DU to Mol

This floe uses OEBio OEDesignUnit to generate a OEMols from a selections of a design unit, the required input is a dataset with an OEDesignUnit.

Extra Required Parameters

  • Dataset with DesignUnit to be modelled (data_source) : The dataset(s) to read records from
  • Output Dataset (dataset_out) : Dataset with Modelled DesignUnit.
    Default: DesignUnitsToMolecules
  • Failure Dataset (dataset_out) : Dataset with DesignUnit that failed to be successfully modelled.
    Default: failed_DesignUnitsToMolecules
  • 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’, ‘nucleic’, ‘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
  • 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: [‘undefined’]
    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
  • 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: [‘undefined’]
    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
  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field
  • 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: [‘ligand’]
    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
  • Convert R-groups to Hydrogen atoms (boolean) : Convert R-groups on ligand and biomolecules to hydrogens from broken covalent bonds. An example could be on glycosylation sites where sugars are excluded from the component selection,another common use case would be for covalent ligands
    Default: True