v0.1.3 December 2022¶
This package is built using
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
The default number of segments being processed per cube instance (
item_count) has been changed from
Added a plot to show the (symmetrized) free energy profile of the molecule along the progress coordinate z.
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.
The tutorial has been updated to explain all 11 auxiliary coordinates that are currently available in the Permeability - Calculate Auxiliary Coordinates (Optional) floe.
Hid a few non-human readable fields on the output records of all floes from the “Analyze” page.
v0.1.2 September 2022¶
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¶
This package is built using
All floes have a new brief parameter and floe categories.
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.
All tutorials have been updated in accord with the floe classification rework.
Fixed an issue regarding running simulations on g5 instances.
Simulation Step Size Unitfield from the output record. Instead, the unit (picosecond, immutable) is added to
Simulation Step Sizeas metadata.
Added the temperature unit (Kelvin, immutable) to the
Temperaturefield of the output record as metadata.
Several bug & typo fixes.
v0.1.0 April 2022¶
This is the first release of OpenEye Permeability Floes.
The package uses
OpenEye-WESTSnowballas well as
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.