pydna_epbd package

Subpackages

• pydna_epbd.monitors package
  • Submodules
  • pydna_epbd.monitors.all_monitors module
    • Monitors
      • Monitors.collect_at_iter()
      • Monitors.collect_at_step()
      • Monitors.collect_at_step_preheat()
      • Monitors.update_state()
  • pydna_epbd.monitors.bubble_monitor module
    • BubbleMonitor
      • BubbleMonitor.MAX_BUB_ELEM
      • BubbleMonitor.MIN_BUB_ELEM
      • BubbleMonitor.TRESHOLDS
      • BubbleMonitor.TRESHOLD_SIZE
      • BubbleMonitor.collect_at_step()
  • pydna_epbd.monitors.coord_monitor module
    • CoordMonitor
      • CoordMonitor.collect_at_step()
  • pydna_epbd.monitors.coord_monitor_verbose module
  • pydna_epbd.monitors.energy_monitor module
    • EnergyMonitor
      • EnergyMonitor.KB
      • EnergyMonitor.collect_at_step()
      • EnergyMonitor.collect_at_step_preheat()
  • pydna_epbd.monitors.flipping_monitor module
    • FlippingMonitor
      • FlippingMonitor.FLIP_CUTOFF
      • FlippingMonitor.collect_at_step()
  • pydna_epbd.monitors.flipping_monitor_verbose module
    • FlippingMonitorVerbose
      • FlippingMonitorVerbose.FLIP_CUTOFF
      • FlippingMonitorVerbose.FLIP_SIZES
      • FlippingMonitorVerbose.collect_at_step()
  • pydna_epbd.monitors.melting_and_fraction_many_monitor module
    • MeltingAndFractionManyMonitor
      • MeltingAndFractionManyMonitor.MELT_FRACTION_SIZES
      • MeltingAndFractionManyMonitor.MELT_FRACTION_TIME_STEPS
      • MeltingAndFractionManyMonitor.MELT_FRACTION_TRESHOLDS
      • MeltingAndFractionManyMonitor.collect_at_step()
  • pydna_epbd.monitors.melting_and_fraction_monitor module
    • MeltingAndFractionMonitor
      • MeltingAndFractionMonitor.MELT_FRACTION_TRESHOLD
      • MeltingAndFractionMonitor.collect_at_iter()
      • MeltingAndFractionMonitor.collect_at_step()
  • pydna_epbd.monitors.monitor module
    • Monitor
      • Monitor.collect_at_iter()
      • Monitor.collect_at_step()
      • Monitor.collect_at_step_preheat()
      • Monitor.collect_at_temp()
      • Monitor.update_state()
  • Module contents
• pydna_epbd.simulation package
  • Submodules
  • pydna_epbd.simulation.aggregate_outputs_and_write module
    • aggregate_outputs_for_single_temp()
  • pydna_epbd.simulation.constants module
  • pydna_epbd.simulation.dna module
    • DNA
      • DNA.reset()
  • pydna_epbd.simulation.mc_simulation module
    • Simulation
      • Simulation.execute()
      • Simulation.init_temp()
    • random()
  • pydna_epbd.simulation.simulation_steps module
    • run_sequences()
    • run_single_iteration()
  • Module contents

Submodules

pydna_epbd.configs module

class pydna_epbd.configs.InputConfigs(temperature: float, sequences: list, outputs_dir: str, n_iterations: int, n_preheating_steps: int, n_steps_after_preheating: int, n_nodes: int, save_full=False, save_runtime=False)

Bases: object

This initializes an input configuration object to use throughout the simulation process.

Parameters:

• temperature (float) – In Kelvin scale.

• sequences (list) – List of tuples of sequences in [(“output_dir”, “seq_id”, “seq”)] format

• outputs_dir (str) – The directory path to save the simulation outputs.

• n_iterations (int) – The number of independent iterations with different initial conditions.

• n_preheating_steps (int) – The number of preheating steps.

• n_steps_after_preheating (int) – The number of post preheating steps.

• n_nodes (int) – The computing nodes where the input sequences are divided equally for faster execution of bulk sequences.

• save_full (bool, optional) – Whether or not save the full outputs of the simulation. If True, first axis denotes n_iterations. Defaults to False.

• save_runtime (bool, optional) – Whether or not save the runtime for each sequence. Defaults to False.

pydna_epbd.input_reader module

pydna_epbd.input_reader.read_all_sequences(input_seqs_dir, is_first_col_id, flanks, outputs_dir)

Read all sequences for the simulation.

Parameters:

• input_seqs_dir (str) – Directory that contains files containing DNA sequences.

• is_first_col_id (bool) – Whether or not the first column of the sequence containing file determines sequence id.

• flanks (str) – Flanks are added at both sides of all input sequences.

• outputs_dir (str) – The output directory for saving simulation outputs.

Returns:

A list containing all sequences in the input directory.

Return type:

list

pydna_epbd.input_reader.read_configurations(configuration_filepath)

Read the configs from the input configuration file.

Parameters:

configuration_filepath (str) – The configurations needed to run MCMC simulations. The structure of the configs are given in the Readme file.

Returns:

The class containing specific format for running the simulations.

Return type:

InputConfigs

pydna_epbd.input_reader.read_sequences_from_a_file(input_seqs_dir, filename_with_ext, is_first_col_id, flanks, outputs_dir)

Read DNA sequences from one input file. This also creates output directories for saving simulation outputs.

Parameters:

• input_seqs_dir (str) – Directory that contains DNA sequences file.

• filename_with_ext (str) – Filename with extension.

• is_first_col_id (bool) – Whether or not the first column of the sequence containing file determines sequence id.

• flanks (str) – Flanks are added at both sides of all input sequences.

• outputs_dir (str) – The output directory for saving simulation outputs.

Returns:

A list of tuples containing all sequences in the input sequence file with seq-id and output directory. If seq-id is not present, 1-indexed incrementally generated seq-id will be attached. Format: [(“seq_output_dir”, “seq_id”, “seq”)]

Return type:

list

pydna_epbd.pickle_utils module

pydna_epbd.pickle_utils.create_necessary_directories()

pydna_epbd.pickle_utils.get_dimension(a)

given a list (of lists) compute the dimension

pydna_epbd.pickle_utils.load_pickle(path)

pydna_epbd.pickle_utils.save_as_pickle(data, path)

pydna_epbd.run module

pydna_epbd.run.parse_args()

pydna_epbd.version module

Module contents