Reaction & Reagent Database - Create from SMILES

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 from a previously uploaded SMI file resource.

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 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 SMI source and filtering used for the structure selection. The Reaction & Reagent Database file generated will be an Orion file resource with the floe user’s credentials in the specified output folder.

Promoted Parameters

Title in user interface (promoted name)

Processing Options

SMI File Resource (SMI_file): A previously uploaded SMILES (.smi) file resource. This should be an Orion file resource that minimally provides a SMILES and a unique ID for each structure. Note that the default Orion ETL (conversion to dataset) activity should be suppressed for such file uploads.

  • Type: file_in

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]

Strip Salts (saltchop): If set, retains only the largest fragment from each input structure prior to indexing.

  • 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’]