Dataset to Reaction & Reagent Database

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Hit to Lead/Generative Design/Reaction-based Libraries

  • Task-based/Library Prep & Design/Reaction-based Enumeration

  • Role-based/Cheminformatician/Medicinal Chemistry Support

  • Role-based/Cheminformatician/Corporate Collection Support

Description

This floe is used to populate a reaction & reagent database with a set of user-provided structures. One (or more) datasets can be selected as input. Each record must have a primary molecule, and a field that identifies a unique reagent identification tag.

Launching the Floe

The floe requires a valid reaction definition file that defines the reactions, and associated reagent chemistry for classification of input structures. A sample reaction definition file, sample_reaction_classification_2022_2.txt is available from the OpenEye Organization resources. At the time of this release, the documentation for generating a custom version of this file is not yet available. If you have the need to undertake this activity, contact OpenEye Support (mailto:support@eyesopen.com) for additional details.

The name of the output reaction & reagent database should be specified with a scheme that serves as a reminder of the class/type/date of the structures used to generate it. The reaction & reagent database file generated will be an Orion file resource with the floe user’s credentials.

Promoted Parameters

Title in user interface (promoted name)

Dataset Processing Options

Molecule Field (molfield): Field containing the unclassified reagent molecules

  • Type: field_parameter::mol

Reagent Id (molid): Field containing the reagent id or catalog number, or use the keyword TITLE to use the primary molecule title as the unique id

  • Required

  • Type: field_parameter::string

Functional Group Transformations (enablefngroups): If ON, allows interconversion of simple functional groups per the reaction definitions during reagent classification

  • Type: boolean

  • Default: True

  • Choices: [True, False]

SMILES Generation Option (gensmi): default:add the smiles field if it does not exist, force:add or update the smiles field regardless of field presence

  • Required

  • Type: string

  • Default: default

  • Choices: [‘default’, ‘force’]

Salt Chop (saltchop): If ON, retains only the largest fragment from the input structures

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Neutralize Charges (neutralize): If ON, removes all formal charges other than quaternary amines, correcting hydrogen counts.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Molecule Filtering (filter_mols): If ON, performs filtering of reagents prior to classification

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Custom Filter File (filter_file): An filter file resource to load (supersedes the default)

  • Type: file_in

Filter Summary Report (filter_summary): if ON, will enable a summary report of the rules for the filtered molecules

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Verbosity (verbosity): Sets the output logging verbosity

  • Type: string

  • Default: warning

  • Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]