Subset Design Unit Within

Category Paths

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

  • Product-based/SPRUCE

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation

Description

This floe uses OEBio function GetComponentsWithin to subset a design unit based on distance to other selected components. The required input is a dataset with an OEDesignUnit.

Titles of required parameters (promoted names)

  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: SubsetWithinDesignUnits
  • Within distance (dist) type: decimal: The within distance in angstroms.
    Default: 5.0
  • Component(s) to subset (subset_choices) type: string: Component(s) to subset.
    Default: [‘solvent’]
    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
  • Within Components (within_choices) type: string: Components to include if they are within the subset distance.
    Default: [‘protein’, ‘nucleic’, ‘ligand’, ‘cofactors’, ‘other_ligands’, ‘other_cofactors’]
    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
  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled
  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_SubsetWithinDesignUnits