Permeability - Analyze Permeability SimulationΒΆ

Analyzes data generated by the permeability floe.

Promoted Parameters

  • ref_perm (string) : This can be a value determined by an experiment or determined by other methods as a reference for comparison. The reference value should have a unit of cm/s and then converted to the log scale. An error can be included in a pair of parentheses, if available. Example input: -6.0 (0.1)
  • ref_src (string) : Source of the reference permeability coefficient, which can be the type of the experiment or the name of the method that used to determine permeability
  • mol_id (string) : This can be any identification number (e.g., CHEMBL ID) associated with the molecule
  • in (data_source) : The dataset(s) to read records from
  • cleanup (boolean) : Clean up intermediate data. The output record can still be used for resuming a simulation or analysis
    Default: True
  • deep_cleanup (boolean) : Remove WESTPA data to save space for permeability results. WARNING: if this option is turned on, the output record cannot be used by the analysis floe.
    Default: False
  • verbosity (string) : The level of logging verbosity
    Default: debug
    Choices: error, warning, info, debug, ddebug
  • average_window (integer) : Number of iterations to generate averaged distributions for calculating their Kullback-Leibler divergence
    Default: 10 Min: 1
  • n_bins (integer) : Number of bins for plotting density distribution
    Default: 100 Min: 10
  • red (boolean) : Whether or not to plot the permeability estimated using the Rate from Event Durations (RED) scheme (if available)
    Default: False
  • out (dataset_out) : Output dataset to write to
  • bayesian (boolean) : Whether or not to apply Bayesian Bootstrap for estimating the confident regions
    Default: False
  • evolution (boolean) : Whether or not to calculate the full evolution of the rate (True) or just the final value (False)
    Default: True
  • fail (dataset_out) : Output dataset to write to in case of errors
  • rerun (boolean) : Whether or not to rerun w_ipa even if data is already present
    Default: True
  • mode (string) : How to calculate time evolution of rate estimates.
    Default: cumulative
    Choices: cumulative, blocked
  • window (integer) : The number of iterations that is either used as the interval for cumulative calculation or the block size for blocked calculation.
    Default: 1 Min: 1
  • compartment_size_scale (decimal) : The scaling factor for the (donor) compartment size (i.e., (simulation box length - membrane width)/2).
    Default: 1.0 Max: 2.0

Extra Required Parameters

  • Final State (string) : The label for the final state
  • Initial State (string) : The label for the initial state
  • State Boundaries (string) : Boundaries of states in terms of progress coordinates
  • States (json) : Progress coordinates of states
  • Final State (string) : The label for the final state
  • Initial State (string) : The label for the initial state