DU to PDB

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 design units. The OEMol is then exported as a PDB file. The required input is a dataset with an OEDesignUnit.

Promoted Parameters

Title in user interface (promoted name)

Outputs

Failure Dataset (failed_dataset): Dataset with design unit that failed to be successfully converted and exported.

  • Required

  • Type: dataset_out

  • Default: failed_pdb_exports

Optional PDB filename prefix (filename_prefix): Prefix for all output PDB files.

  • Required

  • Type: string

  • Default:

Optional PDB filename postfix (filename_postfix): Postfix for all output PDB files.

  • Required

  • Type: string

  • Default:

Output Selection

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’]

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]

Add PDB header data to the output molecule (meta): Adds a header to the PDB file with relevant PDB metadata.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]