Make SiteHopper Patch Database

This floe generates a SiteHopper patch collection based on a collection of OEDesignUnits, it writes a dataset that identifies the collection to be used in the SiteHopper search floe. A tutorial can be found here: Search for Similar Binding Sites with SiteHopper.

Extra Required Parameters

  • Failed output dataset (dataset_out) : Output dataset to write to
    Default: Failed Patch Dataset
  • Enumerate Potential Pockets (boolean) : Enumerate potential pockets on design units
    Default: False
  • Keep only design units on a record (boolean) : Keeps only design units fields on a record
    Default: False
  • Enumerate Potential Pockets (boolean) : Enumerate potential pockets on design units
    Default: False
  • Components to be part of the molecule (string) : Components to make part of the molecule.If set to ‘undefined’, will not be included in output
    Default: [‘protein’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors
  • Discard liganded design units (boolean) : Option to discard liganded design units.
    Default: True
  • Generate surface (boolean) : Option to generate surface for pockets.
    Default: True
  • Local burial factor (decimal) : Option to set local burial factor.
    Default: 1.4
  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field
  • Max surface area (decimal) : Option to set maximum surface area for pocket finding.
    Default: 3000.0
  • Min surface area (decimal) : Option to set minimum surface area for pocket finding.
    Default: 150.0
  • Collection Name (collection_sink) : Name of the collection to create
    Default: SiteHopper Patch DB Collection
  • Shard Format (string) : The format of the data that shards contain
    Default: oedb
    Choices: ism.gz, oedb, oeb, oeb.gz, oez
  • Output Shard Format (string) : The format of the data that shards will contain
    Default: oedb
    Choices: ism.gz, oedb, oeb, oeb.gz, oez
  • records_per_shard (integer) : The target number of records in a shard. 0 indicates to run up to the max_shard_bytes limit per shard
    Default: 0
  • AlphaFold Min Quality Score (decimal) : Option to set minimum Alphafold quality score.
    Default: 70.0
  • AlphaFold Min Residue Coverage (decimal) : Option to set a minimum coverage of residues with min quality score in binding pocket.
    Default: 100.0
  • Components to be part of the molecule (string) : Components to make part of the molecule.If set to ‘undefined’, will not be included in output
    Default: [‘protein’]
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors
  • Discard liganded design units (boolean) : Option to discard liganded design units.
    Default: True
  • Fpocket Drug Score (decimal) : Option to set the minimum f-pocket drug score.
    Default: 0.01
  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field
  • Max surface area (decimal) : Option to set maximum surface area for pocket finding.
    Default: 3000.0
  • Min surface area (decimal) : Option to set minimum surface area for pocket finding.
    Default: 150.0