Regex ProteinMPNN

A wrapper around proteinMPNN to automate sequence generation and allow specifying fixed residues using regex (and ranges). See the included shell scripts for examples of how to use it.

Installation and Usage

1. Clone proteinMPNN and follow their installation instructions.
2. Clone this repository.
3. Activate your conda environment associated with proteinMPNN.
4. Run better_mpnn.py with the desired parameters.

The wrapper has the following usage:

usage: better_mpnn.py [-h] [--input_pattern INPUT_PATTERN] [--design_chains DESIGN_CHAINS] [--fix_pattern FIX_PATTERN] [--fix_ranges FIX_RANGES] [--num_outputs NUM_OUTPUTS]
                      [--sampling_temperature SAMPLING_TEMPERATURE] [--mpnn_path MPNN_PATH]
                      input_dir output_dir temp_dir

Run proteinMPNN on a set of input files

positional arguments:
  input_dir             The directory containing the input files
  output_dir            The directory to save the output files
  temp_dir              The directory to save temporary files

options:
  -h, --help            show this help message and exit
  --input_pattern INPUT_PATTERN
                        The pattern to match for input files
  --design_chains DESIGN_CHAINS
                        The chains to design
  --fix_pattern FIX_PATTERN
                        The pattern to match for fixed residues
  --fix_ranges FIX_RANGES
                        Ranges of residues to fix in the format "chain:res1-res2,chain:res3-res4"
  --num_outputs NUM_OUTPUTS
                        The number of outputs per input file to generate
  --sampling_temperature SAMPLING_TEMPERATURE
                        The "predictability" of the model
  --mpnn_path MPNN_PATH
                        The path to the proteinMPNN directory

Running the script without any arguments will test some of the code, which may be useful if you want to extend this wrapper.