lattice, basis, and unit cell.
todict()	Return dict of constructor parameters.
transform_lattice(scaling_matrix[, ...])	Transform structure lattice.
translate(t[, fix_anchor_points])	Translate crystal cell lattice, basis, and unit cell.
write([xyzfile, atoms, comment_line])	Write xyz file.
write_data(**kwargs)	Write LAMMPS data file.
write_dump(**kwargs)	Write LAMMPS dump file.
write_pdb(**kwargs)	Write pdb file.
write_xyz(**kwargs)	Write xyz file.

Methods Summary

write([xyzfile, atoms, comment_line])

Write xyz file.

Methods Documentation

write(xyzfile=None, atoms=None, comment_line=None, **kwargs)

Write xyz file.

Parameters:

• xyzfile ({None, str}, optional) –
• comment_line (str, optional) – A string written to the first line of xyz file. If None, then it is set to the full path of the output xyz file.