Dataset to Reaction & Reagent Database

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_2021_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.

Extra Required Parameters

  • Input Dataset (data_source) : The dataset(s) to read records from
  • String Key (Field Type: String) : Name of the string field containing the key to deduplicate records on
  • Molecule Filtering (boolean) : If ON, performs filtering of reagents prior to classification
    Default: True
  • Reagent Id (Field Type: String) : Field containing the reagent id or catalog number
  • Smiles Field (Field Type: String) : Name of the string field containing SMILES of the classified structures
  • Output Database Name (file_out) : Name for the Orion file resource being generated
  • Reagent Class Field (Field Type: String) : Name of the field for annotating the reagent class information
    Default: ReagentClass
  • Reagent Id (Field Type: String) : Field containing the reagent id or catalog number
  • Smiles Field (Field Type: String) : Name of the string field containing SMILES for the structures to be classified
  • Reagent Class Field (Field Type: String) : Name of the field for annotating the reagent class information
    Default: ReagentClass
  • SMILES field (Field Type: String) : SMILES field to be updated based on the primary molecule
    Default: smiles
  • SMILES Generation Option (string) : default:add the smiles field if it does not exist, force:add or update the smiles field regardless of field presence
    Default: default
    Choices: default, force
  • Reaction Definition File (file_in) : The name of file resource containing the reaction definitions
  • Output Database Name (file_out) : Name for the Orion file resource being generated