ZINC Download to Reaction & Reagent Database

This floe is used to populate a reaction & reagent database with a user-customized selection of ZINC compounds.

NOTE: The ZINC database is a shared resource for users all over the world - please be considerate in the number of compounds selected for processing, as well as the frequency of the update activity.

The input to the floe is either previously downloaded SMILES tranche file(s) from ZINC, or a set of tranche ids selected by the user based using the powerful tranche filtering capability for [ZINC tranche selection](http://zinc15.docking.org/tranches/home/).

ZINC Subset selection

A common filtering activity is to select “In-Stock” compounds from the Minimum Purchasability drop-down and some molecular weight (or other property) range of interest. In general, a conservative goal to limit the total number of compounds to something less than 10M total compounds should be employed, though higher limits may also be successful. Once the tranche subset/filtered selection has been finalized, choosing the download arrow from the web page will present the user with a list of tranche ids which can be copied to the clipboard from the browser window. This is the only information needed by this update floe. The tranches will be downloaded on the fly when the floe is run, thus no explicit download activity is required by the user.

Launching the Floe

The floe requires a valid reaction definition file that defines the reactions, and associated reagent chemistry for classification of input structures. A sample reaction definition file, sample_reaction_classification_2021_2.txt is available from the OpenEye Organization resources. At the time of this release, the documentation for generating a custom version of this file is not yet available. If you have the need to undertake this activity, contact OpenEye Support (mailto:support@eyesopen.com) for additional details.

The name of the output reaction & reagent database should be specified with a scheme that serves as a reminder of the tranche filtering used for the structure selection. The reaction & reagent database file generated will be an Orion file resource with the floe user’s credentials.

Extra Required Parameters

  • Output Reaction & Reagent Database Name (file_out) : Name for the Orion file resource being generated
  • String Key (Field Type: String) : Name of the string field containing the key to deduplicate records on
  • Reaction Definition File (file_in) : The name of file resource containing the reaction definitions
  • Molecule ID (Field Type: String) : Name of the string field the molecule id
  • Smiles Field (Field Type: String) : Name of the string field containing SMILES of the classified structures
  • Output Reaction & Reagent Database Name (file_out) : Name for the Orion file resource being generated
  • Reagent Class Field (Field Type: String) : Name of the field for annotating the reagent class information
    Default: ReagentClass
  • Molecule Filtering (boolean) : If ON, performs filtering of reagents prior to classification
    Default: True
  • Smiles Field (Field Type: String) : Name of the string field containing SMILES for the structures to be classified
  • Reagent Class Field (Field Type: String) : Name of the field for annotating the reagent class information
    Default: ReagentClass