Reagent Archive - Launch Reaction Enumerations

Category Paths

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

  • Task-based/Library Prep & Design/Reaction-based Enumeration

  • Role-based/Medicinal Chemist

Description

This floe launches individual reaction enumeration floes for all the reaction IDs selected for enumeration from the uploaded reagent collection.

WARNING For reaction libraries of the 100M size or larger, contact support@eyesopen.com for assistance.

General Usage

10^10 products have been enumerated successfully with this approach, but careful investigation using the specific reagent collection of interest is highly encouraged. It is recommended that the Reagent Archive Summary is run on the desired reagent collection to verify the number of potential products before embarking on a large enumeration activity. Preliminary runs with a subset of the potential reaction(s) should be performed to ensure the product dataset contains all the desired output fields.

Reaction ID - The reaction IDs from the specified reagent collection (Reagent Collection ID) to be enumerated. All is an acceptable selection but should be used very cautiously as this can result in a large number of launched floes and a very expensive overall cost for the enumeration.

Append Enumeration Products To Collection - Name of the output collection for output of the product records. If the collection does not exist, it will be created, and if it exists, the product shards will be added to the collection. The append feature means that the specified output collection will never be closed to allow additional product enumerations to populate the collection. It is recommended that ocli be used to close the collection once all the enumerations have been completed. The collection may display with 0 size, but that is simply because the size is not computed until the collection is closed. Regardless of its open/closed state, the product collection can still be used directly in other floes.

Product ID Style - The desired style of output product IDs.

Product ID Delimiter - The delimiter to use for the Custom style of product IDs.

Product Rec/Shard - Desired records/shard for the final output collection shards.

Advanced Usage

Concurrent Enumeration Job Limit - Limits the number of running enumeration floes to this limit (0: unlimited).

Enumeration Cost Budget (Dollars) - The launching floe will not launch any more enumeration jobs once this (dollar)

cost limit (if available) is met from all the child jobs. The launching floe will never kill running floes, however.

Enumeration Time Budget (Minutes) - The launching floe will not launch any more enumeration jobs once this time limit

(if available) is met from all the child jobs. The launching floe will never kill running floes, however.

Enumeration Failure Limit - Enumeration jobs are continued to be launched until this number of failures is reached (0:

no limit).

InFlight Job Priority Limit - This limit caps the number of running enumeration floes to this product limit. For example, if there is a reaction with one billion products launched, this limit can be used to reduce stress on the stack by limiting the launch of additional enumeration jobs until this large reaction completes and required compute instances are freed for use. The limit is a total number of products for all enumeration floes in flight; as floes complete, additional enumeration floes will be launched so long as this in-flight limit is not exceeded.

Reaction Product Minimum, Reaction Product Maximum - Only enumerate reactions limited by this range of products.

Skip Reaction Sizes - Ignore reactions that generate more than this number of products.

Reagent Enumeration Floe - Designates the name or ID of the child floe that enumerates a single reaction ID. This should be the single reaction enumeration floe from this package.

Output Finalization Strategy - using mode Auto (default), the output product collection will be created or opened (if not in the ready state), and will be closed after all child jobs complete. To suppress this activity, use the None option. Auto mode implies that only one launching floe is active at a time.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Reagent Collection (reagent_collection): Designate the input reagent collection by name or id

  • Required

  • Type: collection_source

Outputs

Append Enumeration Products to Collection (coll_append_output): The name or ID of the collection for appending enumeration products.

  • Required

  • Type: string

Enumeration Options

Reaction IDs (reagent_reaction_ids): Either a comma-delimited list of reactions, or keyword ‘All’ to run all reactions from the input collection.

  • Required

  • Type: string

Reaction Product Maximum (numprod_le): Only enumerate reactions having <= this number of products, or 0 for unconstrained.

  • Type: integer

Reaction Product Minimum (numprod_ge): Only enumerate reactions having >= this number of products, or 0 for unconstrained.

  • Type: integer

Product rec/shard (product_records_per_shard): Records per shard for the final emitted product shards. For post-processing with Omega directly, 2500 is optimum. For use in the Prepare Giga Collections Floe, 50K is optimum.

  • Required

  • Type: integer

  • Default: 100000

Product ID Style (prod_style): Which style of product ID to generate.

  • Required

  • Type: string

  • Default: EnamineREALSpace

  • Choices: [‘None’, ‘EnamineREALSpace’, ‘Custom’]

Product ID Delimiter (prod_delim): Reagent delimiter to use for the ‘Custom’ Product ID Style.

  • Type: string

Enumeration Constraints

Enumeration Cost Budget (dollars) (enum_cost_limit): Do not launch any more enumeration jobs once this (dollar) cost limit (if available) is met from all the child jobs

  • Type: decimal

InFlight Job Priority Limit (inflight_limit): Limits in-flight concurrent jobs to <= this threshold

  • Type: integer

  • Default: 10000000000

Enumeration Failure Limit (enum_failure_limit): Enumeration jobs are launched until this number of failures is reached (0: no limit)

  • Type: integer

  • Default: 1

Concurrent Enumeration Job Limit (enum_job_limit): Limit the number of concurrently running enumeration floes to this limit (0: unlimited).

  • Type: integer

  • Default: 1

Enumeration Time Budget (minutes) (enum_min_limit): Do not launch any more enumeration jobs once this (elapsed minute) job limit is met from all the child jobs

  • Type: integer

Skip Reaction Sizes (enum_skip_size_limit): Ignore reactions that generate more than this number of products

  • Type: integer

Advanced Options

Reagent Enumeration Floe (reagent_enumeration_floe): Designate the enumeration floe by title or id for product enumerations

  • Required

  • Type: string

  • Default: _Reagent Archive - Single Reaction Enumerator v0.2.0b7

Enable V2 Collections (coll_v2_output): If ON, uses the high-performance collection API exclusively.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Finalization Strategy (coll_finalize): Finalization strategy for the output collection. Auto: if the output collection was opened or created, close after final child job completes; None: ensure ‘open’ of the output collection for writing, no change to collection status status upon completion; Force: force close of the output collection on job completion.

  • Type: string

  • Default: Auto

  • Choices: [‘None’, ‘Auto’, ‘Force’]

Verbosity (verbosity): Sets the output logging verbosity level.

  • Type: string

  • Default: warning

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