Permeability - Analyze Permeability Simulation¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Hit to Lead/Properties/Permeability
Solution-based/Small Molecule Lead-opt/ADME & Tox/Permeability
Product-based/Molecular Dynamics/WESTPA
Product-based/Molecular Dynamics/OpenMM
Task-based/Molecular Dynamics
Task-based/ADME & Tox Assessment
Description
The Floe analyzes data generated by the Permeability - Run Permeability Simulation Floe and calculates the permeability coefficient based on the probability fluxes simulated using the Weighted Ensemble enhanced sampling strategy. Do not run this Floe on collections while data is being generated by the simulation Floes.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input Collection (collection_in): Collections to use as input to a floe
Required
Type: collection_source
Outputs
Analysis Output (dataset_out): Output dataset to write to
Required
Type: dataset_out
Default: Permeability Analysis
Output Collection (collection_out): Name of the collection to create
Required
Type: collection_sink
Default: Permeability Analysis Data
Floe Report (report): The title for the output floe report.
Required
Type: string
Default: Permeability Analysis Report
Failure Report (fail_report): Output report to generate upon failure
Type: string
Default: Permeability Analysis Failure Report
Permeability Parameters
Start Iteration (Rate Estimation) (first_iter): Starting iteration to be used for calculating the fluxes. Leave empty to start from the first iteration that is available.
Type: integer
Default: 300
End Iteration (Rate Estimation) (last_iter): Last iteration to be used for calculating the fluxes. Leave empty to stop at the last iteration that is available.
Type: integer
Advanced Parameters
Block Size (Rate Estimation) (rate_block_size): The number of iterations that is either used as the interval for cumulative calculation or the block size for blocked calculation.
Required
Type: integer
Default: 1
Block Size (Probability Distribution) (fe_block_size): The number of iterations to be taken average to calculate the free energy profile. If left empty, all iterations will be used.
Type: integer
Rate Calculation Mode (mode): How to calculate time evolution of rate estimates.
Required
Type: string
Default: cumulative
Choices: [‘cumulative’, ‘blocked’]
Bayesian Bootstrap (bayesian): Apply Bayesian Bootstrap for estimating the confident regions
Type: boolean
Default: False
Choices: [True, False]
Rate Evolution (evolution): Calculate the full evolution of the rate (True) or just the final value (False)
Type: boolean
Default: True
Choices: [True, False]
Compartment Size Scaling Factor (compartment_size_scale): The scaling factor for the (donor) compartment size (i.e., (simulation box length - membrane width)/2).
Type: decimal
Default: 1.0
Miscellaneous Parameters
Rerun Analysis (rerun): Rerun analysis even if data is already present.
Required
Type: boolean
Default: True
Choices: [True, False]
Trace Permeation Paths (traj): Trace the history of recycled walkers.
Type: boolean
Default: True
Choices: [True, False]
Log Verbosity (verbosity): verbose level
Type: string
Default: debug
Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]
Additional Information
Reference Permeability Coefficient (Logarithmic, Optional) (ref_perm): 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). Leave the parameter empty to not change it.
Type: string
Reference Permeability Coefficient Source (Optional) (ref_src): 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. Leave the parameter empty to not change it.
Type: string
Identification Number for the Molecule (Optional) (mol_id): This can be any identification number (e.g., CHEMBL ID) associated with the molecule. Leave the parameter empty to not change it.
Type: string
Molecule Name (Optional) (mol_name): The name for the molecule. Leave the parameter empty to not change it.
Type: string