Reaction & Reagent Database - Multi-vendor - Create from BULK SMILES

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.

Multiple vendor inputs are supported to allow tagging and tracking alternate BB vendor selections downstream.

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, 2025_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

Output Parameters

Reaction & Reagent Database Name (rrdb_output): Name for the Orion file resource being generated.

  • Required

  • Type: file_out

VendorA Input

VendorA SMI File (A_SMI): A previously uploaded SMILES (.smi) or CXSMILES (.cxsmiles) file resource. This should be one or more Orion file resource(s) 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. Gzipped input files are also supported but the file resource MUST have the .gz suffix on the name.

  • Required

  • Type: file_in

VendorA ID (A_id): The id or key to use for the vendor.

  • Required

  • Type: string

VendorA Name (A_name): The full or descriptive name for the vendor.

  • Required

  • Type: string

VendorA Version (A_ver): Optional vendor version information.

  • Type: string

VendorB Input

VendorB SMI File (B_SMI): A previously uploaded SMILES (.smi) or CXSMILES (.cxsmiles) file resource. This should be one or more Orion file resource(s) 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. Gzipped input files are also supported but the file resource MUST have the .gz suffix on the name.

  • Type: file_in

VendorB ID (B_id): The id or key to use for the vendor.

  • Type: string

VendorB Name (B_name): The full or descriptive name for the vendor.

  • Type: string

VendorB Version (B_ver): Optional vendor version information.

  • Type: string

VendorC Input

VendorC SMI File (C_SMI): A previously uploaded SMILES (.smi) or CXSMILES (.cxsmiles) file resource. This should be one or more Orion file resource(s) 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. Gzipped input files are also supported but the file resource MUST have the .gz suffix on the name.

  • Type: file_in

VendorC ID (C_id): The id or key to use for the vendor.

  • Type: string

VendorC Name (C_name): The full or descriptive name for the vendor.

  • Type: string

VendorC Version (C_ver): Optional vendor version information.

  • Type: string

VendorD Input

VendorD SMI File (D_SMI): A previously uploaded SMILES (.smi) or CXSMILES (.cxsmiles) file resource. This should be one or more Orion file resource(s) 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. Gzipped input files are also supported but the file resource MUST have the .gz suffix on the name.

  • Type: file_in

VendorD ID (D_id): The id or key to use for the vendor.

  • Type: string

VendorD Name (D_name): The full or descriptive name for the vendor.

  • Type: string

VendorD Version (D_ver): Optional vendor version information.

  • Type: string

Filtering & Processing Options

Functional Group Transformations (enablefngroups): If ON, enables interconversion of simple functional groups per the reaction definitions prior to 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 ON, retains only the largest fragment from each input structure prior to indexing. The default of OFF means that the additional input fragments are retained, which can result in a reduction of classified reagents for some reagent classes due to the presence of competing fragment chemistries.

  • 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’]

CXSMILES Record Handling (cxsmirecs): Requested handling of CXSMILES input records: convert: convert to SMILES - appendix info is added as a title wart, ignore: reject and capture rejected records, retain: keep CXSMILES appendix info (experimental).

  • Type: string

  • Default: convert

  • Choices: [‘convert’, ‘ignore’, ‘retain’, ‘strip’]

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 disk space limit (MiB) to accommodate the input bulk SMILES file plus processing overhead.

  • Required

  • Type: decimal

  • Default: 20000

DB Segment Disk Space Limit (dbsegmentspace): The disk space limit (MiB) to accommodate the generation of each segment of the output R&R database.

  • Required

  • Type: decimal

  • Default: 10000

DB Finalizer Disk Space Limit (dbfinalizespace): The disk space limit (MiB) to accommodate the generation of the final merged output R&R database. Approximately 1Mb disk space per 10,0000 input structures is generally required.

  • Required

  • Type: decimal

  • Default: 15000

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

Emit Counter Records (emit_count_recs): If enabled, emits counter record(s) to the success port(s) for UI visibility of input and processed record counts. Disable this activity for very large input files to reduce unused record traffic.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Verbosity (verbosity): Sets the output logging verbosity.

  • Type: string

  • Default: warning

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

Development Options

SMI Input Record Limit (smimaxrecs): Limit ingestion from the input file(s) to this limit.

  • Type: integer

Reaction & Reagent Database Collection (rrdb_output_coll): Name for a generated output collection to capture segments during the R&R database processing.

  • Type: string

VendorE SMI File (E_SMI): 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. Gzipped input files are also supported but MUST have the .gz suffix on their name.

  • Type: file_in

VendorE ID (E_id): The id or key to use for the vendor.

  • Type: string

VendorE Name (E_name): The full or descriptive name for the vendor.

  • Type: string

VendorE Version (E_ver): Optional vendor version information.

  • Type: string

VendorF SMI File (F_SMI): 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. Gzipped input files are also supported but MUST have the .gz suffix on their name.

  • Type: file_in

VendorF ID (F_id): The id or key to use for the vendor.

  • Type: string

VendorF Name (F_name): The full or descriptive name for the vendor.

  • Type: string

VendorF Version (F_ver): Optional vendor version information.

  • Type: string