Fast Substructure Search with an MDL Query

Category Paths

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

  • Role-based/Medicinal Chemist

  • Task-based/Library Prep & Design/Substructure & Similarity Search

  • Solution-based/Virtual-screening/DB Search/2D Similarity and SubSearch

Description

Searches a collection (prepared by either of the floes Prepare Collection for Fast Similarity or Substructure Search from Dataset or File) using an input query MDL molecule.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Prepared Molecule Collection to Search (input_collection): Input collection, must be prepared using one of the floes: Prepare Collection for Fast Similarity or Substructure Search from Dataset or File.

  • Required

  • Type: collection_source

MDL Query Molecule (data_in): Draw MDL query in popup sketcher.

  • Required

  • Type: fragment_input

Advanced MDL Search Settings

Match stereo (match_stereo): Match stereo centers as drawn in query.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Add bond aliphatic constraint (aliphatic_constraint): Unless specifically annotated with MDL query features, aliphatic bonds can only match aliphatic bonds, aromatic bonds can only match aromatic bonds.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Add bond topology constraint (topology_constraint): Unless specifically annotated with MDL query features, bonds in a ring only match other bonds in a ring.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Outputs

Collection Name (out_coll): Name of the collection to create

  • Required

  • Type: collection_sink

  • Default: MDL Fast Substructure Search Hits Collection

Output Dataset (data_out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: MDL Fast Substructure Search Hits

Floe Report Name (floe_report_name): Name of report containing summary statistics.

  • Type: string

  • Default: MDL Fast Substructure Search Report

Advanced

Maximum Number of Records in Output Dataset (n_records): Dataset size will be restricted to this many records.

  • Type: integer

  • Default: 10000

Records per Shard (records_per_shard): The target number of records in a shard.

0 indicates to run up to the max_shard_bytes limit per shard

  • Required

  • Type: integer

  • Default: 10000