rc

A command line tool to run various biomolecular structural prediction, analysis and design applications using containerized environments.

Overview

rc provides a unified interface for running Rosetta and other biomolecular modeling applications through container engines like Docker, Singularity, or Apptainer.

Installation

cargo install --path .

Basic Usage

Running Rosetta Score

Score a PDB structure file using Rosetta:

rc run -w /path/to/working/directory rosetta score \
    -out:file:scorefile output.sc \
    -in:file:s structure.pdb

This command will:

• Use the default Docker container engine
• Mount the working directory into the container
• Run the Rosetta score application
• Output the score file to output.sc
• Log the executed command to a log file for reproducibility

Specifying a Container Engine

You can specify which container engine to use with the -e flag:

rc run -e singularity rosetta score -in:file:s structure.pdb

Supported container engines:

• docker (default)
• singularity
• apptainer
• none (run natively without containers)

Working Directory

The -w flag specifies the working directory that will be mounted into the container:

rc run -w ./data rosetta score -in:file:s input.pdb

If not specified, the current directory (.) is used by default.

Command Logging

Every command executed by rc is automatically logged to <working-dir>/.NNNN.rc.log, where NNNN is a sequential number incremented with each command run in that directory. This provides:

• Reproducibility - Review and replay exact commands that were run
• Debugging - Trace what commands were executed in case of issues
• Documentation - Keep a record of all operations performed

Each log file contains:

• The exact command line used to invoke rc
• Full output logs from the executed application
• Timestamp and execution details

For example, your first run creates .0000.rc.log, the second creates .0001.rc.log, and so on.

Commands

run

Run an application with optional arguments.

rc run [OPTIONS] <APP> [ARGS]...

Options:

• -w, --working-dir <PATH> - Input directory path (default: current directory)
• -e, --container-engine <ENGINE> - Container engine to use (default: docker)

Available Apps:

• rosetta - Run Rosetta protocols and applications
• score - Run Rosetta score command (shorthand for common scoring tasks)
• pyrosetta - Execute PyRosetta Python scripts with PyRosetta environment
• rfdiffusion - Run RFdiffusion for protein structure generation
• proteinmpnn - Run ProteinMPNN for protein sequence design
• proteinmpnn-script - Run ProteinMPNN helper scripts for preprocessing and analysis
• ligandmpnn - Run LigandMPNN for protein-ligand interface design

install

Install an application (not yet implemented).

rc install <APP>

clean

Clean an app installation (not yet implemented).

rc clean <APP>

App Usage Examples

Rosetta

Score a single structure

rc run rosetta score \
    -out:file:scorefile my_scores.sc \
    -in:file:s my_protein.pdb

Run other Rosetta protocols

rc run rosetta relax \
    -in:file:s input.pdb \
    -relax:fast

PyRosetta

Running PyRosetta Scripts

Execute PyRosetta Python scripts directly using the -c flag for inline code:

rc run pyrosetta -c 'import pyrosetta; pyrosetta.init(); pose=pyrosetta.pose_from_pdb("1brs.pdb"); print("SCORE:", pyrosetta.get_score_function()(pose) )'

Or run a Python script file:

rc run pyrosetta my-pyrosetta-script.py

Run a PyRosetta script file

rc run pyrosetta design_script.py

RFdiffusion

Generate a protein backbone

rc run rfdiffusion inference.py \
    inference.output_prefix=output/sample \
    inference.num_designs=10

Conditional generation with a motif

rc run rfdiffusion inference.py \
    inference.output_prefix=output/motif_scaffold \
    inference.input_pdb=motif.pdb \
    'contigmap.contigs=[10-40/A163-181/10-40]'

ProteinMPNN

Design sequences for a protein structure

rc run proteinmpnn \
    --pdb_path structure.pdb \
    --pdb_path_chains "A B"

This will generate designed sequences in the seqs/ directory within your working directory.

Design with custom parameters

rc run proteinmpnn \
    --pdb_path structure.pdb \
    --pdb_path_chains "A" \
    --num_seq_per_target 10 \
    --sampling_temp 0.1

General Options

Using with different working directory

rc run -w /data/structures rosetta score \
    -out:file:scorefile results/scores.sc \
    -in:file:s protein.pdb

Using Singularity instead of Docker

rc run -e singularity rosetta score \
    -in:file:s structure.pdb

Verbose Mode

Enable verbose output with the -v flag:

rc -v run rosetta score -in:file:s structure.pdb

This will show detailed information including the exact command being executed and where it's being logged.

Requirements

• One of the supported container engines (Docker, Singularity, or Apptainer)
• Appropriate container images for the applications you want to run

License

See LICENSE file for details.

Author

Sergey Lyskov