DU to Mol

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 OEDesignUnit to generate OEMols from a selection of a design units. The required input is a dataset with an OEDesignUnit.

Promoted Parameters

Title in user interface (promoted name)

Primary molecule selection group

Molecule Field (primary_mol_field_param): Field to put the primary molecule onto.

  • Type: field_parameter::mol

  • Default: Complex

Components to be part of the molecule (primary_components): Components to make part of the molecule. If set to ‘undefined,’ will not be included in output.

  • Required

  • Type: string

  • Default: [‘protein’, ‘nucleic’, ‘ligand’, ‘solvent’, ‘cofactors’, ‘other_ligands’, ‘other_cofactors’, ‘other_proteins’, ‘other_nucleics’]

  • 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’]

Molecule selection group 1

None (mol_field_param_1):

  • Type: field_parameter::mol

  • Default: Protein

Components to be part of the molecule (components_1): Components to make part of the molecule. If set to ‘undefined’, will not be included in output.

  • Required

  • Type: string

  • 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’]

Molecule selection group 2

None (mol_field_param_2):

  • Type: field_parameter::mol

  • Default: Optional 1

Components to be part of the molecule (components_2): Components to make part of the molecule. If set to ‘undefined’, will not be included in output.

  • Required

  • Type: string

  • 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’]

Molecule selection group 3

None (mol_field_param_3):

  • Type: field_parameter::mol

  • Default: Optional 2

Components to be part of the molecule (components_3): Components to make part of the molecule. If set to ‘undefined’, will not be included in output.

  • Required

  • Type: string

  • 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’]

DU to Mol Options

Input Design Unit Field (in_du_field):

  • Type: field_parameter::DU

  • Default: designunit

Convert R-groups to Hydrogen atoms (r2h): 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.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Option to add the molecule to the incoming record, otherwise a new one with limited information is generated. (add_to_record):

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]