Subset Design Unit

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 OESubsetDesignUnit to subset a design unit. The required input is a dataset with an OEDesignUnit.

Titles of required parameters (promoted names)

  • Convert R-groups to Hydrogen atoms (r2h) type: boolean: Convert R-groups from broken covalent bonds due to deleted pieces to Hydrogen atoms.
    Default: True
  • Components to keep in the subset (subset_choices) type: string: Different components to keep in the subset.
    Default: [‘protein’, ‘nucleic’, ‘ligand’, ‘cofactors’, ‘solvent’, ‘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
  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: SubsetDesignUnits
  • 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_SubsetDesignUnits

Optional parameters (promoted names)

  • Delete molecule component (delete_pieces) type: string: Delete entire molecule component containing specified residues. (format is RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC] - separate multiple with | delimiter.
  • Delete Residues (delete_residues) type: string: Delete residues specified (format is RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC] - separate multiple with | delimiter.