pyxtal.io module

This module handles reading and write crystal files.

pyxtal.io.get_cif_str_for_pyxtal(struc, header: str = '', sym_num=None, style: str = 'mp')[source]

Get the cif string for a given structure.

The default setting for _atom_site follows the materials project cif format. TODO: make this a method of the pyxtal class

Parameters:

  • struc – PyXtal structure object

  • header – Additional information

  • sym_num – Number of symmetry operations. None means write all symops

  • style – Format type - either ‘icsd’ or ‘mp’ (used in pymatgen)

Returns:

CIF format string representation of the structure

Return type:

str

pyxtal.io.in_merged_coords(wp, pt, pts, cell)[source]

Check if a point is within a set of points.

Parameters:

  • wp – Wyckoff position object

  • pt – Tuple of (coordinates, species) for the point to check

  • pts – List of (coordinates, species) tuples to check against

  • cell – Unit cell matrix

Returns:

True if pt matches any point in pts, False otherwise

Return type:

bool

pyxtal.io.read_cif(filename)[source]

Read a CIF file, primarily designed for PyXtal CIF output format. Warning: Use caution when reading other CIF files.

Parameters:

filename (str) – Path to the CIF structure file

Returns:

(Lattice, list of sites) representing the crystal structure

Return type:

tuple

pyxtal.io.search_molecules_in_crystal(struc, tol=0.2, once=False, ignore_HH=True, max_bond_length=None)[source]

Find molecules within a crystal structure.

Parameters:

  • struc (Structure) – Pymatgen Structure object

  • tol (float) – Bond distance tolerance factor. Default 0.2

  • once (bool) – Whether to find only first molecule. Default False

  • ignore_HH (bool) – Whether to ignore short H-H bonds. Default True

  • max_bond_length (float, optional) – Maximum allowed bond length for missing entries

Returns:

List of pymatgen Molecule objects representing found molecules

Return type:

list[Molecule]

class pyxtal.io.structure_from_ext(struc, ref_mols, tol=0.2, ignore_HH=False, add_H=False, hn=None)[source]

Bases: object

add_Hydrogens(smile, xyz)[source]

add hydrogen for pymtagen molecule

align()[source]

Compute the orientation wrt the reference molecule

make_mol_sites()[source]

Generate the molecular wyckoff sites

resort(molecules)[source]
show(overlay=True)[source]
pyxtal.io.write_cif(struc, filename=None, header='', permission='w', sym_num=None, style='mp')[source]

Export the structure in cif format. The default setting for _atom_site follows the materials project cif

Parameters:

  • struc – pyxtal structure object

  • filename – path of the structure file

  • header – additional information

  • permission – write(w) or append(a+) to the given file

  • sym_num – the number of symmetry operations, None means writing all symops

  • style – icsd or mp (used in pymatgen)