Release Notes

v0.1.6 July 2024

This package is built using OpenEye-orionplatform==6.2.0, OpenEye-toolkits==2024.1.1, OpenEye-Snowball==0.28.0, and OpenEye-orionmdcore==2.4.2.

A bug has been fixed in the Permeability - Analyze Permeability Simulation Floe which caused the error ‘Namespace’ object has no attribute ‘west_step_size_field’.
Weighted ensemble protein sampling data storage has been significantly refactored, which reduces the overall size by half and supports faster data find and read.
The Run a Weighted Ensemble MD Simulation Floe now generates and stores data in a V2 ShardCollection.
The outputs have been changed from the Run a Weighted Ensemble MD Simulation Floe. Now the output dataset contains multiple records (one record per iteration) and only contains summary statistics for the simulation. All simulation data (e.g., weighted ensemble data, MD trajectories, simulation files) are stored in the output shard collection. The collection is now self-contained and required as input for downstream analysis Floes.
The Permeability - Continue Permeability Simulation (Optional) Floe now takes the collection generated by the Permeability - Run Permeability Simulation Floe as the input to resume the weighted ensemble protein sampling simulation.
Both the Permeability - Analyze Permeability Simulation and Permeability - Calculate Auxiliary Coordinates (Optional) Floes now take the collection generated by the Permeability - Run Permeability Simulation Floe as input.

This package is built using OpenEye-orionplatform==5.1.1, OpenEye-toolkits==2023.1.0, and OpenEye-Snowball==0.26.0.

Fixed a bug in the Permeability - Analyze Permeability Simulation floe which caused the error “‘Namespace’ object has no attribute ‘west_step_size_field’”.

This package is built using OpenEye-orionplatform==5.1.0, OpenEye-toolkits==2023.1.0, and OpenEye-Snowball==0.26.0.

Permeability - Run Permeability Simulation:
- The floe now generates and updates one record for the entire course of the simulation, as opposed to generating one record per iteration.
- The job will be properly marked “Failed” if the simulation crashes.
- A few fields are hidden that are for internal use (for example, Box Edges) on the output record.
- The weighted ensemble data (west.h5) has been moved from the dataset to the collection, to avoid exceeding the size limit of the dataset for long simulations. Now the record stores only a link to the west.h5 file.
- Datasets generated by previous versions of this floe can no longer be resumed or restarted with this version of the floe. Attempting to do so will cause the job to abort immediately. Note that this incompatibility applies only to the simulation floe, and the two analysis floes are still compatible with old datasets.
Permeability - Analyze Permeability Simulation:
- A checkbox has been added to switch between the symmetrized and the original free energy profile along the progress coordinate z.
Permeability - Calculate Auxiliary Coordinates (Optional):
- A checkbox has been added to switch between the symmetrized and the original probability distributions.
- The floe report now calculates (if not already calculated) and displays the free energy profile as shown in the Permeability - Analyze Permeability Simulation Floe.

The tutorials have been revised to reflect the changes above.
A section has been added to describe how users can monitor the simulation using the “Analyze” page.

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

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.

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.

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.

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.

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.

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.

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.