Release Notes
v0.14.1 October 2024
General Notice
This package is built using
OpenEye-orionplatform==6.2.0
,OpenEye-toolkits==2024.1.3
, andOpenEye-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
, andOpenEye-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
, andOpenEye-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
, andOpenEye-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
, andOpenEye-Snowball==0.26.0
.
Floe Updates
The Floes SPRUCE - Protein Preparation from PDB Codes Floe and SPRUCE - Protein Preparation from PDB Files Floe have been combined into a single Floe that can take the same input(s) as the previous floes: SPRUCE - Protein Preparation. This Floe is intended to replace the former Floes.
The SPRUCE - Protein Preparation Floe added additional support for apo pocket finding by also including F-pocket search.
The CHOMP - Generate BROOD Fragment Database Floe has been modified to handle larger molecular databases more efficiently. The updated Floe will act as a drop-in replacement for the existing Floe. Conformers are generated from the 2D fragments instead of the input molecules. The input to the new CHOMP Floe can be provided as a dataset, a file, or a collection. The 3D fragment database output from the Floe is still a .tar.gz file. The 2D fragments, however, are written as a collection.
The BROOD - 3D Fragment Replacement Floe can save the input query as a dataset. The user can load a pregenerated query through the Sketcher.
The Substructure Search - Small Scale Substructure Matching Floe now exposes ui_result as a promoted parameter.
A new parameter to specify
Protein mask
is now exposed in the SZYBKI - Ligand Minimization in a Rigid Active Site Floe.The FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI Floe can now be used with user-provided ensemble of conformers.
New parameters for the following are now added to the OMEGA - 3D Conformer Ensemble Generation Floe.
Energy window (EWindow)
RMS
Hydrogen sampling
Nitrogen stereo enumeration
Flag to ignore stereo failures
External fragments library
Fix based on maximum common substructure (MCS)
v0.11.2 December 2022
General Notice
This package is built using
OpenEye-orionplatform==4.5.4
,OpenEye-toolkits==2022.2.2
, andOpenEye-Snowball==0.25.3
.
Floe Updates
The EON - Shape Alignment and Electrostatic Similarity Scoring floe now allows multiple molecules as query.
The
solvent model
parameter in the following floes now has a newPB
option.The
target mask
parameter in the GamePlan - Ligand Design with Water Analysis using SZMAP floe no longer include the solvent particles as part of the target protein by default.A new Floe Filter Docking Hits by Interactions has been added. This annotates docking results and receptor datasets with fields that can be used to filter the results based on the interactions between the docked/posed molecule and the receptor. The floe additionally calculates an interaction fingerprint, and reports the tanimoto score with the receptor bound ligand as the reference (if present). The floe works for both single and multi-receptor results from GigaDocking and the classic docking floes.
v0.10.1 September 2022
General Notice
This package is built using
OpenEye-orionplatform==4.4.0
,OpenEye-toolkits==2022.1.1
, andOpenEye-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
, andOpenEye-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
A new
solvent model
parameter has been added to the following floes. The error handling behavior of these floes have also been improved. These floes are also now robust against input molecules missing explicit hydrogen atoms.The EON - Shape Alignment and Electrostatic Similarity Scoring floe now keeps all the input dataset record fields in the generated output dataset records.
The FreeForm - Bound Ligand Configurational Free Energies with SZYBKI floe now keeps all the input dataset record fields in the generated strains output dataset records, along with having those fields being kept in the generated ensembles dataset records.
The GamePlan - Ligand Design with Water Analysis using SZMAP no longer fails if the input molecule was missing title.
The POSIT - Ligand Guided Small Molecule Posing now reports an additional field containing the
posit method
that was used for a prediction. The floe also now properly passes records tofailed dataset
in cases when positfails
due to low probability or clash as desired.The maximum allowable value for hitlist from the
ROCS - Shape Based Alignment for Virtual Screening
has been increased to 1,000,000.
The POSIT - Ligand Guided Small Molecule Posing floe was modified to produce Interaction Map, Contact Map, and Unpaired Map diagrams.
The following changes were made to the OMEGA - Conformer Generation for Macrocycles floe
Do not expose random_seed_field as a promoted parameter
Do not hide the iter_cycle_size parameter
The OMEGA - 3D Conformer Ensemble Generation Floe was modified to filter macrocycle molecules using the ParallelMacrocycleFilterCube prior to the stereo enumeration process.
The SPRUCE Protein Preparation Floes were modified with a new path where a reference structure can be generated as part of the Floes, instead of being a separate run prior to prep of a larger dataset.
The SPRUCE Protein Preparation Floes were modified such that the failure floe reports is providing more actionable error messages and improved detail logging per structure.
v0.9.0 December 2021
General Notice
This package is built using
OpenEye-orionplatform==4.2.5
,OpenEye-toolkits==2021.2.0
, andOpenEye-Snowball==0.23.0
.
New Floes
A new ROCS Query Model Builder has been added that builds OEShapeQuery from a set of input bound ligands.
Floe Updates
The following modifications have been made to the ROCS - Shape Based Alignment for Virtual Screening floe.
Ability to work with custom color force fields
Floe output no longer suppress hydrogen in the generated hits
The floes SPRUCE - Protein Preparation from PDB Codes Floe and SPRUCE - Protein Preparation from PDB Files Floe have been updated to enable pocket finding in the event that Spruce does not find a ligand during structure preparation. The pocket search is done using OEPocket, and the result will be a set of design units each focused on a detected pocket.
A output hitlist dataset from the OEDocking - Dock into an Active Site for Virtual Screening floe no longer automatically contain the input receptor design unit in the first record. A flag has been added to optionally add that as a separate but first record in the output dataset.
The POSIT - Ligand Guided Small Molecule Posing floe has been modified with the following:
Can now generate multiple poses, and provides an option to use either only the best receptor or all receptors in doing so
The Design Units in the output records now contain receptors
A pose (if generated) is set into the record, even if the record goes to the failure port due to clash or low probability
The SZYBKI - Ligand Minimization in a Flexible Active Site floe can now be used to minimize a ligand dataset against a protein in a separate design unit, in addition to minimizing a ligand and a protein containing within the same design unit.
The following floes are now able to accept custom SMIRNOFF force fields. The latest
OpenFF
forcefieldsage_openff200
has also been added, and is the current default, with internally generatedam1bcc_elf10
charges.The following floes are now able to accept custom SMIRNOFF force fields for small molecule components of a protein-ligand complex optimization, where the protein interactions are defined with the
ff14sb
. A newff14sb_parsley
has also been added, and is the current default.Ionic state can now be choosen in the following
FreeForm
floes:The output records of the
Bound Ligand Configurational Free Energies
datasets from the FreeForm - Bound Ligand Configurational Free Energies with SZYBKI floe now contains following additional fields in the conformer recordsPartner (ensemble) conformer index
Partner (ensemble) conformer relative energy
Partner (ensemble) conformer deltaG
A bug preventing use of
Short Trajectory Molecular Dynamics (STMD) Floes
output to be used as input to theFreeForm
floes have been fixed.A bug in output for the Fingerprint Search - Small Scale 2D Similarity floe has been fixed to properly generate failed outputs and a failure report.
A bug in the Substructure Search - Small Scale Substructure Matching floe was fixed where selected parts of the input query molecule were not searched, and instead the entire query molecule was searched. Now the floe will only search for selected parts of the query input.
The query image in the BROOD - 3D Fragment Replacement floe report is now properly generated irrespective of if the floe was ran with or without a protein input.
FastROCS
has been removed from the list of mode choices in the OMEGA - 3D Conformer Ensemble Generation floe, as the results were not usable as-is in a FastROCS floe.
v0.8.3 June 2021
General Notice
This package is built using
OpenEye-Snowball==0.21.0
and the associatedOpenEye-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
andClassic 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
, andClassic 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 associatedOpenEye-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 associatedOpenEye-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
andClassic 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 andClassic 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 associatedOpenEye-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 associatedOpenEye-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 moleculesNew Floe
Classic Szybki Ligand Hydrogen
has been added to optimize ligand hydrogen atoms positionsNew 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 energiesClassic FreeForm Solvation Energies
: Floe for solvation free energiesClassic Szybki Free Ligand
: Floe for free ligand optimizationClassic Szybki Activesite Ligand
: Floe for active-site ligand optimizationClassic 2D Similarity
: Floe for fingerprint based 2D similarityClassic Gameplan
: Floe to analyze ligands to generate modification hypothesisClassic 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
andClassic 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
andOpenEye-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
andOpenEye-Snowball==0.16.0
v0.3.1 June 2019
General Notice
Upgrades to use
OpenEye-orionplatform==0.2.5
andOpenEye-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
andOpenEye-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
andOpenEye-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.