Focused Library - Core InputΒΆ
This Floe provides a facility to perform library enumeration using reagents from a reaction & reagent database to provide the Rgroup definition(s) for an Rgroup annotated library core molecule.
Library Core Input - Library Core Input invokes the Sketcher. You can select a
record from an existing dataset, or draw/paste a libray core onto the
canvas. The Rgroup sites for the enumeration must be specified as
R1-R4 (max), but any combination of Rgroups are allowed, as long as a
reagent definition is provided for the specified site(s). A numbered
Rgroup site in the Sketcher is generated by selecting an atom and using
the keyboard command r
to toggle through *
, R1
, R2
, R3
, R4
.
For ring closure reactions/reagents, you must specify both R1 and R2, and explicitly select identical reagent definitions for both.
Reaction & Reagent Database - a previously generated reaction & reagent databse. This provides the source of the reagent definitions and the (required) half-reactions that allow prepared reagents (sans leaving groups) to be generated.
Due the potential of huge combinatorial expansion, use small limits on the maximum reagents to verify the correct enumerated products are being produced prior to scale up.
Extra Required Parameters
Check Valences (string) : How to handle valence issues for the final products: reject: reject valence errors, allow: ignore valence errors, fix: repair valence issuesDefault: fixChoices: reject, allow, fix Max Products (integer) : The maximum number of enumerated products allowed to be generated. If the Rgroup reagent limits chosen would generate more than this number of products, the floe will fail.Default: 1000000 Reaction & Reagent Database (file_in) : The name of the reaction & reagent database to use Reaction & Reagent Database (file_in) : The name of the reaction & reagent database to use String Key (Field Type: String) : Name of the string field to deduplicate Rgroup Number (string) : Rgroup number to activate Rgroup Number (string) : Rgroup number to activate Filter Products (boolean) : If ON, performs filtering on the generated productsDefault: True Product Dataset (dataset_out) : Product dataset from the enumerationDefault: libenum_products Output Failure Dataset (boolean) : If OFF, just counts records, but does not output themDefault: False Reaction & Reagent Database (file_in) : The name of the reaction & reagent database to use Rgroup Number (string) : Rgroup number to activate Output Product Dataset (boolean) : If OFF, just counts records, but does not output themDefault: True Library Core Input (fragment_input) : Draw or load a library core to use for a virtual library enumeration. Starting with a lead molecule, edit it to include one or more Rn groups using the sketcher. Each Rgroup will be replaced with a set of reaction-specific reagents per the selection(s) below. Output Duplicate Dataset (boolean) : If OFF, just counts records, but does not output themDefault: False Dedupe Products Switch (boolean) : Simple canonical product SMI deduplication, or suppress if downstream floes will deduplicateDefault: True Reaction & Reagent Database (file_in) : The name of the reaction & reagent database to use Reaction & Reagent Database (file_in) : The name of the reaction & reagent database to use Rgroup Number (string) : Rgroup number to activate