Reaction & Reagent Database - Create from Dataset

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, 2024_2_sample_reaction_classification.txt is available from the OpenEye Organization resources. The documentation for generating a custom version of this file is not currently 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): A 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]

Classifier Memory Limit (classifiermem): The memory limit for the reaction classifier. It may need to be increased for large R&R Databases.

  • Required

  • Type: decimal

  • Default: 10240

Verbosity (verbosity): Sets the output logging verbosity.

  • Type: string

  • Default: warning

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