DU to mmCIF/PDB File

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 mmCIF or 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

Filename Title Field (output_title_field): String field used to name each exported file. Defaults to the design unit title field.

  • Required

  • Type: field_parameter::string

  • Default: du_title

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

  • Required

  • Type: string

  • Default:

Optional mmCIF/PDB filename postfix (filename_postfix): Postfix for all output mmCIF/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]

Conversion Options

Input Design Unit Field (in_du_field):

  • Type: field_parameter::DU

  • Default: designunit

Output file extension (file_ext_param): File extension for output files. We recommend mmCIF as PDB format has been deprecated by the RCSB

  • Required

  • Type: string

  • Default: .cif

  • Choices: [‘.cif’, ‘.pdb’]