Index _ | A | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | W | Z _ __init__() (HammingSpace method) (MotifProductionSpace method) (MotifSpace method) (TimeRGSpace method) (UnstructuredTimeDomain method) A add_zebra_fluctuation_to_motif_vector() (in module src.obj.motif_vector) alphabet (HammingSpace property) (MotifHyphenSpace property) (MotifProductionSpace property) (MotifSpace property) alphabet() (in module src.get.alphabet) analyze_segment() (in module src.infer.dissociation_constant) are_compatible_motif_breakage_trajectories() (in module src.obj.motif_breakage_trajectory) are_compatible_motif_breakage_trajectory_ensembles() (in module src.obj.motif_breakage_trajectory_ensemble) are_compatible_motif_production_trajectories() (in module src.obj.motif_production_trajectory) are_compatible_motif_production_trajectory_ensembles() (in module src.obj.motif_production_trajectory_ensemble) are_compatible_motif_trajectories() (in module src.obj.motif_trajectory) are_compatible_motif_trajectory_ensembles() (in module src.obj.motif_trajectory_ensemble) are_compatible_motif_vectors() (in module src.obj.motif_vector) are_compatible_times_vectors() (in module src.obj.times_vector) are_compatible_timespaces() (in module src.domains.time_space) C calculate_concentration_of_a_single_particle() (in module src.plot.motif_concentrations) calculate_effective_ligation_rate_for_tetramer_creation() (in module src.infer.effective_ligation_rates_from_parameters) categories_indices() (in module src.obj.motif_vector) category_indices() (in module src.obj.motif_vector) collisions_from_motif_concentration_trajectory_and_collision_rate_constants() (in module src.infer.collisions) collisions_from_motif_concentration_trajectory_array_and_collision_rate_constants_array() (in module src.infer.collisions) colorbar_example() (in module src.plot.colors) compute_logc_diff_extended_end_motifs() (in module src.infer.fourmer_production_rates) compute_logc_diff_extending_beginning_motifs() (in module src.infer.fourmer_production_rates) compute_logc_diff_produced_motifs() (in module src.infer.fourmer_production_rates) compute_motif_extensions() (in module src.infer.fourmer_production_rates) compute_total_extension_rates() (in module src.infer.fourmer_production_rates) compute_words() (in module src.plot.motif_concentrations) (in module src.plot.motif_production_rates) config() (in module src.read.config) continuations_trajectories() (in module src.plot.motif_concentrations) convert_dimers_to_tetramers() (in module src.obj.motif_vector) convert_homogeneous_dimers_to_zebra_dimers() (in module src.obj.motif_vector) create_directory_if_not_already_existing() (in module src.utils.save) create_directory_path_if_not_already_existing() (in module src.utils.save) create_motif_production_trajectory_ensemble_path() (in module src.utils.save) create_strand_trajectory_ensemble_path() (in module src.utils.save) create_trajectory_ensemble_path() (in module src.utils.save) D discretized_onset_of_growth() (in module src.infer.onset) dissociation_constant_from_strand_reactor_parameters() (in module src.infer.dissociation_constant) E effective_ligation_rates_from_parameters() (in module src.infer.effective_ligation_rates_from_parameters) energy_continuous_block() (in module src.infer.dissociation_constant) entropy() (in module src.plot.entropy) extract_initial_motif_vector_from_motif_trajectory() (in module src.obj.motif_trajectory) F fourmer_breakage_rates() (in module src.infer.fourmer_breakage_rates) fourmer_trajectory_from_rate_constants() (in module src.infer.fourmer_trajectory_from_rate_constants) G get_overall_length_distribution() (in module src.read.strand_length_distribution) give_shape() (in module src.infer.dissociation_constant) green_colorbar() (in module src.plot.colors) greenish_colorbar() (in module src.plot.colors) H HammingSpace (class in src.domains.hamming_space) hybridization_bond_category() (in module src.infer.dissociation_constant) I individual_motif_zebraness() (in module src.infer.zebraness) isinstance_motifbreakagetrajectory() (in module src.obj.motif_breakage_trajectory) isinstance_motifbreakagetrajectoryensemble() (in module src.obj.motif_breakage_trajectory_ensemble) isinstance_motifbreakagevector() (in module src.obj.motif_breakage_vector) isinstance_motifproductiontrajectory() (in module src.obj.motif_production_trajectory) isinstance_motifproductiontrajectoryensemble() (in module src.obj.motif_production_trajectory_ensemble) isinstance_motifproductionvector() (in module src.obj.motif_production_vector) isinstance_motiftrajectory() (in module src.obj.motif_trajectory) isinstance_motiftrajectoryensemble() (in module src.obj.motif_trajectory_ensemble) isinstance_motifvector() (in module src.obj.motif_vector) isinstance_times_vector() (in module src.obj.times_vector) isinstance_timespace() (in module src.domains.time_space) isunit() (in module src.obj.units) isunits_unit() (in module src.obj.units) L left_reactant_logconcentration() (in module src.infer.motif_production_rates) ligation_rate_constant_from_strand_reactor_parameters() (in module src.infer.dissociation_constant) ligation_spot_formations_from_motifs_array() (in module src.infer.collisions) load_motif_production_trajectory() (in module src.obj.motif_production_trajectory) load_motif_production_trajectory_ensemble() (in module src.obj.motif_production_trajectory_ensemble) load_motif_production_vector() (in module src.obj.motif_production_vector) load_motif_trajectory() (in module src.obj.motif_trajectory) load_motif_trajectory_ensemble() (in module src.obj.motif_trajectory_ensemble) load_motif_vector() (in module src.obj.motif_vector) M make() (MotifHyphenSpace static method) (MotifProductionSpace static method) (MotifSpace static method) make_hamming_dct() (in module src.domains.motif_space) make_hyphen_dct() (in module src.domains.motif_hyphen_space) make_motif_production_dct() (in module src.domains.motif_production_space) make_unit() (in module src.obj.units) makeExtentiveMotifBreakageSpace() (in module src.domains.extentive_motif_breakage_space) mass_correction_rates() (in module src.infer.fourmer_mass_correction) maximum_ligation_window_length (MotifProductionSpace property) mean_length() (in module src.infer.mean_length) module src src.domains src.domains.extentive_motif_breakage_space src.domains.hamming_space src.domains.motif_breakage_space src.domains.motif_hyphen_space src.domains.motif_production_space src.domains.motif_space src.domains.time_space src.domains.trajectory_space src.get src.get.alphabet src.get.motif_breakage_rate_constants src.get.motif_production_rate_constants src.get.strand_length_distribution src.get.strand_motifs_productions_trajectory src.get.strand_motifs_productions_trajectory_ensemble src.get.strand_motifs_trajectory src.get.strand_motifs_trajectory_ensemble src.get.strand_reactor_parameters src.infer src.infer.collisions src.infer.dissociation_constant src.infer.effective_ligation_rates_from_parameters src.infer.fourmer_breakage_rates src.infer.fourmer_mass_correction src.infer.fourmer_production_rates src.infer.fourmer_trajectory_from_rate_constants src.infer.mean_length src.infer.motif_breakage_rate_constants_from_strand_reactor_parameters src.infer.motif_concentration_trajectory src.infer.motif_concentration_vector src.infer.motif_production_rate_constants_extension_matrix src.infer.motif_production_rate_constants_from_strand_reactor_parameters src.infer.motif_production_rates src.infer.motif_production_transition_kernel src.infer.onset src.infer.total_mass src.infer.zebraness src.obj src.obj.motif_breakage_trajectory src.obj.motif_breakage_trajectory_ensemble src.obj.motif_breakage_vector src.obj.motif_concentration_vector src.obj.motif_number_vector src.obj.motif_production_trajectory src.obj.motif_production_trajectory_ensemble src.obj.motif_production_vector src.obj.motif_trajectory src.obj.motif_trajectory_ensemble src.obj.motif_vector src.obj.times_vector src.obj.units src.plot src.plot.colors src.plot.entropy src.plot.motif_concentrations src.plot.motif_production_rates src.plot.motif_trajectory_analysis src.plot.zebraness src.read src.read.config src.read.strand_length_distribution src.read.strand_motifs_productions_trajectory src.read.strand_motifs_productions_trajectory_ensemble src.read.strand_motifs_trajectory src.read.strand_motifs_trajectory_ensemble src.read.strand_reactor_nucleotides src.read.strand_reactor_parameters src.utils src.utils.logc src.utils.manage_strand_reactor_files src.utils.save src.utils.split_config src.utils.transform_vectors_to_fields motif_breakage_rate_constants_from_strand_reactor_parameters() (in module src.get.motif_breakage_rate_constants) (in module src.infer.motif_breakage_rate_constants_from_strand_reactor_parameters) motif_concentration_trajectory_from_motif_number_trajectory() (in module src.infer.motif_concentration_trajectory) motif_concentration_vector_from_motif_number_vector() (in module src.infer.motif_concentration_vector) motif_entropy() (in module src.plot.entropy) motif_production_rate_constants_extension_matrix() (in module src.infer.motif_production_rate_constants_extension_matrix) motif_production_rate_constants_from_strand_reactor_parameters() (in module src.get.motif_production_rate_constants) (in module src.infer.motif_production_rate_constants_from_strand_reactor_parameters) motif_production_rates() (in module src.plot.motif_production_rates) motif_production_rates_array_from_motif_production_counts() (in module src.infer.motif_production_rates) motif_production_rates_array_from_motif_production_rate_constants_array_and_motif_concentrations_array() (in module src.infer.motif_production_rates) motif_production_transition_kernel_from_motif_production_rate_constants_array() (in module src.infer.motif_production_transition_kernel) motif_production_transition_kernel_matrix() (in module src.infer.motif_production_transition_kernel) motif_trajectories() (in module src.plot.motif_concentrations) motif_trajectory_analysis() (in module src.plot.motif_trajectory_analysis) MotifBreakageSpace (class in src.domains.motif_breakage_space) MotifBreakageTrajectory() (in module src.obj.motif_breakage_trajectory) MotifBreakageTrajectoryEnsemble() (in module src.obj.motif_breakage_trajectory_ensemble) MotifBreakageVector() (in module src.obj.motif_breakage_vector) MotifConcentrationVector() (in module src.obj.motif_concentration_vector) MotifHyphenSpace (class in src.domains.motif_hyphen_space) motiflength (MotifHyphenSpace property) (MotifProductionSpace property) (MotifSpace property) MotifNumberVector() (in module src.obj.motif_number_vector) MotifProductionSpace (class in src.domains.motif_production_space) MotifProductionTrajectory() (in module src.obj.motif_production_trajectory) MotifProductionTrajectoryEnsemble() (in module src.obj.motif_production_trajectory_ensemble) MotifProductionVector() (in module src.obj.motif_production_vector) motifs_collisions_array_from_motifs_array() (in module src.infer.collisions) MotifSpace (class in src.domains.motif_space) MotifTrajectory() (in module src.obj.motif_trajectory) MotifTrajectoryEnsemble() (in module src.obj.motif_trajectory_ensemble) MotifVector() (in module src.obj.motif_vector) N nest_mean() (in module src.plot.zebraness) number_of_letters (MotifHyphenSpace property) (MotifProductionSpace property) (MotifSpace property) O onset_of_growth() (in module src.infer.onset) onset_of_growth_from_strand_trajectory_parameters() (in module src.infer.onset) P print_hybridization_site_categories() (in module src.infer.motif_production_transition_kernel) R read_txt() (in module src.utils.manage_strand_reactor_files) S save() (in module src.utils.save) save_motif_production_trajectory() (in module src.obj.motif_production_trajectory) save_motif_production_trajectory_ensemble() (in module src.obj.motif_production_trajectory_ensemble) save_motif_production_vector() (in module src.obj.motif_production_vector) save_motif_trajectory() (in module src.obj.motif_trajectory) save_motif_trajectory_ensemble() (in module src.obj.motif_trajectory_ensemble) save_motif_vector() (in module src.obj.motif_vector) segment_category() (in module src.infer.dissociation_constant) separate_hybridization_and_ligation_parameters() (in module src.infer.effective_ligation_rates_from_parameters) sort_by_length() (in module src.plot.motif_production_rates) split_config() (in module src.utils.split_config) src module src.domains module src.domains.extentive_motif_breakage_space module src.domains.hamming_space module src.domains.motif_breakage_space module src.domains.motif_hyphen_space module src.domains.motif_production_space module src.domains.motif_space module src.domains.time_space module src.domains.trajectory_space module src.get module src.get.alphabet module src.get.motif_breakage_rate_constants module src.get.motif_production_rate_constants module src.get.strand_length_distribution module src.get.strand_motifs_productions_trajectory module src.get.strand_motifs_productions_trajectory_ensemble module src.get.strand_motifs_trajectory module src.get.strand_motifs_trajectory_ensemble module src.get.strand_reactor_parameters module src.infer module src.infer.collisions module src.infer.dissociation_constant module src.infer.effective_ligation_rates_from_parameters module src.infer.fourmer_breakage_rates module src.infer.fourmer_mass_correction module src.infer.fourmer_production_rates module src.infer.fourmer_trajectory_from_rate_constants module src.infer.mean_length module src.infer.motif_breakage_rate_constants_from_strand_reactor_parameters module src.infer.motif_concentration_trajectory module src.infer.motif_concentration_vector module src.infer.motif_production_rate_constants_extension_matrix module src.infer.motif_production_rate_constants_from_strand_reactor_parameters module src.infer.motif_production_rates module src.infer.motif_production_transition_kernel module src.infer.onset module src.infer.total_mass module src.infer.zebraness module src.obj module src.obj.motif_breakage_trajectory module src.obj.motif_breakage_trajectory_ensemble module src.obj.motif_breakage_vector module src.obj.motif_concentration_vector module src.obj.motif_number_vector module src.obj.motif_production_trajectory module src.obj.motif_production_trajectory_ensemble module src.obj.motif_production_vector module src.obj.motif_trajectory module src.obj.motif_trajectory_ensemble module src.obj.motif_vector module src.obj.times_vector module src.obj.units module src.plot module src.plot.colors module src.plot.entropy module src.plot.motif_concentrations module src.plot.motif_production_rates module src.plot.motif_trajectory_analysis module src.plot.zebraness module src.read module src.read.config module src.read.strand_length_distribution module src.read.strand_motifs_productions_trajectory module src.read.strand_motifs_productions_trajectory_ensemble module src.read.strand_motifs_trajectory module src.read.strand_motifs_trajectory_ensemble module src.read.strand_reactor_nucleotides module src.read.strand_reactor_parameters module src.utils module src.utils.logc module src.utils.manage_strand_reactor_files module src.utils.save module src.utils.split_config module src.utils.transform_vectors_to_fields module standard_colorbar() (in module src.plot.colors) steps_and_times_and_complexes_from_complexes_txt() (in module src.read.strand_motifs_trajectory) steps_and_times_and_sequence_trajectory_from_complexes_txt() (in module src.read.strand_motifs_trajectory) strand_length_distribution() (in module src.get.strand_length_distribution) (in module src.read.strand_length_distribution) strand_motifs_productions_trajectory() (in module src.get.strand_motifs_productions_trajectory) (in module src.read.strand_motifs_productions_trajectory) strand_motifs_productions_trajectory_ensemble() (in module src.get.strand_motifs_productions_trajectory_ensemble) (in module src.read.strand_motifs_productions_trajectory_ensemble) strand_motifs_trajectory() (in module src.get.strand_motifs_trajectory) (in module src.read.strand_motifs_trajectory) strand_motifs_trajectory_ensemble() (in module src.get.strand_motifs_trajectory_ensemble) (in module src.read.strand_motifs_trajectory_ensemble) strand_reactor_nucleotides() (in module src.read.strand_reactor_nucleotides) strand_reactor_parameters() (in module src.get.strand_reactor_parameters) (in module src.read.strand_reactor_parameters) symbol_config() (in module src.read.config) system_level_motif_zebraness() (in module src.infer.zebraness) (in module src.plot.zebraness) T template_averaged_dissociation_constant_from_strand_reactor_parameters() (in module src.infer.dissociation_constant) TimeRGSpace (class in src.domains.time_space) TimeSpace() (in module src.domains.time_space) TimesVector() (in module src.obj.times_vector) total_mass() (in module src.infer.total_mass) total_mass_of_motif_concentration_trajectory_array() (in module src.infer.total_mass) total_mass_trajectory() (in module src.infer.total_mass) TrajectorySpace() (in module src.domains.trajectory_space) transform_dict_to_unit() (in module src.obj.units) transform_dicts_to_field() (in module src.utils.transform_vectors_to_fields) transform_execution_time_txt_to_list() (in module src.utils.manage_strand_reactor_files) transform_unit_to_dict() (in module src.obj.units) transform_unit_to_str() (in module src.obj.units) transform_vectors_to_field() (in module src.utils.transform_vectors_to_fields) U units (MotifHyphenSpace property) (MotifSpace property) (TimeRGSpace property) (UnstructuredTimeDomain property) UnstructuredTimeDomain (class in src.domains.time_space) unzero() (in module src.utils.logc) W wordlength (HammingSpace property) Z zebraness() (in module src.plot.zebraness)