src package

Subpackages

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

Module contents