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 toDefault: Failed Patch Dataset Enumerate Potential Pockets (boolean) : Enumerate potential pockets on design unitsDefault: False Keep only design units on a record (boolean) : Keeps only design units fields on a recordDefault: False Enumerate Potential Pockets (boolean) : Enumerate potential pockets on design unitsDefault: 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 outputDefault: [‘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 reportDefault: 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 createDefault: SiteHopper Patch DB Collection Shard Format (string) : The format of the data that shards containDefault: oedbChoices: ism.gz, oedb, oeb, oeb.gz, oez Output Shard Format (string) : The format of the data that shards will containDefault: oedbChoices: 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 shardDefault: 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 outputDefault: [‘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 reportDefault: 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