Index A | B | C | D | G | I | M | O | R | S | U | V | W A Angle (class in atomaton.models) atomaton.analyze module atomaton.models module atomaton.visualize module atomaton.write_lammps_files module Atoms (class in atomaton.models) B bin_data() (in module atomaton.analyze) (in module atomaton.visualize) bind_from_ase() (atomaton.models.Atoms class method) bind_from_file() (atomaton.models.Atoms class method) Bond (class in atomaton.models) build_supercell() (atomaton.models.Crystal method) (atomaton.models.SimulationBox method) C calculate_angles() (atomaton.models.Atoms method) calculate_bonds() (atomaton.models.Atoms method) calculate_bounding_box() (atomaton.models.Atoms method) calculate_dihedrals_and_impropers() (atomaton.models.Atoms method) center_in_cell() (atomaton.models.Atoms method) center_on_position() (atomaton.models.Atoms method) convert_images_to_gif() (in module atomaton.visualize) create_extended_cell() (in module atomaton.analyze) create_extended_cell_minimal() (atomaton.models.Atoms method) (in module atomaton.analyze) create_from_atoms() (atomaton.models.SimulationBox class method) Crystal (class in atomaton.models) D delete_atoms() (atomaton.models.Atoms method) draw_atoms() (in module atomaton.visualize) draw_bonds() (in module atomaton.visualize) draw_unit_cell() (in module atomaton.visualize) G get_angle_properties() (in module atomaton.analyze) get_bond_properties() (in module atomaton.analyze) get_bonds_metadata() (atomaton.models.Atoms method) get_bonds_on_atom() (in module atomaton.analyze) get_cart_to_frac_matrix() (atomaton.models.UnitCell method) get_center_of_cell() (atomaton.models.UnitCell method) get_center_of_positions() (atomaton.models.Atoms method) get_corners() (atomaton.models.UnitCell method) get_frac_to_cart_matrix() (atomaton.models.UnitCell method) get_lammps_box_parameters() (in module atomaton.write_lammps_files) get_masses() (in module atomaton.write_lammps_files) guess_angles() (in module atomaton.analyze) guess_bonds() (in module atomaton.analyze) guess_dihedrals_and_impropers() (in module atomaton.analyze) I Improper (class in atomaton.models) insert_atoms() (atomaton.models.Atoms method) (atomaton.models.SimulationBox method) M module atomaton.analyze atomaton.models atomaton.visualize atomaton.write_lammps_files O overlap_at_point() (atomaton.models.Atoms method) (atomaton.models.SimulationBox method) R remove_atoms_outside_cell() (in module atomaton.analyze) remove_duplicate_atoms() (in module atomaton.analyze) S shift_atoms() (atomaton.models.Atoms method) SimulationBox (class in atomaton.models) split_by_property() (in module atomaton.analyze) U UnitCell (class in atomaton.models) V view() (atomaton.models.Atoms method) (atomaton.models.SimulationBox method) view_structure() (in module atomaton.visualize) W wrap_atoms_outside_cell() (in module atomaton.analyze) write_lammps_data_file() (in module atomaton.write_lammps_files)