Release Notes

v0.14.1 October 2024

General Notice

  • This package is built using OpenEye-orionplatform==6.2.0, OpenEye-toolkits==2024.1.3, and OpenEye-Snowball==0.28.0.

Floe Updates

  • A bug has been fixed in the EON - Shape and Electrostatic Similarity Alignment floe. Previously, the list of all shape and electrostatics overlaid hits, for a given database molecule was not sorted in the combo score to find the best hit for molecule, but instead the best hit for first conformer was written to output. This mistake has been corrected by switching to OpenEye-toolkits==2024.1.3 and the fixes therein.

v0.14.0 July 2024

General Notice

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

  • Updated to latest version of FPocket: fpocket==4.2

Floe Updates

  • A new QUACPAC - Tautomer Enumeration and Analysis Floe has been added to perform tautomer analysis and generate reasonable tautomers of molecules.

  • A new BROOD - Fragments Conformer Generation Floe has been added to generate 3D conformers of molecule fragments.

  • A new BROOD - 3D Fragment Similarity Floe has been added to perform 3D overlay optimization and similarity estimation between molecule fragments.

  • The following improvements and modifications have been made to the BROOD - 3D Fragment Replacement Floe.

    • The Floe has separate inputs for a pre-build query and for building a query on the fly.

    • The Floe accepts a design unit with associated parameters for a target protein.

    • The pre-build query input can now accept a query prepared using the vBROOD application.

    • The performance of the Floe is optimized to better handle queries with multiple attachment points.

  • The BROOD - Query Builder Floe has been expanded with the ability to build a query containing a target protein.

  • The following improvements and modifications have been made to the CHOMP - Generate BROOD Fragment Database Floe.

    • Parameters to use a custom SMARTS for fragmentation and custom filters have been added.

    • The Floe can handle output database names containing spaces.

    • The Floe now optionally generates a 2D fragments dataset.

    • Memory requirements on some of the Cubes in the Floe have been reduced.

  • The QUACPAC - Partial Charges Floe has been extended with the ability to assign am1bccelf10 partial charges, which is also the new default behavior.

  • The FreeForm - Bound Ligand Configurational Free Energies with SZYBKI Floe can now function with externally supplied conformer ensembles.

  • The protein_mask parameter, which designates the appropriate components of a design unit as the protein target, has been added as a parameter in the SZYBKI - Ligand Minimization in a Flexible Active Site Floe.

  • The EON - Shape Alignment and Electrostatic Similarity Scoring Floe has been renamed to be the EON - Shape and Electrostatic Similarity Alignment Floe and updated. It now performs shape and charge density overlay and scoring. By turning a promoted (potential) boolean parameter on, the overlaid geometries are rescored with shape and potential similarity combo.

  • The Filter Docking Hits by Interactions Floe now has better handling of receptor input datasets and is now compatible with the FastROCS+ Floe.

  • The following improvements and modifications have been made to the SPRUCE - Protein Preparation Floe

    • Added a support for saving only biological units.

    • Fixed a bug where turning of pocket enumeration would still send design units into the pocket enumeration cubes.

v0.13.1 February 2024

General Notice

  • This package is built using OpenEye-orionplatform==6.0.0, OpenEye-toolkits==2023.2.3, and OpenEye-Snowball==0.27.0.

Floe Updates

  • The CHOMP - Generate BROOD Fragment Database Floe has been modified to handle databases containing millions of molecules efficiently. The primary output from the Floe is a 3D BROOD fragment database collection that can be used as input for the BROOD - 3D Fragment Replacement Floe. There is also an option to save the BROOD fragment database tar file by turning on the Save BROOD Database Tarfile switch.

  • The BROOD - 3D Fragment Replacement Floe has been modified to generate bioisosteric analogs more efficiently. The input for the updated Floe is a BROOD fragment database collection instead of a BROOD fragment database tar file. The options to run the Floe in ET and linkOnly modes are now available.

  • OpenEye-provided BROOD database files are already available as collections. For your own, existing BROOD database files, you can use the new BROOD - DB File to Collection Floe to convert them into a BROOD database collection before running the BROOD floe.

  • A new BROOD - Query Builder Floe has been added to create BROOD queries for future BROOD runs.

  • The SPRUCE - Protein Preparation Floe has been modified so that it is less likely to fail and will emit biological units if no design units were generated.

  • The OMEGA - 3D Conformer Ensemble Generation Floe has been modified to optionally normalize pKa before proceeding to conformer generation.

  • The following improvements have been made to the ROCS - Shape Based Alignment for Virtual Screening Floe:

    • The Floe can now work with multiple molecules as queries.

    • The Floe now has options to perform random starts for overlay optimization.

  • The POSIT - Ligand Guided Small Molecule Posing Floe now properly handles design units without a receptor.

v0.12.1 September 2023

General Notice

  • This package is built using OpenEye-orionplatform==6.0.0, OpenEye-toolkits==2023.1.1, and OpenEye-Snowball==0.26.1.

v0.12.0 July 2023

General Notice

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

Floe Updates

v0.11.2 December 2022

General Notice

  • This package is built using OpenEye-orionplatform==4.5.4, OpenEye-toolkits==2022.2.2, and OpenEye-Snowball==0.25.3.

Floe Updates

v0.10.1 September 2022

General Notice

  • This package is built using OpenEye-orionplatform==4.4.0, OpenEye-toolkits==2022.1.1, and OpenEye-Snowball==0.24.1.

Floe Updates

  • The Receptor in Design Unit cube mishandled bioDUs. A new parameter and default was set for all SPRUCE floes that use this cube.

v0.10.0 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.

New Floes

  • A new SZYBKI - Single Point MMPBSA has been added that calculates single point MMPBSA scores for ligands in the context of active site.

  • The CHOMP - Generate BROOD Fragment Database floe was added to generate a fragment database for the BROOD floe from a set of input molecules. The floe can be used to fragment molecules, filter the fragments, generate 3D conformations, organize and index the fragments for rapid searching, and write a Brood database.

  • The Calculate Atropisomerism floe was added, which updates an existing dataset to include a boolean field indicating presence of atropisomerism and an image field containing a depiction of molecule torsion.

  • The Calculate Dipole Moment floe was added, which updates a dataset with the dipole moment of molecules.

  • The Assign Partial Charges floe was added, which calculates partial charges of molecules.

Floe Updates

v0.9.0 December 2021

General Notice

  • This package is built using OpenEye-orionplatform==4.2.5, OpenEye-toolkits==2021.2.0, and OpenEye-Snowball==0.23.0.

New Floes

Floe Updates

v0.8.3 June 2021

General Notice

  • This package is built using OpenEye-Snowball==0.21.0 and the associated OpenEye-orionplatform.

New Floes

  • The Classic Szybki Ligand in Flexible Protein Floe was added, which is a tool for optimization of ligands in a flexible protein active site. Both the ligand and the flexible part of the protein are modified to perform the optimization.

  • The Classic ReceptorInDU Floe was added, which creates receptors in input DUs.

  • The Classic Spruce - Import Prepared PDB Files was added, which uses Spruce to generate an OEDesignUnit object used by downstream OpenEye modelling applications in Orion, such as docking, posit, gameplan, or short-trajectory MD.

Floe Updates

  • The Classic OEDocking and Classic Posit floes were adjusted to work properly with both OEB and DU receptors.

  • The Classic OEDocking floe was modified to put the DU on a new field for the first docking record.

  • The Classic Posit, Classic Szybki Ligand in Fixed Protein, Classic Szybki Free Ligand, and Classic Szybki Ligand Hydrogen floes were updated to use the ParallelLigandChargeCube instead of the (deprecated) LigandPrepCube.

  • Fixed bug so that Classic Spruce: ETL Floe now handles input of files with .gz extension correctly.

  • Floe failure report names were changed to include the title of the floe.

  • Improved floe descriptions and floe parameter descriptions.

  • Standardized floe success and failure output behavior with the floe_endgame function from the snowball package.

v0.7.1 November 2020

General Notice

  • This package is built using OpenEye-Snowball==0.20.0 and the associated OpenEye-orionplatform.

Floe Updates

  • The Classic Substructure Search Floe no longer fails when there are no hits.

  • The Classic Macrocycle Omega Floe will produce the same number of conformers when it runs multiple times on the same input molecule.

  • The Classic OMEGA Floe no longer re-flips input molecules. It also no longer flips specified nitrogen stereo centers.

  • Promoted Cube parameters for all Floes now appear in the order specified by the Floe author in the Orion Job Form.

  • The IdeaGroup column in the Classic BROOD Floe results has been renamed to ClusterID.

  • The Classic Gameplan Floe now promotes errors of Gameplan log file to the floe report.

  • The Classic Spruce - Prep from PDB Codes Floe no longer expose “Add Interaction hints as a promoted parameter”

  • The Classic Spruce - Prep from Files Floe no longer expose “Add Interaction hints as a promoted parameter”

v0.6.2 August 2020

General Notice

  • Upgrades to use OpenEye-Snowball==0.19.3.

v0.6.1 August 2020

General Notice

  • Upgrades to use OpenEye-Snowball==0.19.1 and the associated OpenEye-orionplatform

New Floes

  • New Classic Shapequery To Record Floe reads shape query from a file and outputs it to a dataset.

  • New Classic Spruce - OEDesignUnit Type Updater has been added to convert datasets containing design units in the old Blob type to the new Types.Chem.DesignUnit type, which is required if a user wants to visualize the design unit in the 3D viewer. The Floe retains the old Blob type for backwards compatibility for this release, and merely adds the new fields.

Floe Updates

  • Classic Spruce - Prep from PDB Codes and Classic Spruce - Prep from Files Floes now by default include loop modeling for gaps in protein structures. Preparation times are expected to increase, dependent on the number and lengths of the missing loops.

  • Classic Szybki Free Ligand Floe and Classic Szybki Activesite Ligand Floe no longer fail when the solvent model is set to PB.

  • The Classic BROOD Floe has been improved to align depictions of hits with the non-changing part of the BROOD query.

  • The Classic OMEGA Floe now supports ‘fix molecule’ and ‘fix smarts’ to fix an portion of the input molecule.

  • Support of Open FF 1.0 has been added to the following Floes. PARSLEY_OPENFF100, PARSLEY_OPENFF111 and PARSLEY_OPENFF120 are added as predefined choices, and an .offxml file that defines a SMIRNOFF force field can also be used as input.

    • Classic Szybki Activesite Ligand

    • Classic Szybki Free Ligand

    • Classic Szybki Ligand Hydrogen

    • Classic FreeForm Conformer Energies

    • Classic FreeForm Restriction Energies

  • The Classic ROCS Floe has been updated to suport a shape query as well as a query molecule.

  • The Classic Szybki Activesite Ligand Floe now assigns charges to proteins if they are not charged. The Floe used to fail if the protein is not charged.

Removed Floes

  • The Classic Spruce - OEDesignUnit Upload Floe has been removed, as Orion now automatically can ETL OEDU files to records.

v0.5.2 April 2020

General Notice

  • Upgrades to use OpenEye-Snowball==0.18.2 and the associated OpenEye-orionplatform

New Floes

  • The spruce Floes refactored into two new Floes, the old Floes have been removed. The refactor of the Floes has removed the need to run multiple Floes to prepare strutures for modeling, furthermore, the Floes now write a single dataset containing multiple design unit records. The Floe can take multiple files or PDB codes, e.g. it is possible to prepare all the structures for a given target in parallel providing a single optional reference to superpose all the structures to.

    • Classic Spruce - Prep from PDB Codes

    • Classic Spruce - Prep from Files

Floe Updates

  • Classic Posit has been improved to not always require high-memory machines.

  • Classic OEDocking now fails more cleanly on bad receptor input.

  • Classic Substructure Search now generates an additional output of un-matched compounds.

v0.4.0 November 2019

General Notice

  • Upgrades to use OpenEye-Snowball==0.17.2 and the associated OpenEye-orionplatform

  • The Classic Floes BETA package no loger exists. All of the Floes from the BETA package are now merged to the main package.

New Floes

  • New Floe Classic Macrocycle Omega has been added to generate conformers of macrocycle molecules

  • New Floe Classic Szybki Ligand Hydrogen has been added to optimize ligand hydrogen atoms positions

  • New Floe Classic FreeForm Restriction Energies has been added to estimate restriction energies on bound ligands based on Force field based Conformational FreeForm calculation.

  • New Floe Classic EON has been added to rank database molecule against query based on Electrostatics similarity.

  • New Floe Classic Substructure Search has been added to find molecules containing MDL query patterns of interest.

Floe Updates

  • The following Floes have been improved for robustness and are moved from the BETA package to the release package.

    • Classic FreeForm Conformer Energies: Floe for conformer free energies

    • Classic FreeForm Solvation Energies: Floe for solvation free energies

    • Classic Szybki Free Ligand: Floe for free ligand optimization

    • Classic Szybki Activesite Ligand: Floe for active-site ligand optimization

    • Classic 2D Similarity: Floe for fingerprint based 2D similarity

    • Classic Gameplan: Floe to analyze ligands to generate modification hypothesis

    • Classic BROOD: Floe to generate new Leads

  • The Classic Posit Floe modified to use the capabilities of the newly modified Posit toolkit.

  • The Classic ROCS Floe is enhanced with ability to work with multi-conformer query.

  • The Classic Omega Floe enhanced with an optional Maximum Number of Conformers parameter.

  • The Classic ROCS and Classic OEDocking Floes have been enhanced with a switch to turn on/off depiction of images.

v0.3.6 September 2019

General Notice

  • Upgrades to use OpenEye-orionplatform==1.1.4 and OpenEye-Snowball==0.16.6

  • The Classic Floes package is deployed in two parts: (1) OpenEye classic Floes: contains Floes that are robust and well behaved; (2) OpenEye classic Floes BETA: contains Floes that are functional but may be ill-behaved to some inputs. Floes from the BETA package would be moved to the standard package, as they are improved over time.

New Floes

  • A specialized Floe for generating single 3D structure from a 1D/2D molecule.

  • A Floe has been added to convert OEDesignUnits prepared outside of Orion to the format of output datasets produced by Classic Spruce Prep.

  • A set of Floes have been added to prepare Unprepped datasets required for input to Classic Spruce Prep.

Floe Updates

  • The Classic OMEGA Floe is now simplified to generate conformers for predefined use case based modes.

  • The Classic ROCS Floe now produces more focused result fields, and responds properly to the user choice of sorter type field to produce the hitlist.

  • The following Floes have been improved to better respond to bad inputs, and provide a comprehensive report on total or partial failure of the underlying jobs: * Classic Omega * Classic ROCS * Classic Docking * Classic Posit

  • The Classic SPRUCE Prep Floe has been simplified, with many input parameters removed in favor of a robust set of defaults. The primary input to the Classic Spruce Prep Floe is an Unprepped PDB/MTZ dataset. An Unprepped input dataset can be generated using one of the following following Floes also in Classic Spruce: * Classic Spruce: PDB Code * Classic Spruce: PDB Codes File * Classic Spruce: PDB File Each of these Floes produce Unprepped input datasets for Classic Spruce Prep, and require either an input PDB code, a text file of PDB codes, or an input PDB file respectively.

v0.3.3 July 2019

General Notice

  • Upgrades to use OpenEye-orionplatform==1.0.0 and OpenEye-Snowball==0.16.0

v0.3.1 June 2019

General Notice

  • Upgrades to use OpenEye-orionplatform==0.2.5 and OpenEye-Snowball==0.14.0

New Floes

  • A specialized Floe for running Classic ROCS with a single reference.

  • A specialized Floe for running Classic POSIT with a single receptor.

Floe Updates

  • The Multi-receptor Classic POSIT Floe now promotes a parameter to specify the minimum required memory, and another parameter to specify the poser cash size. The Floe also throws exception if sufficient memory for the job is not requested.

  • The Multi-receptor Classic ROCS Floe now promotes a parameter to specify the minimum required memory. The Floe also throws exception if sufficient memory for the job is not requested.

  • The Classic OEDocking Floe now works properly even when the input ligand records contains ‘ConfField: Chemgauss4 Score’ field.

  • The Classic OEDocking Floe no longer produce docked pose with unusually high docking scores.

  • The Classic GamePlan Floe now produces a Floe report to show GamePlan results and app log files.

  • The Classic BROOD Floe now produces a Floe report to show BROOD results and app log files.

  • The Classic Gameplan Floe now takes either a ligand/protein pair or a DesignUnit as input.

v0.2.5 March 2019

General Notice

  • Upgrades to use OpenEye-orionplatform==0.1.14 and OpenEye-Snowball==0.13.6

New Floes

  • New Floe for prepping a protein structure using Spruce.

  • Floes for running wrapped app versions of GamePlan and BROOD.

  • A specialized Macrocycle conformer generation Floe with Omega.

Floe Updates

  • The Classic OEDocking Floe and Classic POSIT Floe now promote a parameter to specify the field on the record in which the receptor can be found.

  • The FreeForm Conf Floe was modified to use new Conformer Splitter and Merger Cubes in Snowball.

  • Every Cube which uses a Expand Confs to Mols Cube now defaults to not exanding conformers.

v0.2.2 September 2018

General Notice

  • Upgrades to use OpenEye-orionplatform==0.1.7 and OpenEye-Snowball==0.13.3

  • Added Release Notes

Floe Updates

  • The Classic OEDocking Floe and Classic ROCS Floe now default to not generating report images, although this functionality can be restored via a parameter on each Floe.