The DDG API runs the Rosetta cartesian-ddg protocol. It takes as input a pre-relaxed PDB and a TSV-formatted mutations file, and outputs a TSV-formatted file containing a new column for scores.

Inputs

• pdb-file

  • must be a pdb which has been run through the ddg-relax endpoint

• Optional - mutations-file

  • TSV-formatted file containing mutations. To create an empty mutations file from an input pdb, run:
    cyrus prepare mutations <pdb-file> --output-dir <output-dir>

• Optional - all-mutations mode

  • you can omit an input mutations-file and instead run in all-mutations mode, where all mutations at each position will be selected

Command Line Examples

Prepare an input pdb file for use with DDG

cyrus submit ddg-relax <pdb-file>

Prepare an input mutations file for use with DDG

cyrus prepare mutations <pdb-file> --output-dir <output-dir>

Run DDG on an input structure with mutations that are included in the input mutations file

cyrus submit ddg <pdb-file> --mutations-file <mutations-file>

Run DDG on an input structure with all mutations selected

cyrus submit ddg <pdb-file> --all-mutations

Python Examples

Prepare an input pdb file for use with DDG

from engine.ddg-relax.client import DdgRelaxClient

client = DdgRelaxClient()
job_id = client.submit(pdb_path="input.pdb")

Run DDG on an input structure with mutations that are included in the input mutations file

from engine.ddg.client import DdgClient

client = DdgClient()
job_id = client.submit(pdb_path="input.pdb", mutations_path="input.tsv")

Outputs

• results.tsv

  • File with one mutation and score per-line

• mutation-input.tsv

  • Input mutations file