Release Notes

3.0.0 Jun 2021 (Orion 2021.1 release)

General Notice

The functionality of the “Multi-Query Ligand-Based Virtual Screening with FastROCS and SubROCS” from the “OpenEye Ligand-Based Virtual Screening” package has been absorbed into the Batch FastROCS (Keywords: Shape, Collection, Virtual Screening) in this package.

New Features

Fixes

  • Fixed issue where floes could not read collections created by very old versions of Orion.

2.0.6 April 2021 (hotfix)

Fixes

  • Fixed issue where a GigaDock job could fail if the Orion stack is under very heavy load.

  • Fixed issue where Prepare Giga Collections ignored the setting of the ‘Mol Title Field’ in some circumstances.

2.0.0 Nov 2020 (Orion 2020.3 release)

General Notice

Parameters for setting the output fields for the docked molecule and score have been temporarily removed along with the parameter specifying the input molecule field. These parameters are very rarely needed and have been set by users not fully understanding their impact. These parameters are planned to return in a future release once the FLOE UI has been improved to provide better clarity on when to set them.

New Features

No new feature in this release.

Fixes

  • Added duplicate checking to ‘Prepare Giga Collections’. Only applied to sequential molecules.

  • Fixed issue with molecules from a dataset (not collection) being docking by ‘Giga Dock’ floe being lost rather than being sent to the Restart Collection if the cost threshold was exceeded.

  • Fixes issue with ‘Prepare Giga Collections’ not deleting its temporary collection.

  • Better ordering of parameters (better categorization is coming in a future release).

  • Improved the efficiency of the Giga-Dock floe by about 15%

  • Protected the giga-docking floe against the unlikely case of 12h timeout docking an individual shard (a full docking collection consists of ~1M shards) of molecule to a gigantic active site (>~2000 cubic Angstroms).

0.1.0 August 2020 (Orion 2020.2 release)

General Notice

Initial release of Large Scale Floes package.

This package include the functionality of the OpenEye Giga Docking Floes and OpenEye Scientific Floes packages, both of which have been deprecated. (Exception: The torsion scanning floes from OpenEye Scientific Floes were moved into the OpenEye QM Floes package).

The Giga Dock (FRED) and Giga Dock (HYBRID) floes from OpenEye Giga Docking Floes have been merged into a single floe Giga Docking which has a parameter to select the docking mode (i.e., FRED or HYBRID).

The Step 1,2 & 3 collection preparation floes from OpenEye Scientific Floes have been merged into a single floe Prepare Giga Collections floe.

New Features

  • The collection preparation floe filters are now significantly more configurable. Some of the new optional filtering options are:

    • Filtering by SMARTS pattern (either exclude or require)

    • Filtering with a custom OEFilter file

    • Random filtering. This allows the creating of collection that contain a random subset of the input molecule for testing purposes.

  • The collection preparation floe now accepts a wider variety of input formats, including tar and zip archive formats.

  • A Filter Collection floe has been added that allows for filtering of existing collection.

  • The Giga Docking floe has a new docking mode Fast-FRED. Fast-FRED uses a simpler scoring function and samples slightly less in the initial stages of docking while using the same Chemgauss4 scoring function for final optimization and scoring. This docking mode can be x2-x4 times faster (and hence less costly) than the standard FRED. Results appear similar to standard FRED, but this docking mode has not been thoroughly validate as of this release in terms of quality of results.

hsp90_compare

Comparison of FRED (x-axis) and Fast-FRED (y-axis) docking scores of 1M random Enamine Real molecules docked to (a) HSP90 and (b) PNPH

Fixes

  • An issue with the collection preparation floes duplicating some input molecules has been addressed.