Reaction & Reagent Database - Multi-vendor - Parallel Export Synthon Collection
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_2_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
Reaction Selection
Reaction List (rxnlist): One or more reaction selections from the sample reaction database list or All for every reaction
Required
Type: string
Default: [‘All’]
Choices: [‘All’, ‘Custom’, ‘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’, ‘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]
Functional Group Reagents (enablefngroupreagents): If ON, enables extraction of functional group equivalent reagents for the synthon conversions from the R&R database.
Type: boolean
Default: False
Choices: [True, False]
Reagent Export Limit (maxreagents): Truncate the exported reagents to this limit, 0=all.
Type: integer
Default: 0
Shard Chunk Size (recordspershard): Cap the records per shard of internally processed reagent shards to this limit - affecting scale-up behavior, 0=unconstrained.
Type: integer
Default: 10000
Verbosity (verbosity): Sets the output logging verbosity.
Type: string
Default: warning
Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]
Advanced Resource Options
Shard Disk Space (shard_disk): The minimum amount of disk space in MiB (1048576 B) for the shard processing cubes.
Type: decimal
Default: 8192
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: 20240
Cube Limit (max_parallel): The maximum number of concurrently running copies of shard processing cubes.
Type: integer
Default: 25
Cube Failure Limit (max_failures): The maximum number of times to attempt processing a work item for the shard processing cubes.
Type: integer
Default: 2
Spot policy (spot_policy): Spot policy for certain key floe cubes - ‘Prohibited’ may improve throughput, but with increased costs.
Type: string
Default: Preferred
Choices: [‘Allowed’, ‘Preferred’, ‘NotPreferred’, ‘Prohibited’, ‘Required’]
Deduplication Options
Deduplicate Synthons (dedupe_synthons): if ON, requests reagent synthon deduplication activity.
Required
Type: boolean
Default: True
Choices: [True, False]
Cross Reaction Dedupe (dedupe_xrxns): If ON, requests deduplication of reagent synthons across all reactions.
Type: boolean
Default: False
Choices: [True, False]
Deduplication Disk Space (dedupe_disk): The minimum amount of disk space in MiB (1048576 B) for the synthon deduplication cube.
Type: decimal
Default: 10240
Deduplication Memory Limit (dedupe_mem): The memory limit for the synthon deduplication cube.
Required
Type: decimal
Default: 20240
Experimental Development Options
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
Deprotection Transforms (deprotxforms): Name of a file resource defining synthon deprotection transformations. Deprotection transforms must be very specifically written to avoid embedded mapping changes within the synthons, arbitrary synthon chemistry conversions, modification of synthon attachment points or performing undesired chemistry changes on other protecting group classes that may be present. Deprotected synthons must have correct valences and cannot comprise more fragments than the unprotected synthon they originated from. Each deprotection transform is performed exhaustively on the original (protected) synthon so multiple sites can/will be deprotected, but only a single protecting group transformation is processed at a time - different bi- or tri-protecting groups within a single synthon will only have a single protecting group type exhaustively deprotected.
Type: file_in
Identify Reagents by Vendor (by_vendor): If ON, extracts reagents by vendor for downstream subsetting and merging.
Type: boolean
Default: False
Choices: [True, False]
Retain Intermediate Files (saveintermediates): If ON, save intermediate collateral to the output collect for analysis/debugging.
Type: boolean
Default: False
Choices: [True, False]
ID Tracking (debugBBids): If provided, add explicit logging info for DB merge operations involving the specified BB id(s) - either a comma, blank or pipe delimited list for multiples, quoted for a singleton containing list delimiters.
Type: string