Release Notes

v0.7.2 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.