Reaction & Reagent Database - Create from BULK 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. The floe assumes a large input SMI file resouce, generally in the 100M or more record size.
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. 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)
Input Parameters
Reaction Definition File (rxndefs): The name of the file resource containing the reaction definitions.
Required
Type: file_in
SMI File Resource (SMI_file): A previously uploaded SMILES (.smi) or CXSMILES (.cxsmiles) 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
Output Parameters
Output Reaction & Reagent Database Name (rrdb_output): Name for the Orion file resource being generated.
Required
Type: file_out
Filtering & Processing Options
Functional Group Transformations (enablefngroups): If ON, allows interconversion of simple functional groups per the reaction definitions during reagent classification.
Type: boolean
Default: False
Choices: [True, False]
Molecule Filtering (filter_mols): If ON, performs filtering of reagents prior to classification.
Required
Type: boolean
Default: False
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]
Structure Normalization Options
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]
Valence Handling (fixvalences): How to handle valence issues for input building blocks: ignore: ignore valence errors, fix: attempt to repair valence issues, reject: reject valence errors. Valence issues after attempted fixes are also rejected.
Type: string
Default: fix
Choices: [‘ignore’, ‘fix’, ‘reject’]
Advanced Options
Record Batch Size (batchsize): The number of records to emit in each shard/block.
Required
Type: integer
Default: 10000
SMI Disk Space Limit (smidiskspace): The minimum amount of disk space in (MiB) to accomodate the input bulk SMILES file.
Required
Type: decimal
Default: 20000
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’]