3.0.0 Jun 2021 (Orion 2021.1 release)¶
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.
All floes now have much improved parameter organization in the floe launch UI.
FastROCS Plus (Keywords: Shape, Docking, Consensus, Collection, Virtual Screening) FastROCS search with optional re-scoring and consensus scoring of best fastROCS molecules with Docking and ROCS.
Batch FastROCS (Keywords: Shape, Collection, Virtual Screening) FastROCS search with ROCS re-score of best FastROCS molecules. A separate hit-list is produce for each query.
FreeForm Pose Calculates the Freeform Delta G of docked poses with optional Delta G filtering of poses.
Cluster Poses Clusters docked poses, or alternatively ROCS overlays, based on the 3D similarity.
Sample Collection Converts a random sample of a FastROCS or GigaDocking collection into a Dataset.
Giga Docking Collection to Hi-res FastROCS Collection Converts a Giga Docking Collection into a fastROCS collection with a max of 200 conformers per molecule, as opposed to a max of 10 conformers per molecule in a standard fastROCS collection.
GigaDock now supports multiple receptors/design units.
Prepare Giga Collections now supports GPU Omega (enabled by default) which can reduce floe cost by up to 40%.
Prepare Giga Collections now retains the original SMILES string when processing SMILES files or command/tab separated files containing SMILES.
Fixed issue where floes could not read collections created by very old versions of Orion.
2.0.6 April 2021 (hotfix)¶
2.0.0 Nov 2020 (Orion 2020.3 release)¶
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.
No new feature in this release.
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)¶
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.
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.
An issue with the collection preparation floes duplicating some input molecules has been addressed.