Rosetta Pair-Energy Pipeline (REF2015_cart)

Repo to compute one-body and two-body pairwise energy terms for any model system of interest.

To use this repo you will need a local installation of Rosetta. Ensure the executables are on your system's PATH (e.g., by adding $ROSETTA3/bin).

Rosetta also needs access to its parameter database. You can achieve this in one of two ways:

1. Set an environment variable:

   export ROSETTA3_DB="$ROSETTA3/main/database"

2. Pass the path as a flag with every Rosetta command:

   -database /path/to/your/rosetta/main/database

Ubiquitin Demo

Generates 1UBQ_relaxed.pdb via relax.xml

rosetta_scripts.linuxgccrelease \
    -s 1UBQ.pdb \
    -parser:protocol relax.xml \
    -database "$ROSETTA3/main/database" \
    -nstruct 1 \
    -out:suffix _relaxed

Dump per-pair energies from the relaxed structure > generates 1UBQ_pair.tbl

residue_energy_breakdown.linuxgccrelease \
    -s 1UBQ_relaxed.pdb \
    -score:weights ref2015_cart \
    -database "$ROSETTA3/main/database" \
    -out:file:silent 1UBQ_pair.tbl

Convert the energy table into JSON matrices > generates the final output, 1UBQ_ref2015_cart.json

python cart_json.py 1UBQ_pair.tbl \
       --out 1UBQ_ref2015_cart.json

PyRosetta Fallback

If you cannot use the compiled Rosetta binaries, you can use the PyRosetta fallback script called cartesian_terms.py. Simply create the required conda environment (this will use approximately 2 GB of disk space):

conda create -n pyrosetta -c conda-forge \
      python=3.13 numpy pandas \
      pyrosetta=2025.23+release.e6f643b818

conda activate pyrosetta

and then run the script via command line.