Design API

The Design API runs the Rosetta FastDesign protocol given an input PDB file and a residue file (resfile). FastDesign performs FastRelax with design enabled to create designed structures for residue parameters defined by the input resfile (See References for more information on the FastDesign protocol)

Command Line Interface

Examples

Run design on an input structure to generate 10 new design models

lev engine submit design \
    --pdb-file=input.pdb \
    --res-file=input.res \
    --repeats 10

Flags

  • --mode (str) (Default = fastdesign)
    • Design mode
    • Options:
      • fastdesign - FastDesign mode
  • --pdb-file (str) (Required)
    • Input PDB file to run design on
    • You can specify this flag as the first positional argument or with the --pdb-file flag
    • The PDB file should be cleaned prior to input using the Clean PDB API.
    • Examples:
      • "input.pdb" - Local PDB file
      • "structures/protein.pdb" - PDB file in subdirectory
      • "/path/to/structure.pdb" - Full path to PDB file
  • --res-file (str) (Required)
    • Input residue file
    • You can specify this flag as the second positional argument or with the --res-file flag
    • The resfile is a standard Rosetta resfile, documented here: Resfile syntax and conventions
  • --repeats (int) (Default = 1)
    • Number of iterations to relax

Python Interface

Examples

Run design on an input structure to generate 10 new design models

from engine import EngineClient

client = EngineClient()
client.authorize()

job_id = client.submit_design(
    pdb_path="input.pdb",
    resfile_path="input.res",
    repeats=10
)

Flags

  • mode (str) (Default = fastdesign)
    • Design mode
    • Options:
      • fastdesign - FastDesign mode
  • pdb_path (str) (Required)
    • Input PDB file to run design on
    • You can specify this flag as the first positional argument or with the --pdb-file flag
    • The PDB file should be cleaned prior to input using the Clean PDB API.
    • Examples:
      • "input.pdb" - Local PDB file
      • "structures/protein.pdb" - PDB file in subdirectory
      • "/path/to/structure.pdb" - Full path to PDB file
  • resfile_path (str) (Required)
    • Input residue file
    • You can specify this flag as the second positional argument or with the --res-file flag
    • The resfile is a standard Rosetta resfile, documented here: Resfile syntax and conventions
  • repeats (int) (Default = 1)
    • Number of iterations to relax

Output

  • models.tgz
    • Designed models

References

Rosetta FastDesign

Rosetta Resfile

Updated: