Release Notes, Version 2025.4.1

The following floe products have new versions for this release. Other packages are unchanged from the previous release.

Release Notes

v0.2.0 December 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.5.0, OpenEye-toolkits==2024.2.1, and OpenEye-Snowball==0.29.2.

Floe Updates

v0.1.1 April 2024

General Notice

  • This package is built using OpenEye-orionplatform==6.0.0, OpenEye-toolkits==2023.2.3, and OpenEye-Snowball==0.27.1.

Floe Updates

v0.1.0 February 2024

General Notice

  • This is the first release of the OpenEye AI Fold Floes.

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

This package contains the following Floe, whose purpose is to generate 3D protein structures from only a sequence input.

Classic Lead Optimization Release Notes

v0.16.3 December 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.4.1, OpenEye-toolkits==2025.2.0, and OpenEye-Snowball==0.31.0.

Legacy Release Notes

4.3.1 December 2025

Fixes

  • The Gigadock Collection to Hi-res FastROCS Collection Floe has been adjusted to create smaller shards to address an out-of-memory error that could occur in the FastROCS Plus Floe.

  • The default name of the output design unit field has been changed from “Design Unit” to “designunit” in the Gigadock and Gigadock Warp Floes.

  • An issue has been fixed where the FastROCS Plus Floe would use FitTversky when RefTversky was specified by the user.

  • In the FastROCS Plus Floe parameter documentation, it has been clarified that color optimization is only supported with Tanimoto scoring, and that if RefTversky and FitTversky are selected, the optimization will be done with shape optimization and color scoring.

  • An out-of-memory error has been fixed in the FastROCS Plus Floe that occurred when the maximum number of rescore molecules (100M) was selected.

  • A rare issue has been fixed that caused some molecules to have Hetero Bemis Murcko cores with invalid valances in the FastROCS Plus Floe output.

4.2.4 March 2025

Fixes

  • Development parameters were removed from floes in Large Scale Floes. These parameters were added for debugging purposes only and are not needed for running these floes.

4.2.3 February 2025

Fixes

  • An issue has been fixed that could cause the Gigadock Warp Floe to fail if a receptor with many constraints caused the vast majority of molecules to fail to dock because they cannot satisfy the constraints.

Changes

  • The Pareto Frontier Consensus Floe has been removed from this package. It has been added to the new Large Scale Floes Hit-to-Lead package.

  • The Multi Query 2D Similarity Floe has been removed from this package. It has been added to the new Large Scale Floes Hit-to-Lead package.

4.2.2 January 2025

Fixes

  • Fixed an issue that could cause the Gigadock Warp to fail if a receptor with many constraints caused the vast majority of molecules to fail to dock because they cannot satisfy the constraints.

Changes

  • Removed “Pareto Frontier Consensus” floe from this package. This floe as been added to the new “large-scale_floes-h2l” package.

  • Removed “Multi Query 2D Similarity” floes from this package. This floe as been added to the new “large-scale_floes-h2l” package.

4.1.10 December 2024

Bugfixes

  • Addressed a rare issue in the Gigadock Warp floe where the GPU memory could become fragmented while training the AI score model causing the floe to fail. The update floe will now complete normally in this circumstance and not fail.

  • Gigadock Warp floe now no longer attempts to use Cadence data center GPUs by default.

4.1.7 July 2024

Highlights

Bug Fixes

  • A bug has been fixed in the Gigadock Warp Floe that could cause the Floe to hang for a long time and then fail if AWS S3 is under load and transferring data slower than expected.

  • The Options: Model Training –> Fraction Train parameter for the Gigadock Warp Floe can now be set as low as 0.001 as stated in the parameter description. A bug in the prior release prevented the value from being set below the default of 0.01.

  • A bug has been fixed in the Gigadock, Gigadock Warp, and FastROCS Plus Floes from including individual dock score components for each molecule in the output when these values are requested by the user. They are only expected to be in the output if the user specifies the parameter output fields for these components; these parameters are in the Output Fields parameter category for all three floes.

  • A typo has been fixed in the tutorial documentation to correctly indicate that the FastROCS Plus Floe produces seven output hit lists. It had incorrectly indicated five.

4.1.5 February 2024

Highlights

The Gigadock Warp Floe has been upgraded with better featurization of the molecules and now uses a neural net model rather than a linear model when docking more than ~100M molecules. Output hit lists from Gigadock Warp should now be expected to even more closely match the hit list that would be created by running the Gigadock Floe and cost 30%-40% less.

Features

  • Gigadock Warp now uses a neural net rather than a linear score model when docking more than 93,460,000 molecules. Below this threshold, it still uses a linear model.

  • Gigadock Warp now uses a 4K Tree fingerprint, FastROCS Shape and Combo Tanimotos, and simple 2D properties to featurize the molecules. The previous version used MACSS166 fingerprints in place of the 4K Tree fingerprint.

Changes

  • The “Predicted Score” field has been removed from the Gigadock Warp output.

  • Gigadock Warp now always uses AWS spot instance for all major parallel cubes that don’t use a GPU.

  • Gigadock Warp now defaults to docking 4% of the molecule in the final docking stage (was 8%).

  • The following parameters have been added to the Gigadock Warp Floe:

    • Options: Model Training -> Fraction Train

    • Options: Model Training -> Final Dock Fraction

    • Options: Hardware -> FastROCS Instance Types

    • Options: Hardware -> FastROCS Spot Policy

Bugfixes

  • A bug was fixed where Gigadock Warp would fail to output a hit list if the Options: Output Fields -> Docked Pose Field was specified.

  • An issue was fixed where the Collection Info Floe could fail when processing a 10B-sized Gigadock collection.

  • An issue was fixed where Collection Info could have negative counts in the report’s histograms if the collection was very large (~>5B).

4.0.2 September 2023 (Large Scale Floes Hotfix)

Changes

  • Filter Collection can now take multiple input collections of the same type (e.g., FastROCS or Gigadock)

Bugfixes

  • Fixed issue with Gigadock Warp hanging when processing extremely large collections.

  • Fixed failure in FastROCS Plus if ROCS re-scoring is turned off and dock re-scoring is not turned on.

  • Fixed issue with ‘Prepare Giga Collection’ intermittently failing in the beginning of the floe if given large input file.

  • Fixed missing Gigadock Warp html documentation

4.0.0 July 2023 (Orion Floe 2023.1 Release)

Highlights

The Gigadock Warp Floe has been upgraded to use an AI model and will now cost less than the previous version and produce hit lists more similar to the hit list the Gigadock Floe would produce given the same input. See Gigadock Warp Floe Details for more details.

Changes

  • The parameter Options: Re-scoring -> Number of Molecules to Re-score can now be set up to 100 M (the previous limit was 10M).

  • Gigadock Warp now requires 1 M or more input molecules to dock in order to ensure it has enough training data to build an AI model of the score.

  • The following parameters have been removed from the Gigadock Warp Floe as part of the internal reworking of Gigadock Warp to now support AI learning of the docking scores.

    • Options: Advanced -> Random Dock Fraction

    • Options: Advanced -> Final Dock Fraction

    • Options: Advanced -> Number of FastROCS Queries

    • Options: Advanced -> Cluster FastROCS Queries

Bugfixes

  • An issue was fixed in FastROCS Plus where the consensus hit lists incorrectly had an extra field named “Pareto Dominance Rank,” in addition to a expected field “Pareto Rank.”

3.4.5 December 2022 (Orion 2022.4 Release)

New Features

  • FastROCS Plus now supports any type of Shape Query in the ROCS Re-scoring step. The core FastROCS screen is still restricted to simpler Shape Queries.

  • FastROCS Plus now supports searching by shape only. I.e, Shape Tanimoto, Ref Shape Tversky and Fit Shape Tversky are now additionally supported as similarity types.

  • The Filter Collection and Prepare Giga Collections floes now create a floe report describing the number of molecules that pass each filtering step.

Bugfixes

3.3.4 September 2022

Bugfixes

  • Collection based cubes now validate that downloaded shard data is the correct size, and retry the download if it is not. This protects against an extremely remote possibility that shard reads could lose data or hang the floe.

  • Cluster poses now properly clusters poses when ‘Options -> Single Conformer/Pose Input’ is switched from its default value of ‘On’ to ‘Off’.

  • The parameter ‘Options: Advanced -> Final Dock Fraction’ in the Gigadock Warp can no longer be set higher than 0.1. (There was an accidental regression in 3.3.0.) The default value of 0.08 is unchanged.

3.3.0 June 2022 (Orion 2022.2 release)

Features

  • New Floe : Multi Query 2D Similarity.

  • FastROCS Plus now automatically outputs two additional datasets by default, ‘FastROCS Novelty Hit List’ and ‘ROCS Novelty Hit List’. These hit lists contain molecules from the FastROCS and the ROCS Re-scoring computations respectively that tend to have high 3D and low 2D similarity.

  • The Filter Collection and Prepare Giga Collections floes can now optionally take a set of known molecules and then filter the collection molecules based on their 2D similarity to the known molecules (see the ‘Options: Known Molecules’ parameter group in both these floes).

  • The Prepare Giga Collections now optionally accepts a dataset as input.

  • FastROCS Plus output hit lists now includes a field with the 2D Tanimoto similarity to the query.

Changes

Bugfixes

3.2.0 April 2022 (Orion 2022.1 release)

Changes

Minor Features

  • The Prepare Giga Collections floe now by default adds a field “Enantiomer Title” to the output collections that contains the title of the molecule with a postfix index to identify enantiomers of input molecule with unspecified stereo that were stereochemically enumerated.

  • The FastROCS Plus floe now has an option to output a collection of up to 10M of the top scoring FastROCS molecules.

Bugfixes

  • Fixed a bug where the FastROCS Plus floe could fail due to an out of memory error if Options: Advanced: Number of Molecules to Re-score is set to a value much higher than the default.

  • Fixed an issue where Prepare Giga Collections could hang and the end of the floe waiting for the docking collection to close. This issue only affected preparation of large collections (e.g., Billions) and when using CPU rather than GPU Omega.

  • Fixed an issue in FastROCS Plus that caused more than one docked pose per molecule to be used when ‘Options: Advanced -> Query Conformer Generation Mode’ was set to ‘dock’.

  • Fixes several grammatical error in the FastROCS Plus and Batch FastROCS floe and parameter descriptions.

  • Fixed an issue in the documentation of floe in the large scale floes package where the python names of parameters were not correct. (The python name of the parameter is the name used when launching a job with ocli).

3.1.7 Dec 2021 (Orion 2021.2.1 release)

Highlights

This release contains a new floe Gigadock Warp that approximates a full Gigadock run using a combination of Docking and FastROCS. Gigadock Warp is ~8-10x less costly to run than a full Gigadock job and when docking billions of molecule recovers 70% of the same molecules the full Gigadock job does in the top 10K hit list.

See also

General Notice

GPU instances on Amazon Web Services (AWS) have been in high demand recently. This can result in long run times for floes that uses GPUs, i.e., FastROCS Plus, Batch FastROCS, Prepare Giga Collections and Gigadock Warp. To help reduce the chance of encountering this issue these floes have been modified to by default use older AWS GPU instances that are generally more available but slight less cost efficient (~25% more GPU cost). These floes now expose parameters to allow specifying more the more efficient, but sometimes less available instances when a floe is run. See the Changes section of these release notes for details on individual floes.

New Features

Changes

  • The FastROCS Plus no longer outputs the Similarity Combo, Color Similarity and Shape Similarity fields. These fields were duplicates of the output fields Tanimoto Combo, Color Tanimoto, and Shape Tanimoto (or fields with Tversky instead of Tanimoto if Tversky scoring is used) which were and continue to be outputted.

  • The GigaDock floe has been renamed the Gigadock floe.

  • The Giga Docking Collection to Hi-res FastROCS Collection has been renamed the Gigadock Collection to Hi-res FastROCS Collection floe.

  • The FastROCS Plus (Keywords: Shape, Docking, Consensus, Collection, Virtual Screening) floe has been renamed the FastROCS Plus floe.

  • The Batch FastROCS (Keywords: Shape, Collection, Virtual Screening) floe has been renamed the Batch FastROCS floe.

  • The FastROCS Plus floe now uses AWS g3 GPU instance by default (previous it used g4dn.2xlarge). Parameters for choosing the AWS GPU instance to use are now exposed (see the GPU Hardware parameter group).

  • The Batch FastROCS floe now uses AWS g3 GPU instance by default (previous it used g4dn.xlarge). Parameters for choosing the AWS GPU instance to use are now exposed (see the GPU Hardware parameter group).

  • The Prepare Giga Collections now uses CPU Omega by default (previously it used GPU Omega). This can be adjusted with the Conformer Generation Settings -> Use GPU Omega setting.

  • When processing a tab or comma separated file Prepare Giga Collections will now, by default, name the field on the output giga docking collection ‘Molecule’ rather than using the column title from the csv/tsv file (see the new Format Specific Settings -> Molecule Field Name For TSV/CSV parameter). This change was made because in practice the column is often named ‘SMILES’ and this field name propagates to the docked pose field of the output hit lists of the Gigadock floe, where ‘SMILES’ is not an appropriate name.

Fixes

  • Fixed a bug in the Batch FastROCS floe that causes it not to write out the fields with the standard names for ROCS scores, i.e., Tanimoto Combo, Color Tanimoto, and Shape Tanimto or Tversky Combo, Color Tversky, and Shape Tvserky when Tversky similarity is selected. The floe was previously writing out fields with Similarity in place of Tanimoto or Tversky in the field names.

  • In the FastROCS Plus floe, fixed the description of the parameter Options: Advances -> Query Conformer Generation Modes which incorrectly referred to ‘freeform’ as an available conformer generation mode.

  • Fixed a bug in the FastROCS Plus floe that caused it to ignore all design units supplied to the Inputs -> Design Unit(S) (Optional) parameter if Options: Advanced -> ROCS Re-Scoring Mode was set to ‘Off’.

  • Fixed a bug in Filter Collection that causes it to lose compression on the molecules of FastROCS collections. In practice this resulted in a functional but slightly larger than necessary output collection when processing FastROCS collections (these collections were not functional in the older deprecated Multi-Query Ligand-Based Virtual Screening with FastROCS and SubROCS floe).

  • Fixed a bug in the Collection Info, Prepare Giga Collections and Filter Collection floes that causes them to use more bandwidth than necessary reading collections.

  • Suppressed rare XlogP calculation warning for individual atoms when running Prepare Giga Collections and Filter Collection. While rare, when processing billions of molecules they tended to flood the log with thousands of un-actionable warnings.

3.0.3 Oct 2021 (hotfix)

Fixes

  • Fixed a bug that could cause docking to fail when running in multi-receptor Hybrid mode.

  • Removed a development parameter that was accidentally exposed in the 3.0.2 release.

3.0.2 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 in this package.

New Features

  • All floes now have much improved parameter organization in the floe launch UI.

  • New Floes

    • FastROCS Plus FastROCS search with optional re-scoring and consensus scoring of best fastROCS molecules with Docking and ROCS.

    • Batch FastROCS 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.

    • Gigadock 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.

  • Minor Features

    • Prepare Giga Collections now has a option to accept the input tautomer state rather than setting an appropriate tautomer state.

    • Collection Info can now accept files or datasets as input in addition to collections.

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.

  • The Pareto Frontier Consensus Floe has been removed from this package. It has been added to the new Large Scale Floes Hit-to-Lead package.

  • The Multi Query 2D Similarity Floe has been removed from this package. It has been added to the new Large Scale Floes Hit-to-Lead package.

Protein Modeling Release Notes

v1.0.0 February 2025

General Notice

This is a new package as a part of the Orion Floes reorganization. It includes Floes previously found in the Biomodeler Floes package.

  • This package is built using OpenEye-orionplatform==6.3.1, OpenEye-toolkits==2024.2.1, and OpenEye-Snowball==0.29.1.

  • The SiteHopper Search Floe has improvements to the GPU prescreen to generate hits with higher accuracy. Options have been added to filter hits based on a sequence similarity cutoff and a patch score cutoff.

Small Molecule Modeling Release Notes

v2.1.1 August 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.1.0, and OpenEye-Snowball==0.30.0.

Floe Updates

  • The OEDocking - Dock into an Active Site for Virtual Screening Floe has the following updates:

    • There is an option to fail optimized poses for excessive bending of aromatic rings in the Refined and STMD quality options.

    • The AUTO docking mode now uses FRED or HYBRID for docking based on the similarity of the molecule to the bound ligand.

      • FRED is used if the receptor is apo, or if the molecule has low similarity to the bound ligand.

      • HYBRID is used if the receptor is holo, and if the molecule has high similarity to the bound ligand.

    • You can now use the same protein mask in the Docking, Optimization, and Check Clashes Cubes.

    • These changes have been made in the STMD mode. You can now:

      • Generate 50 poses using exhaustive docking with FRED.

      • Perform pose clustering before optimization (in addition to one after optimization) using the ChemGauss4 Score for ranking the pose before optimization, and an RMS threshold of 1.0 for deduplication.

      • Perform deduplication of a pose as it is, without doing any overlay.

  • The SZYBKI - Ligand Minimization in a Rigid Active Site Floe and SZYBKI - Ligand Minimization in a Flexible Active Site Floe have a new parameter, bent_ring_check, to set whether or not to fail the optimization when there is excessive deviation from planarity in aromatic rings.

v2.0.1 February 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.2.0, OpenEye-toolkits==2024.2.0, and OpenEye-Snowball==0.29.1.

Floe Updates

Legacy Release Notes

v0.31.1 December 2025

General Notice

  • This package is built using OpenEye-orionplatform=6.7.0, OpenEye-toolkits==2025.2.1, OpenEye-szmap==1.7.1.1, and OpenEye-szybki==2.8.0.1.

Cube Updates

  • The new MacroCycle Prep Cube has been added to check and prepare molecules for conformer generation with distance geometry using OMEGA.

  • The Flex-Protein Ligand Minimization Cube now properly updates the coordinates of the design unit components after optimization.

  • Version checking in Input PDB Codes for Spruce Cube has been removed to prevent failures due to endpoint changes at the RCSB.

v0.30.2 Sept 2025

Cube Updates

v0.30.1 August 2025

General Notice

  • This package is built using OpenEye-orionplatform=6.6.0, OpenEye-toolkits==2025.1.0, OpenEye-szmap==1.7.1.1, and OpenEye-szybki==2.8.0.1.

New Cubes

  • The new Docking Method Selector (Single Receptor) Cube has been added to select the docking method (FRED or Hybrid) based on similarity to the bound ligand and to emit the record to the corresponding port.

Cube Updates

v0.29.1 February 2025

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=6.2.0,<7.0.0.

    • OpenEye-Toolkits>=2024.2.0.

    • OpenEye-szmap>=1.7.1,<2.0.0.

    • OpenEye-szybki>=2.8.0,<3.0.0.

New Cubes

Cube Updates

v0.28.0 July 2024

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=5.1.1,<7.0.0.

    • OpenEye-Toolkits>=2024.1.1.

    • OpenEye-szmap>=1.7.0,<2.0.0.

    • OpenEye-szybki>=2.7.1,<3.0.0.

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

New Cubes

Cube Updates

v0.27.0 February 2024

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=5.1.1,<7.0.0.

    • OpenEye-Toolkits>=2023.2.3.

    • OpenEye-szmap>=1.6.7,<2.0.0.

    • OpenEye-szybki>=2.7.0,<3.0.0.

  • The Cubes FastROCS Molecule Preparation and Parallel FastROCS Molecule Preparation have been removed from exports in the snowball and snowball.shape namespaces. They will need to be explicitly imported when used, that is, with snowball.shape.frocs_prep import FastROCSDataPrepCube, ParallelFastROCSDataPrepCube.

New Cubes

  • The new Chomp Report Cube writes a Floe Report containing BROOD fragment database information.

Cube Updates

v0.26.1 September 2023

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=5.1.1,<7.0.0.

    • OpenEye-Toolkits>=2023.1.0.

    • OpenEye-brood>=3.2.1.0,<4.0.0.

    • OpenEye-szmap>=1.6.6.0,<2.0.0.

    • OpenEye-szybki>=2.6.0.0,<3.0.0.

v0.26.0 July 2023

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=5.1.0,<6.0.0

    • OpenEye-Toolkits>=2023.1.0

    • OpenEye-brood>=3.2.1.0,<4.0.0

    • OpenEye-szmap>=1.6.6.0,<2.0.0

    • OpenEye-szybki>=2.6.0.0,<3.0.0

New Cubes

  • The new BroodDBMergeCube Cube uses the brooddbmerge app to merge the 3D BROOD databases sent to its intake port to produce a merged 3D BROOD database.

  • The new Find Target Name Cube ensures a target name is properly attached to an MMDS target record. If not found, the information will be inferred from header information.

  • A new cube, Brood DB Reader, has been added that reads contents of a BROOD database provided as a tarball and converts that into a set of records.

  • New cubes Brood DB Records Packer and Brood DB Records Unpacker have been added that packs sets of BROOD database records into shards and back.

  • A new cube, BroodMatchCube, has been added that performs a match between a BROOD database fragment against a given query.

  • A new cube, Brood Hit list, has been added that generates a hit list from a given set of BROOD matches.

Cube Updates

  • The following additional parameters are now available in Omega Conformation, Omega Conformation (Modes), Omega Conformation (ROCS mode), Omega Conformation (pose mode), and Omega Conformation (dense mode):

    • External fragments library

    • Fix based on maximum common substructure (MCS)

    • Nitrogen stereo enumeration

    • Ring enumeration

    • Flag to ignore stereo failures

    • Hydrogen sampling

  • The Enumerate Stereo Centers Cube can now handle enhanced stereo information.

  • The Enumerate Nitrogen parameter in the Enumerate Stereo Centers Cube now defaults to False.

  • The ChompMergeFragmentsCube Cube stores fragment information more efficiently to reduce its memory consumption.

  • The ChompLibraryCube Cube has been modified to generate conformers from the 2D fragments instead of working with the molecular conformers passed to the cube.

  • The Atom Potentials Cube fixed an issue with the atom potentials not being properly set on the output record.

  • The Torsion Scan Cube exposes the options for the “Penalty force constant” as well as the new “Number of Starts” and “Overlap divider between starts” torsion options which were added to Szybki TK in the 2023.1.0 toolkit release. This cube also has the option to calculate partial charges, in order to properly support the Parsley and Sage force fields.

  • The Bound Ligand Entropy Cube has been modified to take design units as input, and the cube can now work with FF14SB-Sage and similar custom force-fields.

  • The Ligand Entropy Cube has been modified to enable working with custom OpenFF force-fields.

  • The MMPBSA (Series) Cube now performs calculation on each of the conformers of a given ligand, when ligands with multiple conformers are passed.

  • The Freeform Ligand Strain Cube output records now contain both the free ligand and the restrained ligand conformers corresponding to a tracked ligand conformer.

v0.25.3 December 2022

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=4.5.4,<5.0.0

    • OpenEye-Toolkits>=2022.2.2

    • OpenEye-brood>=3.2.0.1,<4.0.0

    • OpenEye-szmap>=1.6.5.1,<2.0.0

    • OpenEye-szybki>=2.5.1.1,<3.0.0

New Cubes

  • Two new cubes Index Generator and Sorting Records by Index have been added that adds new field with integer indices and sorts based on indices respectively.

  • New cubes Interaction Hint Fingerprint Calculator Cube, and Receptor InteractionHint Fingerprint Annotation Cube have been added. These annotated docking results and receptor datasets, respectively, with fields that can be used for filtering in Orion based on interactions between a docked/posed molecule and the receptor. Additionally, an interaction fingerprint is calculated along with a Tanimoto score to the fingerprint of the ligand bound in the receptor as a reference (if available).

  • A new cube Spruce DU to Mol Simple has been added that subsets a design unit to desired components as a single molecule. A parallel version is also available.

  • A new cube Record to PDB File Converter has been added that converts a molecule to a PDB file and writes it to an Exports folder in the users “My Data” folder. A parallel version is also available.

  • Two new cubes Structure Standardization and DU Validator, and their parallel equivalents were added. The functionality for these cubes have been removed from Spruce Prep and divided into these separate cubes that are used before and after the prep cube. This is to more clearly denote where a structure fails in the standardization and preparation process. Parallel versions of these cubes are also available.

  • A Check for Partial Charges Cube was added that can check if an input molecule has been assigned partial charges. The record will be emitted through the success port if charges are present and through the failure port if not.

Cube Updates

v0.24.1 September 2022

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=4.4.0,<5.0.0

    • OpenEye-Toolkits>=2022.1.1

    • OpenEye-brood>=3.1.7,<4.0.0

    • OpenEye-szmap>=1.6.4,<2.0.0

    • OpenEye-szybki>=2.5.0,<3.0.0

Cube Updates

v0.24.0 July 2022

General Notice

  • This package is built using the following dependencies:

    • openeye-orionplatform>=4.4.0,<5.0.0

    • OpenEye-Toolkits>=2022.1.1

    • OpenEye-brood>=3.1.7,<4.0.0

    • OpenEye-szmap>=1.6.4,<2.0.0

    • OpenEye-szybki>=2.5.0,<3.0.0

New Cubes

Cube Updates

  • A new solvent model parameter has been added to the following cubes. The error handling behavior of these cubes have also been improved.

  • The Ligand Charges now properly handles 2D molecule inputs. The cube also now activates explicit hydrogen atoms irrespective of if the cube was assigning charges or if it was passing forward the available input charges.

  • The Posit now reports an additional field containing the posit method that was used for a prediction. The cube also now properly passes records through the failure port in cases when posit fails due to low probability or clash as desired.

  • The EON Score now keeps all the input record fields in the generated output record.

  • The Freeform Ligand Strain now keeps all the input record fields in the generated strains output record, along with having those fields being kept in the generated ensembles record.

  • The Overlap and Overlap with Grid Query cubes now prepares the input molecules with addition of color atoms and removal of hydrogen atoms, if the molecule did not have any color atoms.

  • The Find Protein cube was modified to add the found protein as a new field in the existing record instead of creating a new record.

  • The Torsion Scan has been improved to include a new force field parameter. The boolean parameter to allow using PB single point energies have been dropped in favor of a new solvent model parameter, that provides additional option to perform a gas-phase calculation.

  • The Spruce Prep has been improved to incorporate the new OESpruceFilter toolkit function, which standardize a structure read from a PDB or MMCIF file, but also fails the structure if specific problems are detected. An option is available to allow failures to pass. Additionally, the new OEValidateDesignUnit toolkit function is used to both style problematic areas of a design unit, and log messages to a validation floe report.

  • The Spruce Prep has been improved to no longer query for the loop database file, but now takes the file ID as initializer input from Loop Database File Look-up. This improves the cubes behavior at large scale use.

  • The Spruce DU to Mol has been improved, to properly mark the first generated molecule as the primary molecule on the record, making export of design units as molecules easier.

  • The Update Design Unit Style has been improved to fail early if the query record does not contain a valid design unit query.

  • The SiteHopper DB Prep and SiteHopper Search have been improved to store and retrieve, respectively, the PDB code, DU title, and target name if available with the data being used to build the database from.

v0.23.1 December 2021

General Notice

  • This package is built using openeye-orionplatform>=4.2.4,<5.0.0 and OpenEye-Toolkits==2021.2.0.

New Cubes

  • The new Field Type Conversion Cube converts a field of one basic type (integer, float, boolean, or string) to a field of another basic type.

  • The new String Field Comparison to Sets of Strings compares the value of a string field to a set of strings and routes records based on whether the value of that string field is contained in the set.

  • The new Process Every N records cube samples every N records from its input, emits those to its success, and others to the failure port.

  • The new Add hydrogens to design unit cube adds protons and optimizes the hydrogen bond network on the input design units or molecules.

  • The new Create DU From Pockets cube takes a design unit and searches for potential binding sites on the protein structure using OEPocket.

  • The new Create DU from f-pocket pockets cube takes a design unit and searches for potential binding sites on the protein structure using F-pocket.

  • The new ROCS Query Model cube builds OEShapeQuery model from bound ligands in the design unit(s)

  • The new Check Design Unit cube identifies if a record contains design unit field and emits the record through different ports accordingly.

  • The new Chemgauss4 Score (Individual) cube calculates checmgauss4 score between the ligand and receptor contained in the input design unit.

  • The new BINT Individual Score and Bint Series Score cubes calculate bint scores between the ligand and receptor contained in the input design unit.

Cube Updates

Deprecated Cubes

The following cubes have been deprecated and will be removed in a future release.

  • DatasetReaderOptCube. This cube is no longer relevant as the DatasetReaderCube in OpenEye-orionplatform has been updated to allow this functionality.

  • ShardReaderOptCube. This cube is no longer relevant as the ShardReaderCube in OpenEye-orionplatform has been updated to allow this functionality.

  • GPU SiteHopper Search. This cube should no longer be used as the toolkit does not allow search directly with a GPU, but only uses it as a pre-screening method.

v0.20.1 June 2021

  • Upgrades to OpenEye-orionplatform==4.0.0 and the associated OpenEye Toolkits

New Cubes

Cube Updates

  • The Find Receptor was updated to be able to find and emit a DU-receptor.

  • The FRED/HYBRID Exhaustive Docking Cube, and similar cubes, were updated to work with DU-receptors.

  • The Exception Handler was updated to avoid processing a fatal error log also being processed as regular failed record log.

  • The Posit was updated to check more thoroughly for input ligand molecules, and to work with DU-receptors.

  • The ROCS Receptor Selector Cube was updated to adjust to the switch to DU receptors.

  • The Omega Macrocycle was updated to not allow output of molecules with dimension less than three.

  • The Freeform Ligand Strain was updated to fix a bug that was producing negative local strain and global strain values.

  • The Posit was updated to output the Chemgauss4 Score for the posed molecule and the number of good interactions as measured by BINT.

  • The AddContexts cube was updated to skip adding targets to MMDS if another target with their same parent name alrady exists.

  • The Spruce DU to Mol cube was updated to use sensible defaults for field names. It was also updated to give users more control and the ability to output additional mol components into separate fields.

  • The Float Hit List cube, Integer Hit List cube, and String Hit List cube were updated to use their specific respective field parameter types.

  • A bug with the URL in the GenerateProasisFamilyTreeData cube was fixed.

  • The superposition method selection for families was fixed in DefineFamilyReferenceStructure cube.

  • The Input Files for Spruce cube was updated to properly read in .gz files.

v0.20.1 November 2020

  • Upgrades to OpenEye-orionplatform==3.1.0 and the associated OpenEye Toolkits

New Cubes

A number of cubes have been added to support SiteHopper patch database generation and searching.

  • New SiteHopperPatchDBGenCube Cube that reads in a collection of prepared OEDesignUnits on records and creates SiteHopper patches from the binding site of each OEDesignUnit. A parallel version also exists ParallelSiteHopperPatchDBGenCube.

  • New SiteHopperPatchDBDatasetCube Cube that ties in the prepared OEDesignUnit collection with the collection of patches into a single record during patch databse generation. The SiteHopperUnpackDBDatasetCube Cube is used during search to extract the proper collection IDs for use by the search and related cubes.

  • New SiteHopper Search Cube, that performs a SiteHopper search on a supplied patch database using a reference OEDesignUnit as the query. A parallel version of this Cube also exists, Parallel SiteHopper Search. In addition a serial and parallel version that utilizes the GPU to search exists GPU SiteHopper Search and Parallel GPU SiteHopper Search.

  • New SiteHopperResultTransformation Cube, that performs a normal CPU re-scoring of the patches, as well as the option to normalize the patches against the query patch and re-score the similarly sized patches. The cube transforms the OEDesignUnits onto the reference frame, with the overlay provided by SiteHopper. A parallel version of this cube is also provided, ParallelSiteHopperResultTransformation.

  • New DUSequenceScore Cube, that compares the sequence of the SiteHopper query OEDesignUnit to the hits, with the ability to filter out results that are too similar in sequence. A parallel version of this cube is also provided, ParallelDUSequenceScore.

  • New Update Design Unit Style Cube, that colors the OEDesignUnits for each hit in the output records with random colors to ensure easier visualization in 3D.

A number of cubes have been added to support populating MMDS using Floe. This includes generating a collection of prepared OEDesignUnits, datasets of targets and target families as well as cubes that allow uploading data into MMDS (for MMDS admins only).

  • New Create Structure Collection Cube that either creates or updates an existing collection. The Cube emits the collection and existing shards via different ports.

  • New Fetch all current PDB codes Cube that retrieves all known PDB codes from the RCSB and makes a record for each with the code and the latest revision.

  • New Check for collection dupes Cube that reads all the shards in a provided collection and checks whether a PDB code and revision already exists in the collection. Only codes not already present are emitted. Shards that are present but where the code has been deprecated or a new revision has been added are deleted from the collection.

  • New PDB codes to Records Cube that works similarly to the existing Input PDB Codes for Spruce Cube, but instead of input parameters takes input from records provided via the intake port. A parallel version of this cube is also provided, Parallel PDB codes to Records.

  • New Convert Structure Records to shards Cube that takes records with PDB data and converts them into a shard each. The shard is named by the PDB code for easier look-up later and the PDB revision (ordinal) is stored in the shard metadata. A parallel version of this cube is also provided, Parallel Convert Structure Records to Shards.

  • New GenerateGtoPFamilyTreeData Cube that reads the family hiearchy from the Guide to Pharmacology database and generates a dataset from it.

  • New GenerateGtoPTargetData Cube that reads the target information from Guide to Pharmacology and maps the target UniProtKb IDs to PDB codes.

  • New UpdateTargetStructures Cube that can update a dataset of targets if new structures have been added to that target since last updated.

  • New DefineTargetReferenceStructure Cube that attempts to find a common reference structure for a given target based on a consensus biological unit and binding site location. A parallel version of this cube is also provided, Parallel Define Target Reference Structure.

  • New DefineFamilyReferenceStructure Cube that reads the reference structures for each target in a family and looks to see if they can all be superposed to a common reference frame. It subsequently checks whether each family member node can be superposed with other family members at the same level in the tree.

  • New TargetStructureMappingCube Cube that takes a dataset of targets and matches up the reference structure for a given target to each of the PDB codes belonging to that target for structure preparation. A parallel version of this cube is also provided, Parallel Target Structure Mapping.

  • New Spruce Prep for MMDS Cube that works identically to the existing Spruce Prep, but instead of records operates on shards. An output shard contains all the prepared OEDesignUnit records for a given PDB code. A parallel version of this cube is also provided, Parallel Spruce Prep for MMDS.

  • New Spruce depiction cube for MMDS Cube that works identically to the existing Spruce Depiction, but instead of records operates on shards. A parallel version of this cube is also provided, Parallel Spruce Depiction Cube for MMDS.

  • New AddFamilies Cube that takes a dataset and builds a family tree from it.

  • New AddContexts Cube that takes a dataset and adds every context (target) at the proper location in the family tree. A parallel version of this cube is also provided, Parallel Inject Target Tree into MMDS.

  • New AddExperimentsAndSites Cube that reads a collection of data for each PDB code and merges it into MMDS. It also reads a collection of prepared OEDesignUnits and uploads these as well. A parallel version of this cube is also provided, Parallel Inject Experiment and Site into MMDS.

  • New AddReceptorForFrame Cube that adds OEDocking receptors to every frame in MMDS. A parallel version of this cube is also provided, Parallel Add receptor for a frame in MMDS.

  • New AddContextSeqAlign Cube that pulls all the frames for each context and generates a sequence alignment for all the structures. Contexts with an existing alignment are skipped, unless the context has had new structures added. A parallel version of this cube is also provided, Parallel Add Sequence Alignment to a Context in MMDS.

  • New GetContextIDs Cube that outputs a dataset of existing context (target) IDs from MMDS.

  • New GetFrames Cube that outputs a dataset of existing frame IDs from MMDS.

A number of cubes have also been added that instead of reaching out to public sources instead can extract data from a Proasis server based on a user provided host url.

  • New GetProasisCodes Cube, mimics Fetch all current PDB codes. A specialization of this cube has also been added that instead of reading all existing codes just reads the latest codes based on a number of days in the past, GetRecentProasisUpdates Cube.

  • New ProasisCodesToInputRecords2 Cube, mimics PDB codes to Records Cube. A parallel version of this cube is also provided, Parallel Structure IDs to Records.

  • New GenerateProasisFamilyTreeData Cube, mimics GenerateGtoPFamilyTreeData.

  • New GenerateProasisTargetData Cube, mimics GenerateGtoPTargetData.

  • New DeletePDBCodesCube Cube that removes a bad PDB code from MMDS, the prepared OEDesignUnit collection and the PDB file collection.

Cube Updates

  • The Input PDB Codes for Spruce now adds the revision number (ordinal) when pulling data from the RCSB.

  • The Assign Partial Charges Cube was improved. A parameter was added to specify whether to use input conformers or not for am1bccelf10 charges. If not, Omega will be used to generate conformers.

  • The Gameplan was updated to handle failures to the fatal port.

  • The Exhaustive Docking (Single Receptor) no longer emits a record with emtpy molecule when the docking produces no results.

  • The Freeform Solvation Energy was updated so that the output molecule from the solvation is on the output record. Parameters were also added for chosing the ionic states for the calculation and if the input 3D structure should be solvated without further optimization.

v0.19.3 August 2020

Cube Updates

  • The Spruce Depiction was updated to handle modeled structures where Iridium data is not available on the DesignUnit

  • The Spruce Prep was updated to resolve issues with modeled loops.

v0.19.1 August 2020

  • Upgrades to OpenEye-orionplatform==3.0.0 the associated OpenEye Toolkits

New Cubes

  • New Spruce Depiction which generates multiple interactive depictions of the design unit. The depictions are target-ligand interactions, b-factor visualization, 3) Iridium data visualization, and if electron density data is available, 4) ligand density coverage.

  • New DesignUnit Type ETL. OEDesignUnit have gotten native support in datarecord as Types.Chem.DesignUnit. This cube converts fields with the old design unit blob type and adds a new field with the native type. For backwards compatibility it currently preserves the existing field.

  • New Named Dataset Reader, Named File Reader, and Named Collection Reader read dataset, file and collection specified by their names. They allow floe developers to permenently customize their floes to utilize a specific resource.

  • New Calculate RMSD performs RMSD calculation between a 3D reference molecule and multi-conformation molecules.

  • New Find ShapeQuery identifies shape query in a record. If a shape query is not found, the cube looks for the primary molecule and creates a shape query from that molecule.

  • New Convert Shape Query to Record reads a shape query file (.sq) and converts the shape query to a record.

  • New Single File Reader reads a single file and emits its contents in a stream. It will throw a runtime error if two or more files are used as input.

  • New Record Splitting By Charges splits records into two streams by whether the molecule is charged.

Cube Updates

Removed Cubes

  • Removed DUFileToRecords cube which is no longer needed as Orion will automatically, upload and ETL an OEDU file to a record.

v0.18.2 April 2020

General Notice

  • Upgrades to OpenEye-orionplatform==2.4.5

New Cubes

  • New Record Counter Switch added that can switch floe path based on the number of records in the initializer port.

  • New Rotate Surface rotates a surface by a 3x3 matrix specified as a 9-element array in row-major order.

  • New Transform Surface transforms a surface using a supplied OETrans object.

  • New Translate Surface translates the surface using the supplied 3-element translation vector.

  • New Dataset Reader Optional to allow a user to pass an optional reference design unit to use when preparing new structures in Spruce.

  • New Input Files for Spruce, which is a re-work of the older and removed PDBFileToInputRecord. This cube takes a set of input PDB files, optional MTZ files, and optional metadata JSON files and pairs them up as input records for Spruce structure preparation.

  • New Input PDB Codes for Spruce, which is a re-work of the older and removed PDBCodeToInputRecords. This cube downloads PDB (fall-back to MMCIF) files and any associated MTZ files and puts them into records for Spruce structure preparation.

  • New Molecule Filtering cube has been added that filters molecules based on a user-defined filter type.

  • New Uncolor Molecule Graph cube has been added that uncolors molecular graphs i.e. removes certain atom and bond properties.

  • New Random N Record Selection cube has been added that randomly selects N records.

  • New Concatenate Records cube has been added that concatenates datasets.

  • New Classification Based on String Field cube has been added that allows classification of records based an a specified string field.

  • New String Fields Comparison to Sets of Strings cube has been added that filters out records based on the string data of reference records.

The following cubes have been added to mimic some of the stages of biomolecule preparation being done automatically in Spruce. They all, except the Spruce BioUnit Extract, take a dataset with designunits as input. The editing cubes updates the design units on the record. To be able to use them for downstream cubes or floes, after editing, the design units on the records must be converted to molecules or receptors (see conversion cubes section following this section).

  • New Spruce BioUnit Extract, which generates biological units from an input asymmetric unit crystal structure.

  • New Spruce sidechain builder cube, takes a dataset of designunits and builds out partial or missing sidechains.

  • New Spruce capping cube, takes a dataset of designunits and caps any chain breaks.

  • New Spruce swamp metal cube, takes a dataset of designunits and converts specified metals, e.g. Zn to Mg.

  • New Spruce mutation cube, takes a dataset of designunits and attempts to mutate specified residues.

  • New Spruce residue state cube, takes a dataset of designunits and changes the state of specified titratable residues.

  • New Spruce rotamers cube, takes a dataset of designunits and returns multiple records per design unit each with different rotamers of a specified residue (non-clashing is default, but optional).

  • New Spruce subset cube, takes a dataset of designunits and subsets them based on inputs, to remove entire design unit components or remove pieces specified by residue identifiers.

  • New Spruce subset within cube, takes a dataset of designunits and subsets a component of each design unit, e.g. subset the solvent to include only those within 5A of the protein and ligand components.

  • New Spruce Superpose, takes a dataset with a reference design unit and a dataset of designunits, and superposes each design unit in the dataset to the reference. Several superposition methods are available.

  • New Spruce Minimize Design Unit Cube, takes a dataset of designunits and minimizes parts of the designunits based on input parameters.

The following cubes have been added that convert design units to molecules or receptors, for use in subsequent cubes or floes.

  • New Spruce DU to Mol, which converts the design unit to a molecule and optionally splits out the ligand to a separate field. All the content in the design unit is output to the molecule, if less is required, first subset the design unit with the cubes: Spruce subset cube or Spruce subset within cube.

  • New DUToReceptor, is a cube split out from the old DUtoReceptorMDRecord, to split the two operations therein. This cube takes a DU and writes a receptor for use in docking.

  • New DUToMDRecord, is a cube split out from the old DUtoReceptorMDRecord, to split the two operations therein. This cube takes a DU and writes an complex (not including the ligand), that can be used in MD floes, e.g. Short Trajectory MD floes.

Cube Updates

  • The DUFileToRecords, has been updated to take multiple input files.

  • The Spruce Prep, has been updated, to take an optional reference design unit using the initializer port, additional options for preparation have been exposed, and several of the input parameters have been updated to make parameter selection easier.

  • The MDL Substructure Map now emits unmatched molecules through the failure port.

  • The Exhaustive Docking (Single Receptor) now exits properly when initialization fails.

  • The Torsion Scan now has a torsion increment option to change the resolution of the torsion drive. It also fails more gracefully when coordinates cannot be generated or the torsion cannot be identified.

  • The Splitting Conformers now has the option to move conformer fields to the primary record after splitting.

  • The Prepare Molecule for 2D Depiction cube now can keep the coordinates of the primary molecule and store the 2D coordinates in a new field specified by a new string parameter.

  • The following changes have been made for the Move Field cube:

    • It now handles cases when the specified field does not exist on the record.

    • A new parameter has been added that allows to move records with missing field to the success port.

    • A fatal port has been added in order to handle cases when no field was renamed in any of the records.

  • The following changes have been made for the Structure to SMILES cube:

    • Meta.Hints.Chem.SMILES meta data is added to the SMILES field

    • It re-perceives all necessary perception upon request.

    • It noew generates the following SMILES: non-canonical, non-isomeric-canonical, and isomeric-canonical (default)

Removed Cubes

  • Removed DUtoTgtLigRecords cube which was unused.

  • The following cubes have been removed and replaced with the new Input PDB Codes for Spruce: GetPDBplusMap, PDBCodeToUrl, UrlToFile, PDBCodeToInputRecord, MultiplePDBCodesToInputRecord.

  • The following cubes have been removed and replaced with the new Input PDB Codes for Spruce: PDBFileToInputRecord, InputRecordtoDataset.

  • The following cubes have been removed and replaced with new DUToReceptor and new DUToMDRecord: DUtoReceptorMDRecord, ReceptorMDRecordToDataset, DUtoReceptorMDDataset.

v0.17.2 November 2019

General Notice

New Cubes

Cube Updates

v0.16.6 September 2019

General Notice

  • Upgrades to OpenEye-orionplatform==1.1.4

  • Upgrades to OpenEye-floereport==0.1.5

  • Static variables are no longer used, other than as the parameter variables.

New Cubes

Cube Updates

v0.16.0 July 2019

General Notice

  • Upgrades to OpenEye-orionplatform==1.0.0

v0.15.0 June 2019

General Notice

  • Upgrades to OpenEye-orionplatform==0.3.2

v0.14.0 June 2019

General Notice

New Cubes

  • New Gameplan Report Cube to report Gameplan results and app generated log files.

  • New Brood Report Cube to report Brood results and app generated log files.

  • New ROCS with Multi-conformer Query cube that works with a multi conformer query molecule.

  • New SingleReceptorPositCube specifically for single receptor pose prediction.

  • New DUtoTgtLigRecords to extract target and ligand DataRecords from OEDesignUnits.

  • New DatasetReaderOpt to read records with an optional data source.

Cube Updates

  • Exhaustive Docking (Single Receptor) no longer produce docked pose with unusually high docking scores.

  • ROCS, SubROCS and Best Overlay Transform now works with a single conformer query molecule only and no longer produce a Query Conformer field in the output record.

  • OEStructureBasedLigandDesignCube now checks for memory limits corresponding to the number of receptors and poser cash size before starting to pose.

  • Updated BroodCube documentation.

  • Updated Gameplan documentation.

  • Spruce cubes have been updated to use and output OEChem::OEDesignUnit object files (.oedu), which are new to the 2019.Apr release of the OpenEye Toolkits.

v0.13.6 March 2019

General Notice

  • Upgrades to OpenEye-orionplatform==0.1.14

New Cubes

Cube Updates

v0.13.4 November 2018

General Notice

Cube Updates

  • Minor fix to Omega Conformation to preserve molecule titles.

  • Speed up fix for many of the FreeFormConf cubes.

  • Updated the Hermite shape cubes for compatibility with the 2018.Oct release of the OpenEye Toolkits

v0.13.3 September 2018

General Notice

  • Upgrades to use OpenEye-orionplatform==0.1.7

New Cubes

Cube Updates

  • CalculateXLogPCube now calculates XLogP on the neutral form of the molecule. A new parameter has been added to the cube, called Keep Neutral Form, which controls whether to keep the neutral form of the molecule after the calculation or restore the original input form.

v0.13.0 August 2018

General Notice

  • Upgrades to use OpenEye-orionplatform==0.1.0

Utility Floes Release Notes

v2.1.4 December 2025

  • This package is built using OpenEye-orionplatform==6.8.0, OpenEye-toolkits==2025.2.1, and OpenEye-Snowball==0.31.1.

v2.1.2 September 2025

  • This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.1.1, and OpenEye-Snowball==0.30.2.

v2.1.1 August 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.1.1, and OpenEye-Snowball==0.30.0.

Floe Updates

  • The following improvement has been made to the OMEGA - 3D Conformer Ensemble Generation Floe: A new Conformer Generation Mode option, ROCS-TS, has been added which uses Thompson Sampling to generate conformers suitable for ROCS calculations.

v2.0.1 February 2025

General Notice

This is a new package as a part of the Orion Floes reorganization. It includes floes previously found in the Classic, Cheminfo, and Biomodeler Floes packages.

  • This package is built using OpenEye-orionplatform==6.3.1, OpenEye-toolkits==2024.2.1, and OpenEye-Snowball==0.29.1.

Floe Updates

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

    • Metadata handling has been improved. Metadata file input is promoted with improved descriptions and better logging if a metadata file was not matched to an input structure file.

    • The Add Ligand Smiles parameter has been added to better identify global ligand metadata and tautomer states.

    • The handling of receptors for covalently bonded ligands has been improved.

    • MTZ data handling has been updated after recent changes to the RCSB offerings of the EDMAPS Announcement.

  • The Calculate Average Precision Floe has been removed.

Recent Release History