Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __init__() (smc_lammps.generate.default_parameters.Parameters method) (smc_lammps.generate.generator.AtomGroup method) (smc_lammps.generate.generator.AtomType method) (smc_lammps.generate.generator.BAI method) (smc_lammps.generate.generator.BAI_Type method) (smc_lammps.generate.generator.Generator method) (smc_lammps.generate.generator.Generator.DynamicCoeffs method) (smc_lammps.generate.generator.PairWise method) (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration.PostProcessParameters method) (smc_lammps.generate.structures.dna.dna.DnaParameters method) (smc_lammps.generate.structures.dna.dna.Doubled method) (smc_lammps.generate.structures.dna.dna.Folded method) (smc_lammps.generate.structures.dna.dna.InteractionParameters method) (smc_lammps.generate.structures.dna.dna.Line method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.RightAngle method) (smc_lammps.generate.structures.dna.dna.Safety method) (smc_lammps.generate.structures.dna.dna.Tether method) (smc_lammps.generate.structures.dna.dna.Tether.Gold method) (smc_lammps.generate.structures.dna.dna.Tether.Wall method) (smc_lammps.generate.structures.polymer.Polymer method) (smc_lammps.generate.structures.smc.smc.SMC method) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos method) (smc_lammps.post_process.smc_perspective.Atom method) (smc_lammps.reader.lammps_data.Box method) (smc_lammps.reader.lammps_data.LammpsData method) (smc_lammps.reader.lammps_data.Plane method) (smc_lammps.reader.parser.Parser method) (smc_lammps.run.TaskDone method) _index (smc_lammps.generate.generator.BAI_Type attribute) _set_up_atom_group_map() (in module smc_lammps.generate.generator.Generator) A add() (smc_lammps.generate.structures.polymer.Polymer method) add_atom_groups() (smc_lammps.generate.generator.Generator method) add_bead_to_dna() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) add_interaction() (smc_lammps.generate.generator.PairWise method) add_interactions() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.Tether method) (smc_lammps.generate.structures.dna.dna.Tether.Gold method) (smc_lammps.generate.structures.dna.dna.Tether.Obstacle method) add_repel_interactions() (smc_lammps.generate.structures.smc.smc.SMC method) add_RNA_polymerase (smc_lammps.generate.default_parameters.Parameters attribute) add_side_site (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) add_stopper_bead (smc_lammps.generate.default_parameters.Parameters attribute) add_tagged_atom_groups() (smc_lammps.generate.structures.polymer.Polymer method) add_tagged_atoms() (smc_lammps.generate.structures.polymer.Polymer method) add_tether_interactions() (smc_lammps.generate.structures.dna.dna.Tether method) AdvancedObstacleSafety (class in smc_lammps.generate.structures.dna.dna) all_dna_groups (smc_lammps.generate.structures.dna.dna.DnaConfiguration property) all_indices_list() (smc_lammps.generate.structures.polymer.Polymer method) all_tests() (in module smc_lammps.generate.generator) ANGLE (smc_lammps.generate.generator.BAI_Kind attribute) angle (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) angles (smc_lammps.generate.structures.dna.dna.Tether attribute) apply() (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos method) arm_length (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) arms_angle_ATP (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) arms_stiffness (smc_lammps.generate.default_parameters.Parameters attribute) asymmetry_stiffness (smc_lammps.generate.default_parameters.Parameters attribute) Atom (class in smc_lammps.post_process.smc_perspective) ATOM_FORMAT (smc_lammps.reader.parser.Parser attribute) atom_group_map (smc_lammps.generate.generator.Generator attribute) atom_type (smc_lammps.generate.generator.AtomGroup attribute) AtomGroup (class in smc_lammps.generate.generator) AtomIdentifier (in module smc_lammps.generate.generator) atomIds_to_LAMMPS_ids() (in module smc_lammps.generate.lammps.util) atoms (smc_lammps.generate.generator.BAI attribute) AtomType (class in smc_lammps.generate.generator) AtomType.UnusedIndex attach() (in module smc_lammps.generate.structures.structure_creator) attach_chain() (in module smc_lammps.generate.structures.structure_creator) average_steps_per_cycle() (smc_lammps.generate.default_parameters.Parameters method) B BAI (class in smc_lammps.generate.generator) BAI_Kind (class in smc_lammps.generate.generator) BAI_Type (class in smc_lammps.generate.generator) bais (smc_lammps.generate.generator.Generator attribute) BOND (smc_lammps.generate.generator.BAI_Kind attribute) bond (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) bonds (smc_lammps.generate.structures.dna.dna.Tether attribute) Box (class in smc_lammps.reader.lammps_data) box_width (smc_lammps.generate.generator.Generator attribute) bridge_width (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) C change_dna_stiffness() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) charge (smc_lammps.generate.generator.AtomGroup attribute) charge_override (smc_lammps.generate.generator.Generator attribute) check_charges() (smc_lammps.generate.generator.Generator method) check_length() (in module smc_lammps.generate.structures.dna.dna_creator) class_decorator_factory() (in module smc_lammps.generate.structures.dna.dna) clean() (in module smc_lammps.run) coefficients (smc_lammps.generate.generator.BAI_Type attribute) combine_by_ids() (smc_lammps.reader.lammps_data.LammpsData method) convert_ratio() (smc_lammps.generate.structures.polymer.Polymer method) convert_units_distance() (in module smc_lammps.post_process.average_plot) convert_units_time() (in module smc_lammps.post_process.average_plot) COORD_TYPE (in module smc_lammps.generate.generator) create_box() (smc_lammps.reader.lammps_data.LammpsData method) create_dna_polymer() (smc_lammps.generate.structures.dna.dna.DnaParameters method) create_figure_raw() (in module smc_lammps.post_process.average_plot) create_figure_units() (in module smc_lammps.post_process.average_plot) create_files() (in module smc_lammps.post_process.process_displacement) create_from_pairwise() (smc_lammps.generate.generator.Generator.DynamicCoeffs class method) create_perspective_file() (in module smc_lammps.run) create_phase() (in module smc_lammps.generate.util) create_phase_wrapper() (in module smc_lammps.generate.util) create_plot() (in module smc_lammps.post_process.process_displacement) create_tether() (smc_lammps.generate.structures.dna.dna.Tether class method) cutoff4 (smc_lammps.generate.default_parameters.Parameters attribute) cutoff5 (smc_lammps.generate.default_parameters.Parameters attribute) cutoff6 (smc_lammps.generate.default_parameters.Parameters attribute) cycles (smc_lammps.generate.default_parameters.Parameters attribute) D default (smc_lammps.generate.generator.PairWise attribute) delete_outside_box() (smc_lammps.reader.lammps_data.LammpsData method) delete_side_of_plane() (smc_lammps.reader.lammps_data.LammpsData method) diameter (smc_lammps.generate.default_parameters.Parameters attribute) distance() (smc_lammps.reader.lammps_data.Plane method) DNA_bond_length (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) dna_config (smc_lammps.generate.default_parameters.Parameters attribute) dna_indices_list (smc_lammps.generate.structures.dna.dna.DnaConfiguration.PostProcessParameters attribute) dna_indices_list_get_all_dna() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) dna_indices_list_get_dna_from_to() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) dna_indices_list_get_dna_to() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) DNA_mass (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) dna_tether_id (smc_lammps.generate.structures.dna.dna.Tether attribute) DnaConfiguration (class in smc_lammps.generate.structures.dna.dna) DnaConfiguration.PostProcessParameters (class in smc_lammps.generate.structures.dna.dna) DnaParameters (class in smc_lammps.generate.structures.dna.dna) Doubled (class in smc_lammps.generate.structures.dna.dna) E elbow_attraction (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) elbow_spacing (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) elbows_stiffness (smc_lammps.generate.default_parameters.Parameters attribute) empty() (smc_lammps.reader.lammps_data.LammpsData class method) end_points (smc_lammps.generate.structures.dna.dna.DnaConfiguration.PostProcessParameters attribute) epsilon3 (smc_lammps.generate.default_parameters.Parameters attribute) epsilon4 (smc_lammps.generate.default_parameters.Parameters attribute) epsilon5 (smc_lammps.generate.default_parameters.Parameters attribute) epsilon6 (smc_lammps.generate.default_parameters.Parameters attribute) epsilon_DNA_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) epsilon_SMC_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) epsilon_upper_site_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) execute() (in module smc_lammps.run) F file (smc_lammps.reader.parser.Parser attribute) fill_between_runtime_lines() (in module smc_lammps.post_process.matplotlib.draw) filter() (smc_lammps.reader.lammps_data.LammpsData method) filter_by_types() (smc_lammps.reader.lammps_data.LammpsData method) find_simulation_base_directory() (in module smc_lammps.run) first_id() (smc_lammps.generate.structures.polymer.Polymer method) Folded (class in smc_lammps.generate.structures.dna.dna) folding_angle_APO (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) folding_angle_ATP (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC attribute) folding_stiffness (smc_lammps.generate.default_parameters.Parameters attribute) force (smc_lammps.generate.default_parameters.Parameters attribute) freeze_indices (smc_lammps.generate.structures.dna.dna.DnaConfiguration.PostProcessParameters attribute) full_list() (smc_lammps.generate.structures.polymer.Polymer method) full_list_length() (smc_lammps.generate.structures.polymer.Polymer method) G gamma (smc_lammps.generate.default_parameters.Parameters attribute) generate() (in module smc_lammps.run) Generator (class in smc_lammps.generate.generator) Generator.DynamicCoeffs (class in smc_lammps.generate.generator) get_absolute_index() (smc_lammps.generate.structures.polymer.Polymer method) get_all_atom_types() (smc_lammps.generate.generator.Generator method) get_all_BAI_styles() (smc_lammps.generate.generator.Generator method) get_all_groups() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.Tether method) (smc_lammps.generate.structures.dna.dna.Tether.Gold method) (smc_lammps.generate.structures.dna.dna.Tether.Obstacle method) (smc_lammps.generate.structures.dna.dna.Tether.Wall method) get_all_interaction_pairs() (smc_lammps.generate.generator.PairWise method) get_all_interactions() (smc_lammps.generate.generator.PairWise method) get_all_types() (smc_lammps.generate.generator.Generator method) get_amounts() (smc_lammps.generate.generator.Generator method) get_angles() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.Tether method) (smc_lammps.generate.structures.smc.smc.SMC method) get_arms() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_array() (smc_lammps.reader.parser.Parser static method) get_atom_index() (smc_lammps.generate.generator.Generator method) get_atom_style() (smc_lammps.generate.generator.Generator method) get_atom_style_command() (smc_lammps.generate.generator.Generator method) get_atoms_header() (smc_lammps.generate.generator.Generator method) get_averages() (in module smc_lammps.post_process.average_plot) get_BAI_coeffs_header() (smc_lammps.generate.generator.Generator method) get_bai_dict_by_type() (smc_lammps.generate.generator.Generator method) get_BAI_header() (smc_lammps.generate.generator.Generator static method) get_BAI_style_command_name() (smc_lammps.generate.generator.Generator static method) get_BAI_styles_command() (smc_lammps.generate.generator.Generator method) get_bead_distances() (in module smc_lammps.post_process.process_displacement) get_best_match_dna_bead_in_smc() (in module smc_lammps.post_process.process_displacement) get_bonds() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.Tether method) (smc_lammps.generate.structures.smc.smc.SMC method) get_bridge() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_circle_segment() (in module smc_lammps.generate.structures.structure_creator) get_circle_segment_unit_radius() (in module smc_lammps.generate.structures.structure_creator) get_closest() (in module smc_lammps.generate.util) get_colored_axis_segments() (in module smc_lammps.post_process.matplotlib.draw) get_cum_runtimes() (in module smc_lammps.post_process.util) get_data_raw() (in module smc_lammps.post_process.average_plot) get_def_dynamically() (in module smc_lammps.generate.lammps.parameterfile) get_dna_config() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety class method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration class method) (smc_lammps.generate.structures.dna.dna.Doubled class method) (smc_lammps.generate.structures.dna.dna.Folded class method) (smc_lammps.generate.structures.dna.dna.Line class method) (smc_lammps.generate.structures.dna.dna.Obstacle class method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety class method) (smc_lammps.generate.structures.dna.dna.RightAngle class method) (smc_lammps.generate.structures.dna.dna.Safety class method) get_dna_coordinates() (in module smc_lammps.generate.structures.dna.dna_creator) get_dna_coordinates_advanced_safety_belt() (in module smc_lammps.generate.structures.dna.dna_creator) get_dna_coordinates_advanced_safety_belt_plus_loop() (in module smc_lammps.generate.structures.dna.dna_creator) get_dna_coordinates_doubled() (in module smc_lammps.generate.structures.dna.dna_creator) get_dna_coordinates_safety_belt() (in module smc_lammps.generate.structures.dna.dna_creator) get_dna_coordinates_straight() (in module smc_lammps.generate.structures.dna.dna_creator) get_dna_coordinates_twist() (in module smc_lammps.generate.structures.dna.dna_creator) get_equal_def() (in module smc_lammps.generate.lammps.parameterfile) get_gold_mass() (smc_lammps.generate.structures.dna.dna.Tether static method) get_groups() (smc_lammps.generate.structures.smc.smc.SMC method) get_heads_kleisin() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_hybrid_or_single_style() (smc_lammps.generate.generator.Generator method) get_id_from_list_index() (smc_lammps.generate.structures.polymer.Polymer method) get_impropers() (smc_lammps.generate.structures.smc.smc.SMC method) get_index_def() (in module smc_lammps.generate.lammps.parameterfile) get_indices_array() (in module smc_lammps.post_process.util) get_interaction_sites() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_interpolated() (in module smc_lammps.generate.structures.structure_creator) get_lammps_args_list() (in module smc_lammps.run) get_mass_per_atom() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_molecule_ids() (smc_lammps.generate.structures.smc.smc.SMC method) get_moving_average() (in module smc_lammps.post_process.util) get_msd_obstacle() (in module smc_lammps.post_process.process_displacement) get_next() (smc_lammps.generate.generator.MoleculeId class method) get_normal_direction() (in module smc_lammps.reader.lammps_data) get_npz_files_from_args() (in module smc_lammps.post_process.average_plot) get_obstacle() (smc_lammps.generate.structures.dna.dna.Tether class method) get_opposite() (smc_lammps.reader.lammps_data.Plane.Side class method) get_parameters() (in module smc_lammps.generate.util) get_parser() (in module smc_lammps.run) get_percent_id() (smc_lammps.generate.structures.polymer.Polymer method) get_position_from_index() (smc_lammps.reader.lammps_data.LammpsData method) get_post_process_parameters() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.Doubled method) (smc_lammps.generate.structures.dna.dna.Folded method) (smc_lammps.generate.structures.dna.dna.Line method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.RightAngle method) (smc_lammps.generate.structures.dna.dna.Safety method) get_post_processing_parameters() (in module smc_lammps.post_process.util) get_project_root() (in module smc_lammps.generate.util) get_repulsive_groups() (smc_lammps.generate.structures.smc.smc.SMC method) get_runtime_lines() (in module smc_lammps.post_process.matplotlib.draw) get_scaled_cum_runtimes() (in module smc_lammps.post_process.util) get_scaling() (in module smc_lammps.post_process.util) get_script_bai_command_name() (smc_lammps.generate.generator.Generator.DynamicCoeffs static method) get_site_cycle_segments() (in module smc_lammps.post_process.util) get_smc() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_stopper_ids() (smc_lammps.generate.structures.dna.dna.AdvancedObstacleSafety method) (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) (smc_lammps.generate.structures.dna.dna.Doubled method) (smc_lammps.generate.structures.dna.dna.Folded method) (smc_lammps.generate.structures.dna.dna.Line method) (smc_lammps.generate.structures.dna.dna.Obstacle method) (smc_lammps.generate.structures.dna.dna.ObstacleSafety method) (smc_lammps.generate.structures.dna.dna.RightAngle method) (smc_lammps.generate.structures.dna.dna.Safety method) get_straight_segment() (in module smc_lammps.generate.structures.structure_creator) get_string() (smc_lammps.generate.generator.BAI_Type method) get_string_def() (in module smc_lammps.generate.lammps.parameterfile) get_timer_accumulator() (in module smc_lammps.reader.util) get_times() (in module smc_lammps.generate.lammps.runtimes) get_times_with_max_steps() (in module smc_lammps.generate.lammps.runtimes) get_toroidal_hinge() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator method) get_total_atoms() (smc_lammps.generate.generator.Generator method) get_universe_def() (in module smc_lammps.generate.lammps.parameterfile) get_version() (in module smc_lammps.run) H handle_dna_bead() (in module smc_lammps.post_process.process_displacement) handle_end_points() (smc_lammps.generate.structures.dna.dna.Tether method) handle_negative_index() (smc_lammps.generate.structures.polymer.Polymer method) has_side_site() (smc_lammps.generate.structures.smc.smc.SMC method) has_toroidal_hinge() (smc_lammps.generate.structures.smc.smc.SMC method) header (smc_lammps.generate.generator.PairWise attribute) highs (smc_lammps.reader.lammps_data.Box attribute) hinge_opening (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) hinge_radius (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc.SMC property) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) hybrid_styles (smc_lammps.generate.generator.Generator attribute) I ID_TYPE (in module smc_lammps.reader.lammps_data) IdArray (in module smc_lammps.reader.lammps_data) ids (smc_lammps.reader.lammps_data.LammpsData attribute) IMPROPER (smc_lammps.generate.generator.BAI_Kind attribute) index (smc_lammps.generate.generator.AtomType property) (smc_lammps.generate.generator.BAI_Type property) indices (smc_lammps.generate.generator.BAI_Type attribute) indices_list_from_to() (smc_lammps.generate.structures.polymer.Polymer method) indices_list_from_to_percent() (smc_lammps.generate.structures.polymer.Polymer method) indices_list_to() (smc_lammps.generate.structures.polymer.Polymer method) indices_list_to_percent() (smc_lammps.generate.structures.polymer.Polymer method) initialize() (in module smc_lammps.run) INSIDE (smc_lammps.reader.lammps_data.Plane.Side attribute) InteractionParameters (class in smc_lammps.generate.structures.dna.dna) is_in_box() (smc_lammps.reader.lammps_data.Box method) is_on_side() (smc_lammps.reader.lammps_data.Plane method) is_sorted() (in module smc_lammps.post_process.process_displacement) iter() (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos method) K k_align_site (smc_lammps.generate.structures.smc.smc.SMC attribute) k_arm (smc_lammps.generate.structures.smc.smc.SMC attribute) k_asymmetry (smc_lammps.generate.structures.smc.smc.SMC attribute) k_bond (smc_lammps.generate.structures.smc.smc.SMC attribute) k_bond_DNA_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) k_elbow (smc_lammps.generate.structures.smc.smc.SMC attribute) k_fold (smc_lammps.generate.structures.smc.smc.SMC attribute) k_hinge (smc_lammps.generate.structures.smc.smc.SMC attribute) kB (smc_lammps.generate.default_parameters.Parameters attribute) keep_every() (in module smc_lammps.run) keep_every_n() (in module smc_lammps.post_process.util) kind (smc_lammps.generate.generator.BAI_Type attribute) kleisin_radius (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) L LammpsData (class in smc_lammps.reader.lammps_data) last_id() (smc_lammps.generate.structures.polymer.Polymer method) length_lookup() (smc_lammps.generate.generator.BAI_Kind class method) Line (class in smc_lammps.generate.structures.dna.dna) linear() (in module smc_lammps.post_process.average_plot) linear_fit() (in module smc_lammps.post_process.average_plot) list_to_space_str() (in module smc_lammps.generate.lammps.parameterfile) loop (smc_lammps.generate.default_parameters.Parameters attribute) lower_site_h (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) lower_site_v (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) lows (smc_lammps.reader.lammps_data.Box attribute) M main() (in module smc_lammps) (in module smc_lammps.generate.generator) (in module smc_lammps.post_process.process_displacement) (in module smc_lammps.post_process.smc_perspective) (in module smc_lammps.run) map() (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos method) map_to_atom_id() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) max_bond_length (smc_lammps.generate.structures.smc.smc.SMC attribute) MAX_ITER (smc_lammps.run.MaxIterationExceeded attribute) max_steps (smc_lammps.generate.default_parameters.Parameters attribute) MaxIterationExceeded merge() (in module smc_lammps.run) merge_lammpstrj() (in module smc_lammps.post_process.util) middle_site_h (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) middle_site_v (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) mode (smc_lammps.reader.parser.Parser attribute) module smc_lammps smc_lammps.console smc_lammps.generate smc_lammps.generate.default_parameters smc_lammps.generate.generator smc_lammps.generate.lammps smc_lammps.generate.lammps.parameterfile smc_lammps.generate.lammps.runtimes smc_lammps.generate.lammps.util smc_lammps.generate.parameters_template smc_lammps.generate.structures smc_lammps.generate.structures.dna smc_lammps.generate.structures.dna.dna smc_lammps.generate.structures.dna.dna_creator smc_lammps.generate.structures.polymer smc_lammps.generate.structures.smc smc_lammps.generate.structures.smc.smc smc_lammps.generate.structures.smc.smc_creator smc_lammps.generate.structures.structure_creator smc_lammps.generate.util smc_lammps.post_process smc_lammps.post_process.average_plot smc_lammps.post_process.matplotlib smc_lammps.post_process.matplotlib.draw smc_lammps.post_process.process_displacement smc_lammps.post_process.smc_perspective smc_lammps.post_process.types smc_lammps.post_process.util smc_lammps.reader smc_lammps.reader.lammps_data smc_lammps.reader.parser smc_lammps.reader.util smc_lammps.run mol_DNA (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) molecule_index (smc_lammps.generate.generator.AtomGroup attribute) molecule_override (smc_lammps.generate.generator.Generator attribute) MoleculeId (class in smc_lammps.generate.generator) move() (smc_lammps.generate.structures.dna.dna.Tether method) (smc_lammps.generate.structures.dna.dna.Tether.Gold method) (smc_lammps.generate.structures.dna.dna.Tether.Obstacle method) (smc_lammps.generate.structures.dna.dna.Tether.Wall method) (smc_lammps.generate.structures.polymer.Polymer method) move_all_atoms() (smc_lammps.generate.generator.Generator method) N N (smc_lammps.generate.default_parameters.Parameters attribute) n (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.generator.AtomGroup property) nDNA (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) next_step() (smc_lammps.reader.parser.Parser method) next_step_raw() (smc_lammps.reader.parser.Parser method) non_random_steps (smc_lammps.generate.default_parameters.Parameters attribute) Nx3Array (in module smc_lammps.generate.generator) O Obstacle (class in smc_lammps.generate.structures.dna.dna) obstacle (smc_lammps.generate.structures.dna.dna.Tether attribute) ObstacleSafety (class in smc_lammps.generate.structures.dna.dna) output_steps (smc_lammps.generate.default_parameters.Parameters attribute) OUTSIDE (smc_lammps.reader.lammps_data.Plane.Side attribute) P pair_in_inter() (smc_lammps.generate.generator.PairWise method) pair_interactions (smc_lammps.generate.generator.Generator attribute) pairs (smc_lammps.generate.generator.PairWise attribute) PairWise (class in smc_lammps.generate.generator) Parameters (class in smc_lammps.generate.default_parameters) parse() (in module smc_lammps.run) parse_with_double_dash() (in module smc_lammps.run) Parser (class in smc_lammps.reader.parser) Parser.EndOfLammpsFile perform_run() (in module smc_lammps.run) Plane (class in smc_lammps.reader.lammps_data) Plane.Side (class in smc_lammps.reader.lammps_data) Polymer (class in smc_lammps.generate.structures.polymer) polymer (smc_lammps.generate.structures.dna.dna.Tether attribute) polymer_angle_type (smc_lammps.generate.generator.AtomGroup attribute) polymer_bond_type (smc_lammps.generate.generator.AtomGroup attribute) pos (smc_lammps.generate.structures.smc.smc.SMC attribute) pos_from_id() (in module smc_lammps.generate.util) positions (smc_lammps.generate.generator.AtomGroup attribute) (smc_lammps.reader.lammps_data.LammpsData attribute) post_process() (in module smc_lammps.run) prepend_or_empty() (in module smc_lammps.generate.lammps.parameterfile) process() (in module smc_lammps.post_process.average_plot) Q quiet_print() (in module smc_lammps.run) qzip() (in module smc_lammps.post_process.util) R r_arm_dl (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_arm_dr (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_arm_ul (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_arm_ur (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_ATP (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_hinge (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_kleisin (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_lower_site (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_middle_site (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_side_site (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) r_upper_site (smc_lammps.generate.structures.smc.smc_creator.SMC_Pos attribute) random_shift (smc_lammps.generate.generator.Generator attribute) rcut_DNA_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) rcut_lower_site_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) rcut_SMC_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) read_lammpstrj() (in module smc_lammps.post_process.smc_perspective) remove_outside_planar_n_gon() (in module smc_lammps.post_process.process_displacement) restart_run() (in module smc_lammps.run) RightAngle (class in smc_lammps.generate.structures.dna.dna) rigid_hinge (smc_lammps.generate.default_parameters.Parameters attribute) rigid_transform_3D() (in module smc_lammps.post_process.smc_perspective) RNA_polymerase_size (smc_lammps.generate.default_parameters.Parameters attribute) RNA_polymerase_type (smc_lammps.generate.default_parameters.Parameters attribute) rounding (smc_lammps.post_process.smc_perspective.Atom attribute) run() (in module smc_lammps.run) run_and_handle_error() (in module smc_lammps.run) runs (smc_lammps.generate.default_parameters.Parameters attribute) S Safety (class in smc_lammps.generate.structures.dna.dna) scale_indices() (in module smc_lammps.post_process.util) scale_times() (in module smc_lammps.post_process.util) seed (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) set_parameters() (smc_lammps.generate.structures.dna.dna.DnaConfiguration class method) set_smc() (smc_lammps.generate.structures.dna.dna.DnaConfiguration class method) set_system_size() (smc_lammps.generate.generator.Generator method) shielded_site_template() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator static method) sigma (smc_lammps.generate.default_parameters.Parameters attribute) sigma_DNA_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) sigma_SMC_DNA (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) sigma_upper_site_DNA (smc_lammps.generate.structures.dna.dna.InteractionParameters attribute) site_cycle_period (smc_lammps.generate.default_parameters.Parameters attribute) site_cycle_when (smc_lammps.generate.default_parameters.Parameters attribute) site_stiffness (smc_lammps.generate.default_parameters.Parameters attribute) site_toggle_delay (smc_lammps.generate.default_parameters.Parameters attribute) skip_to_atoms() (smc_lammps.reader.parser.Parser method) small_noise (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) SMC (class in smc_lammps.generate.structures.smc.smc) SMC_Creator (class in smc_lammps.generate.structures.smc.smc_creator) smc_force (smc_lammps.generate.default_parameters.Parameters attribute) smc_lammps module smc_lammps.console module smc_lammps.generate module smc_lammps.generate.default_parameters module smc_lammps.generate.generator module smc_lammps.generate.lammps module smc_lammps.generate.lammps.parameterfile module smc_lammps.generate.lammps.runtimes module smc_lammps.generate.lammps.util module smc_lammps.generate.parameters_template module smc_lammps.generate.structures module smc_lammps.generate.structures.dna module smc_lammps.generate.structures.dna.dna module smc_lammps.generate.structures.dna.dna_creator module smc_lammps.generate.structures.polymer module smc_lammps.generate.structures.smc module smc_lammps.generate.structures.smc.smc module smc_lammps.generate.structures.smc.smc_creator module smc_lammps.generate.structures.structure_creator module smc_lammps.generate.util module smc_lammps.post_process module smc_lammps.post_process.average_plot module smc_lammps.post_process.matplotlib module smc_lammps.post_process.matplotlib.draw module smc_lammps.post_process.process_displacement module smc_lammps.post_process.smc_perspective module smc_lammps.post_process.types module smc_lammps.post_process.util module smc_lammps.reader module smc_lammps.reader.lammps_data module smc_lammps.reader.parser module smc_lammps.reader.util module smc_lammps.run module SMC_Pos (class in smc_lammps.generate.structures.smc.smc_creator) SMC_spacing (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) spaced_beads_custom_stiffness (smc_lammps.generate.default_parameters.Parameters attribute) spaced_beads_full_dna (smc_lammps.generate.default_parameters.Parameters attribute) spaced_beads_interval (smc_lammps.generate.default_parameters.Parameters attribute) spaced_beads_size (smc_lammps.generate.default_parameters.Parameters attribute) spaced_beads_smc_clearance (smc_lammps.generate.default_parameters.Parameters attribute) spaced_beads_type (smc_lammps.generate.default_parameters.Parameters attribute) split() (smc_lammps.generate.structures.polymer.Polymer method) split_data() (smc_lammps.reader.parser.Parser static method) split_into_index_groups() (in module smc_lammps.post_process.process_displacement) ssangle (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) start_visualize_script() (in module smc_lammps.run) steps_ADP (smc_lammps.generate.default_parameters.Parameters attribute) steps_APO (smc_lammps.generate.default_parameters.Parameters attribute) steps_ATP (smc_lammps.generate.default_parameters.Parameters attribute) str_to_config() (smc_lammps.generate.structures.dna.dna.DnaConfiguration static method) strand_concat() (smc_lammps.generate.structures.dna.dna.DnaConfiguration static method) StrandId (in module smc_lammps.generate.structures.dna.dna) stretching_forces_array (smc_lammps.generate.structures.dna.dna.DnaConfiguration.PostProcessParameters attribute) style (smc_lammps.generate.generator.BAI_Type attribute) T T (smc_lammps.generate.default_parameters.Parameters attribute) t_arms_heads (smc_lammps.generate.structures.smc.smc.SMC attribute) t_atp (smc_lammps.generate.structures.smc.smc.SMC attribute) t_hinge (smc_lammps.generate.structures.smc.smc.SMC attribute) t_kleisin (smc_lammps.generate.structures.smc.smc.SMC attribute) t_lower_site (smc_lammps.generate.structures.smc.smc.SMC attribute) t_middle_site (smc_lammps.generate.structures.smc.smc.SMC attribute) t_ref_site (smc_lammps.generate.structures.smc.smc.SMC attribute) t_shield (smc_lammps.generate.structures.smc.smc.SMC attribute) t_side_site (smc_lammps.generate.structures.smc.smc.SMC attribute) t_upper_site (smc_lammps.generate.structures.smc.smc.SMC attribute) TaskDone (class in smc_lammps.run) template (smc_lammps.generate.generator.PairWise attribute) test_simple_atoms() (in module smc_lammps.generate.generator) test_simple_atoms_polymer() (in module smc_lammps.generate.generator) test_with_bonds() (in module smc_lammps.generate.generator) test_with_pairs() (in module smc_lammps.generate.generator) Tether (class in smc_lammps.generate.structures.dna.dna) Tether.Gold (class in smc_lammps.generate.structures.dna.dna) Tether.Obstacle (class in smc_lammps.generate.structures.dna.dna) Tether.Wall (class in smc_lammps.generate.structures.dna.dna) time_it (smc_lammps.reader.parser.Parser attribute) timer() (in module smc_lammps.reader.util) timestep (smc_lammps.generate.default_parameters.Parameters attribute) to_string() (smc_lammps.post_process.smc_perspective.Atom method) transform_atoms() (in module smc_lammps.post_process.smc_perspective) transpose_rotate_transpose() (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator static method) type (smc_lammps.generate.structures.dna.dna.DnaParameters attribute) TYPE_TYPE (in module smc_lammps.reader.lammps_data) TypeArray (in module smc_lammps.reader.lammps_data) types (smc_lammps.reader.lammps_data.LammpsData attribute) U update_tether_bond() (smc_lammps.generate.structures.dna.dna.DnaConfiguration method) upper_site_h (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) upper_site_v (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) use_charges (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.generator.Generator attribute) use_rigid_hinge (smc_lammps.generate.structures.smc.smc.SMC attribute) use_toroidal_hinge (smc_lammps.generate.default_parameters.Parameters attribute) (smc_lammps.generate.structures.smc.smc_creator.SMC_Creator attribute) V visualize() (in module smc_lammps.run) visualize_datafile() (in module smc_lammps.run) visualize_follow() (in module smc_lammps.run) W warn() (in module smc_lammps.console) with_tether() (in module smc_lammps.generate.structures.dna.dna) write() (in module smc_lammps.post_process.process_displacement) (smc_lammps.generate.generator.PairWise method) write_amounts() (smc_lammps.generate.generator.Generator method) write_atoms() (smc_lammps.generate.generator.Generator method) write_bai() (smc_lammps.generate.generator.Generator method) write_BAI_coeffs() (smc_lammps.generate.generator.Generator method) write_coeffs() (smc_lammps.generate.generator.Generator method) write_full() (smc_lammps.generate.generator.Generator method) write_header() (smc_lammps.generate.generator.Generator method) write_if_non_zero() (in module smc_lammps.generate.generator) write_lammpstrj() (in module smc_lammps.post_process.smc_perspective) write_masses() (smc_lammps.generate.generator.Generator method) write_pair_interactions() (smc_lammps.generate.generator.Generator method) write_positions_and_bonds() (smc_lammps.generate.generator.Generator method) write_script_bai_coeffs() (smc_lammps.generate.generator.Generator.DynamicCoeffs method) write_system_size() (smc_lammps.generate.generator.Generator method) write_types() (smc_lammps.generate.generator.Generator method) X xyz (smc_lammps.post_process.smc_perspective.Atom attribute)