Release Notes

v0.4.0 December 2021 (Orion Release 2021.2.1)

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 enhancments

  • 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

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 (Orion Release 2021.1.2)

  • 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 (Orion Release 2021.1)

  • 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.