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PPM Python: Positioning of Proteins in Membranes Python Wrapper

Python installable package for the set of ppm tools for orientation and placement of membrane proteins in lipid membranes.

For a description of the method see: https://doi.org/10.1093/nar/gkr703

This is a derivative work from the PPM 2 code from this repository: https://cggit.cc.lehigh.edu/biomembhub/ppm2_server_code from the BioMembHub.

The goal is to have a python packaged version of the software with some light wrappers around it to make it easier to use.

Installation

pip install git+https://github.com/examol-corp/ppm2.git

Usage

In PPM2 and PPM3 the executable is named immers in both. Wheel builds of this project disambiguate this with immers2 for PPM2 and immers3 for PPM3. These are the exact executables provided by the original project.

(PPM3 is not implemented in this repo yet.)

To use the wrapper CLIs see the names ppm2 and ppm3.

Note that to use the original immers2 CLI you will need a copy of the res.lib file in your current working directory, which can be found at src/ppm2/_pkg_data/res.lib.

Examples

Raw immers executable

Run the raw bundled executable:

$ cd tests/examples/testA
$ immers2 < input.inp
$ cd -

Note that you need to have a res.lib file in the cwd when executing.

Wrapped Executor CLI

  $ ppm2 run --help
  $ ppm2 run \
    tests/examples/test-wrapped-cli/integral/input/1gzm.pdb \
    tests/examples/test-wrapped-cli/integral/output/1gzm_oriented.pdb \
    --topology in > tests/examples/test-wrapped-cli/integral/output/1gzm.ppm_report.json

This outputs the PDB to your desired location and the other metadata that would come out have been parsed and transformed into the JSON output on stdout.

Python Library

from pathlib import Path
import ppm2

output = ppm2.run_wrapped_immers(
    input_pdb=Path("path/to/my.pdb"),
    output_pdb=Path("path/to/oriented.pdb"),
    topology="in",
    keep_heterogens=False,
)

# the path to the output pdb
output.output_pdb.exists()

# the placement data (thickness, tilt angle etc.)
output.placement

# the transmembrane regions identified in the protein
output.transmembrane_regions

Contributing

just build
just test
just test-cli