ESS - Reaction & Reagent Database - Export Synthon Collection (Dev Floe)

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Role-based/Cheminformatician/Medicinal Chemistry Support

  • Role-based/Cheminformatician/Corporate Collection Support

Description

This floe is used to export previously generated Reaction & Reagent Database. The floe allows subset selection of the desired reagents, as well as all reagents.

Launching the Floe

The floe requires a valid Reaction & Reagent Database. The name of the output Output Synthon Collection should be specified with a scheme that serves as a reminder of the R&R database used to generate it.

A separate floe is available to generate a directory and counts for the reagents in any Reaction & Reagent Database which should be consulted and verified before attempting the export collection creation.

The Reaction List parameter is a pick list of the reactions and reagents from the most recently released sample reaction definition file, 2025_1_sample_reaction_classification.txt. For R&R databases generated from alternate reaction definition files, the Custom Reaction List paramater accepts a blank-delimited string of reactions to export when the picklist choices are insufficient.

Promoted Parameters

Title in user interface (promoted name)

Input Parameters

Reaction & Reagent Database (rxndb): Name of the input R&R database.

  • Required

  • Type: file_in

Output Parameters

Output Synthon Collection (synthoncoll): Name for the generated output collection of reagent synthons.

  • Required

  • Type: string

Output Synthon CSV File (synthoncsv): Name for an optional File resource for the reagent synthons.

  • Type: file_out

Reaction Selection

Reaction List (rxnlist): One or more reaction selections from the sample reaction database list or All for every reaction

  • Type: string

  • Default: [‘All’]

  • Choices: [‘All’, ‘3-nitrile-pyridine’, ‘Buchwald-Hartwig’, ‘Buchwald_cross_coupling1’, ‘Buchwald_cross_coupling2’, ‘Ester_hydrolysis-amide_synthesis1’, ‘Ester_hydrolysis-amide_synthesis2’, ‘Grignard_alcohol’, ‘Grignard_carbonyl’, ‘Heck_non-terminal_vinyl’, ‘Heck_terminal_vinyl’, ‘Huisgen_disubst-alkyne’, ‘Mitsunobu_imide’, ‘Mitsunobu_phenol’, ‘Mitsunobu_sulfonamide’, ‘Mitsunobu_tetrazole_1’, ‘Mitsunobu_tetrazole_2’, ‘N-alkylation1’, ‘N-alkylation2’, ‘N-arylation_heterocycles_1’, ‘N-arylation_heterocycles_2’, ‘Negishi’, ‘Niementowski_quinazoline’, ‘O-alkylation’, ‘O-biarylation’, ‘Pictet-Spengler’, ‘Reductive_amination1’, ‘Reductive_amination2’, ‘Schotten-Baumann_amide’, ‘SnAr1’, ‘SnAr2’, ‘Sonogashira’, ‘Stille’, ‘Suzuki_cross_coupling’, ‘Wittig’, ‘benzimidazole_derivatives_aldehyde’, ‘benzimidazole_derivatives_carboxylic-acid/ester’, ‘benzofuran’, ‘benzothiazole’, ‘benzothiophene’, ‘benzoxazole_arom-aldehyde’, ‘benzoxazole_carboxylic-acid’, ‘decarboxylative_coupling’, ‘heteroaromatic_nuc_sub’, ‘imidazole’, ‘indole’, ‘nucl_sub_aromatic_ortho_nitro’, ‘nucl_sub_aromatic_para_nitro’, ‘oxadiazole’, ‘phthalazinone’, ‘piperidine_indole’, ‘pyrazole’, ‘spiro-chromanone’, ‘sulfon_amide’, ‘tetrazole_connect_regioisomere_1’, ‘tetrazole_connect_regioisomere_2’, ‘tetrazole_terminal’, ‘thiazole’, ‘triaryl-imidazole’, ‘urea’]

Custom Reaction List (customrxnlist): One or more specific reactions from the reaction database (blank delimited)

  • Type: string

Advanced Options

Strict Export (strictexport): If ON, and an explicitly specified reaction lacks one or more reagents, generate a failure/error. For an ‘All’ export, silently ignore incomplete reactions.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Synthon Reagent Form. (synthonreags): if ON, apply return the reagent building blocks in sython form. If OFF, unprocessed reagents are returned.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Synthon Validation (synthonchecking): If ON, and saving reagent in synthon form, perform minimal chemistry validations on the generated synthons.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Functional Group Deprotections. (synthonfuncgroups): If ON, performs functional group transforms on the extracted reagents.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Synthon Index Version (synthonindexversion): Synthon index version exported to the collection.

  • Type: string

  • Default: v3

  • Choices: [‘v2’, ‘v3’]

Reagent Export Limit (maxreagents): Truncate the exported reagents to this limit, 0=all.

  • Type: integer

  • Default: 0

Input Half-reaction Definitions (halfrxns): Name of an alternate reaction definition file to use for half-reaction defintions, if none, the database definition is used.

  • Type: file_in

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

Classifier Disk Space (classifierdisk): The amount of disk space limit available for the reaction classifier activities. It may need to be increased for large R&R Databases.

  • Required

  • Type: decimal

  • Default: 32240

Verbosity (verbosity): Sets the output logging verbosity.

  • Type: string

  • Default: warning

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