Release Notes

v0.9.3 July 2024

Updates to the Generative Design Floes - Base & Advanced Packages

All packages have been built using OpenEye-orionplatform==6.2.0, OpenEye-toolkits==2024.1.1, and OpenEye-Snowball==0.28.0.
The Reaction & Reagent Database - Create from BULK SMILES Floe, used to index structures from SMILES file resources, has been improved and modified for better performance. Defaults for several indexing parameters have been altered from the prior version to better match standard indexing activites.
The Reaction & Reagent Database - Create from SMILES Floe has been replaced by the improved Reaction & Reagent Database - Create from BULK SMILES Floe.
A logic error that did not allow disabling filtering and/or deduplication has been fixed. This error impacted the Focused Library - Core Input Floe.
The Reaction & Reagent Database - Directory Listing Floe, which is used to generate a directory of reactions from a Reaction & Reagent database, has a new parameter that can be used to suppress reaction depictions from the Floe Report to expedite the report generation. Another new parameter can enable the export of the reaction definitions from an existing database.
General internal code changes and improvements have been made to support new floes in upcoming releases.

v0.7.1 September 2023

Updates to the Generative Design Floes - Base & Advanced Packages

A run-time error in the initialization of the molecule classifier cube was fixed. This error impacted Focused Library - Molecule Input, Focused Library - Synthon Analogs, and Reaction & Reagent Database - Reagent Molecule Classification.
Options previously added to Reaction & Reagent Database - Retrieve Reaction Reagents induced floe errors in a related floe, Focused Library - Reagent Join, which has been repaired.

v0.7.0 July 2023

Updates to the Generative Design Floes - Advanced Package

A new experimental floe has been added that can be used to launch product enumerations, Reaction & Reagent Database - Launch Product Enumerations.

Bug fixes and features

All packages have been built using OpenEye-orionplatform==5.1.0, OpenEye-toolkits==2023.1.0, and OpenEye-Snowball==0.26.0.
Floes having a Reaction & Reagent Database input parameter now fail more gracefully if an incorrect resource is erroneously provided.
All instance pinning specifications have been removed to make floes more stack agnostic.
A parameter has been promoted to control memory limits for reaction classifiers for user control in relevant floes.
A parameter has been promoted to control memory limits for structure deduplication activities for user control in relevant floes.
A new parameter that allows exporting reagents as an Orion File resource in CSV format has been added to Reaction & Reagent Database - Retrieve Reaction Reagents.
A new parameter that exposes the maximum hits per query has been added to MaaS Available Analogs.
Numerous floes have been renamed to ensure related floes appear together in a floe listing of the package(s).
New parameter groups have been added to the Reaction & Reagent Database - Reaction Definition Validator Floe to improve usability.
Internal bug fixes and improvements have been made.

v0.6.0 December 2022

Bug fixes and features

All packages were built using OpenEye-orionplatform==4.5.4, OpenEye-toolkits==2022.2.1, and OpenEye-Snowball==0.25.2.
A defect that did not allow the use of a custom filter file specification has been repaired.
A number of new parameter groups have been added to the “Focused Library” floes to improve usability.
Promoted a parameter that controls memory limits for structure deduplication for user control in relevant floes.
Updated copyright headers for non-sample code
Internal bug fixes and improvements

v0.5.1 September 2022

Bug fixes and features

A defect that resulted in run-time errors for the Reaction & Reagent Database Validator floe has been repaired.
The SMILES, Zinc, and Dataset indexing floes used to create Reaction & Reagent databases now support two trivial input structure normalizations: salt chopping and charge neutralization, default: disabled.
The Focused Library - Molecule Input floe now supports the ability select specific functional group transformation(s) to be applied to the Lead Molecule input structure(s). If the reaction definitions include deprotection transformations, the modified/deprotected lead molecules can then be transformed by the selected reactions.
The Focused Library - Molecule Input floe parameter “Allow Functional Group Conversions” has been moved to the “Focused Library Options” parameter group for greater visibility.
The Focused Library - Molecule Input floe has a few new option parameter groups to increase visibility and segregate unrelated parameters for better usability.

v0.5.0 July 2022

Enhancements to reaction definitions

Explicit functional group transformation(s) can now be defined allowing simple group transformations to be considered during reagent classifications. This can dramatically increase the size of the reagent pool(s) for defined reactions by allowing more general (or equivalent) input reagent chemistry.

General enhancements

All floes have a new brief parameter and floe categories.
All packages were built using OpenEye-orionplatform==4.4.0, OpenEye-toolkits==2022.1.1, and OpenEye-Snowball==0.24.0.
Various changes to ordering and arrangement of promoted parameters was undertaken for several floes to increase usability and control.
New 2022.2 sample reaction definition file for use in indexing and customization.
New 2022.2 versions of the low complexity and high medchem interest sample ZINC databases.
New 2022.2 version of MMP transforms extracted from chembl_30 structures with solubility data.
New 2022.2 version of MMP transforms extracted from the 2022 June Enamine Building Block Rush delivery US+EU structures.
New 2022.2 version of the Graft index for the chembl_30 structures with solubility data.
New 2022.2 version of the Graft index for the 2022 June Enamine Building Block Rush delivery US+EU structures.

Updates to the Generative Design Floes package

Added parameter control for enabling or disabling new Functional Group transformations to relevant floes.

Updates to the Generative Design Floes - Advanced package

Added parameter control for enabling or disabling new Functional Group transformations to several reaction floes.
New floe added: SMILES File to Reaction & Reagent Database which supports use of non-ETL’d SMILES file resources for Reaction & Reagent Database creation.
Added the keyword TITLE allowing the use of the primary molecule title pseudo-field as the unique id for Reaction & Reagent Database creation.

Updates to the Generative Design Floes - MaaS package

Added a text parameter that allows specification of MaaS databases that are customer-specific additions to the 2022.2 MaaS database list. See MaaS Available Analogs and MaaS Substructure Search
Promoted several cube-level parameters for MaaS Available Analogs for easier control over the floe actions.
Support explicit SMARTS vs SMILES substructure query typing to suppress issues with attempted automatic typing.
The “Known Analog Reader” option in the analog and substructure floes is now functional.
Updated the database list to reflect 2022.2 MaaS service offerings.

v0.4.0 December 2021

Enhancements to reaction definitions

Retro-reaction transformation(s) can now be defined for reactions.
Added support for a reaction depiction example specification for each reaction definition.
Added valence correction options for transformations as a placeholder for future implementation work.
Reaction & Reagent databases retain backward compatibility with prior versions.

Additional enhancements

New 2021.2 sample version of the reaction definition file for use in indexing and customization.
New 2021.2 versions of the lowcomplexity and high medchem interest sample ZINC.
Updated package dependencies to the latest Orion-platform and OpenEye Toolkits versions.
Numerous internal error handling and code refinements.

Updates to the Generative Design Floes package

New floe added: Focused Library - Synthon Analogs.
Generative Structure Floe.
- Fixed an issue with the Graft method that inadvertantly lost structures specific to this method.

Updates to the Reaction Floes - Advanced package

Reaction & Reagent Database Validator
- Preliminary validation of retro-reactions added to validation floe report.
- Gracefully handle missing (optional) indexing statistics table from the db.
- General cleanup and improvements to the validation floe report.
Reaction & Reagent Database Directory
- Added a reaction depiction column to the floe report that either displays the reaction depiction example (if defined), or samples reagents to obtain a trivial example reaction to use as the depiction image.
- Removed information about mapping and classifying ratios from the directory listing to reduce user confusion. This information is available in the reaction validation floe report.
ZINC Download to Reaction & Reagent Database
- Increased a max_parallel option to support indexing of larger tranche selections.
- Increased the default memory limit of the deduplication cube to support a greater number structure deduplications without requiring explicit user manipulation of cube parameters.
Dataset to Reaction & Reagent Database
- Increased the default memory limit of the deduplication cube to support a greater number structure deduplications without requiring explicit user manipulation of cube parameters.

v0.3.2 July 2021

Fixed a run-time failure in the “Reagent Molecule Classification” floe for uncategorized molecules
Rename input parameter(s) to match “Reaction & Reagent Database”

v0.3.1 June 2021

Updated dependencies for Orion-platform and Orion-maasclient
Added new reaction floes to complement existing Generative Design floes
Numerous fixes and updates for the application of Graft/MMP/Sprout/Trim/Join methods were made to the Generative Structure Floe and the Generative Structure Floe - Site selection floes to prepare for incorporation into larger floes.
Updates to the Generative Design Floes package
- moved indexing floes to the Generative Design Floes - Advanced package
- new floe added
  - Focused Library - Core Input
Updates to the Generative Design Floes - MaaS package
- new floe added
  - MaaS Substructure Search
    
    Added a MaaS substructure search floe that performs a simple substructure search of MaaS databases given a set of input SMARTS queries. The hits are annotated with the query and database, so duplicate hits (from different sources) are possible in the output dataset.
Added a new Generative Design Floes - Advanced package
- relocated indexing floes from the Generative Design Floes package here
  - Graft Database Generator
  - MMP Molecule Indexer
  - MMP Transform Extractor
- new floes added
  - Dataset to Reaction & Reagent Database
  - ZINC Download to Reaction & Reagent Database
  - Focused Library - Molecule Input
  - Focused Library - Reagent Join
  - Reaction & Reagent Database Directory
  - Reagent Molecule Classification
- new experimental floes added
  - Reaction & Reagent Database Validator
  - Reagent Definition Generator
  - Half Reaction Generator
  - Retrieve Reaction Reagents

v0.2.14 November 2020

OEAssignMDLHydrogens is preferred call for valence corrections

v0.2.13 November 2020

Updated dependencies for Orion-platform and Orion-maasclient

v0.2.12 August 2020

Added a new generative method, Join for reagent joining and a default reagent set based on Topliss fragments. This method is only available for the Generative Structure Floe - Site selection floe as it requires user input to indicate the site of the modifications.
Added a new generative method, Sprout for simple sprouting of customizable atoms.
Added a new generative method, Trim for single atom clipping/edits of customizable atom types.
Added an optional ability to perform molecule filtering on the generated analogs.
Added a fast and cached version of structure deduplication. The cached version is appropriate for small numbers of analogs, and provides an annotation of which method(s) generated each analog. The fast version should be used for large generated analog sets, but lacks the ability to annotate each analog with all methods that generated it.

v0.2.11 May 2020

Preliminary release of a package providing Generative Structure Design. Two generative methods are provided, Graft and Matched Molecular Pairs. Default indices are provided for each, as well as separate indexing (& extraction) floes that provide the ability to generate indices based on user-provided chemical structures. Optional property calculations can be enabled on the generated analogs.