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’]