Release Notes

v0.1.3 December 2022

General Notice

• This package is built using OpenEye-orionplatform==4.5.4, OpenEye-toolkits==2022.2.1, and OpenEye-Snowball==0.24.0.

Floe Updates

• Permeability - Run Permeability Simulation:

  • Added a warning in the floe description so users are aware of the potentially high cost of running the floe.

  • The default spot policy has been changed from Allowed to Preferred.

  • The default number of segments being processed per cube instance (item_count) has been changed from 2 to 1.

• Permeability - Analyze Permeability Simulation:

  • Added a plot to show the (symmetrized) free energy profile of the molecule along the progress coordinate z.

• Permeability - Calculate Auxiliary Coordinates (Optional):

  • The floe now calculates and displays three more auxiliary coordinates: the desolvation penalty of the drug molecule calculated by OEZAP Toolkit, the solvation energy, and the surface area of the drug molecule.

  • The overall cost of running the floe has been reduced through optimization of collecting and storing segment data.

Documentation Updates

• The tutorial has been updated to explain all 11 auxiliary coordinates that are currently available in the Permeability - Calculate Auxiliary Coordinates (Optional) floe.

Minor Changes

• Hid a few non-human readable fields on the output records of all floes from the “Analyze” page.

v0.1.2 September 2022

General Notice

• Fixed a critical bug in the dipole moment calculation in the Permeability - Calculate Auxiliary Coordinates (Optional) floe. Now the angle of the molecule with respect to the membrane normal should be calculated and displayed correctly.

v0.1.1 July 2022

General Notice

• This package is built using OpenEye-orionplatform==4.4.0, OpenEye-toolkits==2022.1.1, and OpenEye-Snowball==0.24.0.

• All floes have a new brief parameter and floe categories.

Floe Updates

• The Permeability - Analyze Permeability Simulation floe now calculates and displays a symmetrized probability distribution (inverted) of the molecule along z.

• The Permeability - Calculate Auxiliary Coordinates (Optional) floe now calculates and displays three more auxiliary coordinates: the number of waters near the target molecule, and the number of hydrogen bonds formed between the molecule and the waters when the molecule is the donor or the acceptor, respectively.

• The Permeability - Calculate Auxiliary Coordinates (Optional) floe now has a section to show the 2D structure of the molecule and the permeability coefficients including predicted and reference values if available.

• Added default output names for all permeability floes.

Documentation Updates

• All tutorials have been updated in accord with the floe classification rework.

Minor Changes

• Fixed an issue regarding running simulations on g5 instances.

• Removed the Simulation Step Size Unit field from the output record. Instead, the unit (picosecond, immutable) is added to Simulation Step Size as metadata.

• Added the temperature unit (Kelvin, immutable) to the Temperature field of the output record as metadata.

• Several bug & typo fixes.

v0.1.0 April 2022

General Notice

• This is the first release of OpenEye Permeability Floes.

• The package uses OpenEye-WESTSnowball as well as OpenEye-orionplatform.

• The packages contains the following floes, which are useful for modeling passive small molecule membrane permeability.

  • Permeability - Run Permeability Simulation: A floe to run a permeability simulation.

  • Permeability - Analyze Permeability Simulation: A floe to analyze a permeability simulation.

  • Permeability - Calculate Auxiliary Coordinates (Optional): A floe to calculate the auxiliary coordinates and show how the probability is distributed over them.