Permeability - Calculate Auxiliary Coordinates (Optional)

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/OpenMM

  • Product-based/Molecular Dynamics/WESTPA

  • Task-based/Molecular Dynamics

  • Task-based/ADME & Tox Assessment


This floe calculates a pre-defined set of auxiliary coordinates for simulated permeation trajectories. The floe takes a dataset generated by Permeability - Run Permeability Simulation but also requires the associated collection to be accessible.

Check the documentation for a full list of supported auxiliary coordinates.

Promoted Parameters

Title in user interface (promoted name)


Input Dataset (in): The dataset(s) to read records from

  • Required

  • Type: data_source


Output Dataset (out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Permeability Auxiliary

Output Collection (collection): Name of the collection in which to store the simulation output.

  • Required

  • Type: collection_sink

  • Default: Permeability Auxiliary Data

Floe Report (report): The title for the output floe report.

  • Required

  • Type: string

  • Default: Permeability Auxiliary Report

Failure Report (fail_report): Output report to generate upon failure

  • Type: string

  • Default: Permeability Auxiliary Failure Report

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

Miscellaneous Parameters

Rerun (rerun): Rerun the calculations even if the result is already present on the input record

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Clean Up (cleanup): Clean up the original west.h5 data.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Log Verbosity (verbosity): verbose level

  • Type: string

  • Default: debug

  • Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]