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

Calculates the auxiliary coordinates and shows how the probability is distributed over them. The floe takes a dataset output by the permeability simulation floe but also requires the associated collection to be accessible. Check the documentation for [a full list of supported auxiliary coordinates](https://docs.eyesopen.com/floe/modules/permeability-floe/docs/source/tutorials/small_mol_permeability.html#run-the-auxiliary-coordinates-calculation-floe).

Promoted Parameters

Title in user interface (promoted name)

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

Clean Up (cleanup): Whether or not to clean up the original west.h5 data.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Rerun (rerun): Whether or not to rerun the calculations even if the result is already present on the input record

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Log Verbosity (verbosity): The level of logging verbosity.

  • Type: string

  • Default: debug

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