Prepare Collection for Fast Similarity or Substructure Search from File¶
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
From input file, prepares collection for fast similarity or substructure search. This floe screens molecules for filtering characteristics so that they can be subsequently searched more quickly in the Fast Substructure Search floe, and generates a collection with multiple types of fingerprints, so that they can be searched in the Fast Similarity Search floe.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input Molecule File (in): Input file, containing molecules. Must be an OpenEye supported format.
Required
Type: file_in
Advanced Parallelism Settings
Maximum Parallel Cube Instances (max_parallel_central): Maximum number of cubes at any one time for the parallel part of search prep computation.
Type: integer
Default: 1000
Number of messages to distribute at a time (item_count_central): Maximum units of work sent to each parallel cube
Type: integer
Default: 1
Outputs
Substructure Search Input Collection Name (coll_name): Name of fast substructure search prepared collection.
Required
Type: collection_sink
Default: Fast Substructure Search Input Collection
Similarity Search Input Collection Name (sim_coll_name): Name of fast similarity search prepared collection.
Required
Type: collection_sink
Default: Fast Similarity Search Input Collection
Advanced: Large Inputs
Number of Molecules per Shard (mols_per_shard): Number of molecules per shard. Since each shard is searched in parallel this controls the granularity of the subsequent fast similarity or substructure search floe run.
Type: integer
Default: 250000
File Reader Disk Space (MiB) (disk_space): This size (in MiB) must be larger than the total size of the file(s) provided as input.
Type: decimal
Default: 5120