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

Description

This Floe calculates a pre-defined set of auxiliary coordinates for simulated permeation trajectories using collections generated by the Permeability - Run Permeability Simulation Floe. Do not run this Floe on collections while data is being generated by the simulation Floes.

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

Promoted Parameters

Title in user interface (promoted name)

Inputs

Collection (in): Collections to use as input to a floe

  • Required

  • Type: collection_source

Outputs

Output Collection (collection): Name of the collection to create

  • 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

Advanced Parameters

Start Iteration (first_iter): The start iteration of WE segments to be extracted. Leave empty to extract from the first iteration that is available.

  • Type: integer

End Iteration (last_iter): The end iteration of WE segments to be extracted. Leave empty to stop extracting at the last iteration that is available.

  • Type: integer

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 Analysis (rerun): Rerun analysis even if data is already present.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Log Verbosity (verbosity): verbose level

  • Type: string

  • Default: debug

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