print_logo()
pyxtal
pyxtal.apply_perturbation()
pyxtal.build()
pyxtal.check_H_coordination()
pyxtal.check_distance()
pyxtal.check_mapping()
pyxtal.check_short_distances()
pyxtal.check_short_distances_by_dict()
pyxtal.copy()
pyxtal.find_matched_lattice()
pyxtal.from_CSD()
pyxtal.from_json()
pyxtal.from_random()
pyxtal.from_seed()
pyxtal.get_1D_comp()
pyxtal.get_1D_representation()
pyxtal.get_XRD()
pyxtal.get_alternatives()
pyxtal.get_density()
pyxtal.get_dimensionality()
pyxtal.get_disps_optim()
pyxtal.get_disps_sets()
pyxtal.get_disps_single()
pyxtal.get_dof()
pyxtal.get_forcefield()
pyxtal.get_free_axis()
pyxtal.get_init_translations()
pyxtal.get_intermolecular_energy()
pyxtal.get_neighboring_dists()
pyxtal.get_neighboring_molecules()
pyxtal.get_num_torsions()
pyxtal.get_site_labels()
pyxtal.get_spherical_images()
pyxtal.get_std_representation()
pyxtal.get_structure_factor()
pyxtal.get_transition()
pyxtal.get_transition_by_path()
pyxtal.get_zprime()
pyxtal.has_special_site()
pyxtal.is_duplicate()
pyxtal.load_dict()
pyxtal.make_transitions()
pyxtal.optimize_lattice()
pyxtal.remove_species()
pyxtal.remove_water()
pyxtal.resort()
pyxtal.resort_species()
pyxtal.save_dict()
pyxtal.set_cutoff()
pyxtal.set_site_coordination()
pyxtal.show()
pyxtal.show_mol_cluster()
pyxtal.sort_sites_by_mult()
pyxtal.sort_sites_by_numIons()
pyxtal.subgroup()
pyxtal.subgroup_by_path()
pyxtal.subgroup_once()
pyxtal.substitute()
pyxtal.substitute_linear()
pyxtal.supergroup()
pyxtal.supergroups()
pyxtal.to_ase()
pyxtal.to_atomic_xtal()
pyxtal.to_file()
pyxtal.to_json()
pyxtal.to_molecular_xtal()
pyxtal.to_pymatgen()
pyxtal.to_pyxtal_center()
pyxtal.to_standard_setting()
pyxtal.to_subgroup()
pyxtal.transform()
pyxtal.translate()
block_crystal()
random_crystal
random_crystal.check_wp()
random_crystal.set_crystal()
random_crystal.set_elemental_volumes()
random_crystal.set_lattice()
random_crystal.set_sites()
random_crystal.set_volume()
in_merged_coords()
read_cif()
search_molecules_in_crystal()
structure_from_ext
structure_from_ext.add_Hydrogens()
structure_from_ext.align()
structure_from_ext.make_mol_sites()
structure_from_ext.resort()
structure_from_ext.show()
write_cif()
Lattice
Lattice.add_vacuum()
Lattice.apply_transformation()
Lattice.check_mismatch()
Lattice.copy()
Lattice.encode()
Lattice.find_transition_to_orthoslab()
Lattice.from_1d_representation()
Lattice.from_matrix()
Lattice.from_para()
Lattice.generate_matrix()
Lattice.generate_para()
Lattice.generate_point()
Lattice.get_diff()
Lattice.get_dofs()
Lattice.get_lengths()
Lattice.get_matrix()
Lattice.get_para()
Lattice.get_permutation_matrices()
Lattice.get_transformation_matrices()
Lattice.get_worst_angle()
Lattice.is_valid_matrix()
Lattice.mutate()
Lattice.optimize_multi()
Lattice.optimize_once()
Lattice.reset_matrix()
Lattice.scale()
Lattice.search_transformation()
Lattice.search_transformations()
Lattice.set_matrix()
Lattice.set_para()
Lattice.set_volume()
Lattice.standardize()
Lattice.swap_angle()
Lattice.swap_axis()
Lattice.transform()
Lattice.transform_multi()
gaussian()
generate_cellpara()
generate_cellpara_0D()
generate_cellpara_1D()
generate_cellpara_2D()
matrix2para()
para2matrix()
random_shear_matrix()
random_vector()
molecular_crystal
molecular_crystal.set_crystal()
molecular_crystal.set_lattice()
molecular_crystal.set_molecules()
molecular_crystal.set_orientations()
molecular_crystal.set_sites()
molecular_crystal.set_volume()
Box
Box.operate()
Orientation
Orientation.change_orientation()
Orientation.copy()
Orientation.get_Euler_angles()
Orientation.get_matrix()
Orientation.get_op()
Orientation.load_dict()
Orientation.random_orientation()
Orientation.reset_matrix()
Orientation.rotate_by_matrix()
Orientation.save_dict()
compare_mol_connectivity()
find_rotor_from_smile()
generate_molecules()
get_inertia_tensor()
has_non_aromatic_ring()
is_compatible_symmetry()
make_graph()
pyxtal_molecule
pyxtal_molecule.align()
pyxtal_molecule.apply_inversion()
pyxtal_molecule.copy()
pyxtal_molecule.get_box()
pyxtal_molecule.get_box_coordinates()
pyxtal_molecule.get_center()
pyxtal_molecule.get_coefs_matrix()
pyxtal_molecule.get_energy()
pyxtal_molecule.get_orientation()
pyxtal_molecule.get_orientations_in_wp()
pyxtal_molecule.get_orientations_in_wps()
pyxtal_molecule.get_principle_axes()
pyxtal_molecule.get_radius()
pyxtal_molecule.get_rmsd()
pyxtal_molecule.get_rmsd2()
pyxtal_molecule.get_symbols()
pyxtal_molecule.get_symmetry()
pyxtal_molecule.get_tols_matrix()
pyxtal_molecule.get_torsion_angles()
pyxtal_molecule.list_molecules()
pyxtal_molecule.load_str()
pyxtal_molecule.perturb_torsion()
pyxtal_molecule.rdkit_mol()
pyxtal_molecule.rdkit_mol_init()
pyxtal_molecule.relax()
pyxtal_molecule.reset_positions()
pyxtal_molecule.save_str()
pyxtal_molecule.set_labels()
pyxtal_molecule.set_torsion_angles()
pyxtal_molecule.show()
pyxtal_molecule.show_box()
pyxtal_molecule.swap_axis()
pyxtal_molecule.to_ase()
random()
reoriented_molecule()
OperationAnalyzer
OperationAnalyzer.affine_matrix
OperationAnalyzer.are_conjugate()
OperationAnalyzer.det
OperationAnalyzer.get_order()
OperationAnalyzer.is_conjugate()
OperationAnalyzer.m
OperationAnalyzer.op
OperationAnalyzer.order
OperationAnalyzer.rotation_order
OperationAnalyzer.tol
OperationAnalyzer.type
aa2matrix()
angle()
apply_ops()
apply_ops_diagonal()
are_equal()
check_distance()
check_images()
create_matrix()
distance()
distance_matrix()
distance_matrix_no_PBC()
filtered_coords()
filtered_coords_euclidean()
find_ids()
get_best_match()
get_inverse()
get_inverse_ops()
is_orthogonal()
rotate_vector()
verify_distances()
representation
representation.from_pyxtal()
representation.from_string()
representation.get_dist()
representation.same_smiles()
representation.to_pyxtal()
representation.to_standard_setting()
representation.to_string()
representation_atom
representation_atom.from_pyxtal()
representation_atom.to_array()
representation_atom.to_pyxtal()
representation_atom.to_standard_setting()
representation_atom.to_string()
find_mapping()
find_mapping_per_element()
find_xyz()
new_path()
new_structure()
search_G1()
search_G2()
supergroup
supergroup.calc_disps()
supergroup.get_coord_H()
supergroup.get_initial_mask()
supergroup.make_pyxtal_in_supergroup()
supergroup.make_pyxtals_in_subgroup()
supergroup.make_supergroup()
supergroup.print_detail()
supergroup.print_wp()
supergroup.search_supergroup()
supergroup.sort_solutions()
supergroup.symmetrize()
supergroup.symmetrize_dist()
supergroup.symmetrize_site_double_k()
supergroup.symmetrize_site_double_t()
supergroup.symmetrize_site_multi()
supergroup.symmetrize_site_single()
supergroups
supergroups.get_transformation()
supergroups.print_solutions()
supergroups.struc_along_path()
supergroups.write_cifs()
write_poscars()
Group
Group.add_k_transitions()
Group.cellsize()
Group.check_compatible()
Group.clean_lists()
Group.get_alternatives()
Group.get_ferroelectric_groups()
Group.get_free_axis()
Group.get_index_by_letter()
Group.get_lattice_dof()
Group.get_lists()
Group.get_lists_mol()
Group.get_max_k_subgroup()
Group.get_max_subgroup()
Group.get_max_subgroup_numbers()
Group.get_max_t_subgroup()
Group.get_min_supergroup()
Group.get_site_dof()
Group.get_splitters_from_relation()
Group.get_splitters_from_structure()
Group.get_symmetry_directions()
Group.get_valid_solutions()
Group.get_wp_by_letter()
Group.get_wp_list()
Group.get_wyckoff_position()
Group.get_wyckoff_position_from_xyz()
Group.is_valid_combination()
Group.list_groups()
Group.list_wyckoff_combinations()
Group.path_to_general_wp()
Group.path_to_subgroup()
Group.search_subgroup_paths()
Group.search_supergroup_paths()
Group.short_path_to_general_wp()
Hall
Wyckoff_position
Wyckoff_position.apply_ops()
Wyckoff_position.are_equivalent_pts()
Wyckoff_position.copy()
Wyckoff_position.distance_check()
Wyckoff_position.equivalent_set()
Wyckoff_position.from_dict()
Wyckoff_position.from_group_and_index()
Wyckoff_position.from_group_and_letter()
Wyckoff_position.from_index_quick()
Wyckoff_position.from_symops()
Wyckoff_position.from_symops_wo_group()
Wyckoff_position.gen_pos()
Wyckoff_position.get_all_positions()
Wyckoff_position.get_dof()
Wyckoff_position.get_euclidean_generator()
Wyckoff_position.get_euclidean_symmetries()
Wyckoff_position.get_free_xyzs()
Wyckoff_position.get_frozen_axis()
Wyckoff_position.get_hm_number()
Wyckoff_position.get_hm_symbol()
Wyckoff_position.get_label()
Wyckoff_position.get_ops_from_transformation()
Wyckoff_position.get_position_from_free_xyzs()
Wyckoff_position.get_site_symm_ops()
Wyckoff_position.get_site_symm_wo_translation()
Wyckoff_position.get_site_symmetry()
Wyckoff_position.get_site_symmetry_object()
Wyckoff_position.has_equivalent_ops()
Wyckoff_position.is_pure_translation()
Wyckoff_position.is_standard_setting()
Wyckoff_position.load_dict()
Wyckoff_position.merge()
Wyckoff_position.print_ops()
Wyckoff_position.process_ops()
Wyckoff_position.project()
Wyckoff_position.save_dict()
Wyckoff_position.search_all_generators()
Wyckoff_position.search_generator()
Wyckoff_position.search_generator_dist()
Wyckoff_position.set_euclidean()
Wyckoff_position.set_generators()
Wyckoff_position.set_ops()
Wyckoff_position.short_distances()
Wyckoff_position.swap_axis()
Wyckoff_position.transform_from_matrices()
Wyckoff_position.transform_from_matrix()
Wyckoff_position.update()
Wyckoff_position.update_hall()
Wyckoff_position.update_index()
abc2matrix()
are_equivalent_ops()
check_symmetry_and_dim()
check_wyckoff_position()
choose_wyckoff()
choose_wyckoff_mol()
find_axis_order()
get_all_polar_space_groups()
get_close_packed_groups()
get_generators()
get_pbc_and_lattice()
get_point_group()
get_symbol_and_number()
get_symmetry_directions()
get_symmetry_from_ops()
get_wyckoff_symmetry()
get_wyckoffs()
identity_ops()
index_from_letter()
jk_from_i()
letter_from_index()
op_transform()
op_translation()
organized_wyckoffs()
para2ferro()
rf()
search_cloest_wp()
site_symm()
site_symmetry
site_symmetry.get_highest_symmetry()
site_symmetry.get_name()
site_symmetry.ref_symmetry()
site_symmetry.set_full_hm_symbols()
site_symmetry.set_short_symbols()
site_symmetry.set_table()
site_symmetry.to_beautiful_matrix_representation()
site_symmetry.to_matrix_representation()
site_symmetry.to_one_hot()
site_symmetry.unique_symmetry()
swap_xyz_ops()
swap_xyz_string()
symmetry_element_from_axis()
transform_ops()
trim_ops()
Tol_matrix
Tol_matrix.from_file()
Tol_matrix.from_matrix()
Tol_matrix.from_radii()
Tol_matrix.from_single_value()
Tol_matrix.get_tol()
Tol_matrix.set_tol()
Tol_matrix.to_file()
addBox()
addlines()
display_atomic()
display_cluster()
display_crystals()
display_mol_crystals()
display_molecular()
display_molecular_site()
display_molecule()
display_molecules()
atom_site
atom_site.check_with_ws2()
atom_site.copy()
atom_site.encode()
atom_site.equivalent_set()
atom_site.get_disp()
atom_site.get_translations()
atom_site.load_dict()
atom_site.perturbate()
atom_site.save_dict()
atom_site.search_position()
atom_site.shift_by_swap()
atom_site.substitute_with_linear()
atom_site.substitute_with_single()
atom_site.swap_axis()
atom_site.to_mol_site()
atom_site.update()
mol_site
mol_site.encode()
mol_site.from_1D_dicts()
mol_site.get_coords_and_species()
mol_site.get_distances()
mol_site.get_dists_WP()
mol_site.get_dists_auto()
mol_site.get_ijk_lists()
mol_site.get_min_dist()
mol_site.get_mol_object()
mol_site.get_neighbors_auto()
mol_site.get_neighbors_wp2()
mol_site.is_valid_orientation()
mol_site.load_dict()
mol_site.perturbate()
mol_site.rotate()
mol_site.save_dict()
mol_site.short_dist()
mol_site.short_dist_with_wp2()
mol_site.show()
mol_site.show_molecule_in_box()
mol_site.to_1D_dicts()
mol_site.to_atom_site()
mol_site.translate()
mol_site.update()
mol_site.update_lattice()
mol_site.update_molecule()
mol_site.update_orientation()
in_lists()
wyckoff_split
wyckoff_split.check_orbits()
wyckoff_split.parse_wp2()
wyckoff_split.sort()
wyckoff_split.split_k()
wyckoff_split.split_t()
wyckoff_split.translation_generator()
Profile
Profile.get_profile()
Similarity
Similarity.cosineFunction()
Similarity.show()
Similarity.triangleFunction()
XRD
XRD.all_dhkl()
XRD.by_hkl()
XRD.draw_hkl()
XRD.get_profile()
XRD.get_unique_families()
XRD.intensity()
XRD.load()
XRD.plot_pxrd()
XRD.plotly_pxrd()
XRD.pxrdf()
XRD.save()
create_index()
get_all_intensity()
get_all_intensity_par()
get_intensity()
lorentzian()
mod_pseudo_voigt()
pseudo_voigt()
similarity_calculate()