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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

  • Optional - dump-pdb mode

    • run with this flag to output the PDB for each mutation as well as the score

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

Run DDG on an input structure with all mutations selected and output the PDBs as well as scores

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

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")

Run DDG on an input structure and dump the output PDB files

from engine.ddg.client import DdgClient

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


Outputs

  • results.tsv

    • file with one mutation and score per-line

  • mutation-input.tsv

    • input mutations file

  • pdbresults.tar.gz

    • output PDB files, will be empty if --dump-pdb omitted

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