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’]