Command-line tools for protein structure analysis: convert PDB, mmCIF, PDBML, or XYZR files into atomic sphere data, then compute volumes, channels, cavities, and tunnel geometry using grid-based methods. Intended for researchers in structural biology and molecular biophysics who need reproducible, scriptable analyses of protein 3D structure.
- docs/INSTALL.md: setup steps and build requirements.
- docs/USAGE.md: how to run the executables and common flags.
- docs/QUICKSTART.md: end-to-end workflow walkthrough.
- docs/CODE_ARCHITECTURE.md: system design and data flow.
- docs/FILE_STRUCTURE.md: directory map and generated assets.
- docs/CHANGELOG.md: chronological record of changes.
- docs/RELEASE_HISTORY.md: released versions and highlights.
- docs/REPO_STYLE.md: repo organization and naming conventions.
- docs/PYTHON_STYLE.md: Python conventions for the repo.
- docs/MARKDOWN_STYLE.md: documentation formatting rules.
Build the executables:
cd src
make
cd ..Confirm the CLI is available:
./bin/Volume.exe -hSee docs/USAGE.md for workflows and examples.
./tests/test_volume.shruns the volume regression check../tests/test_pdb_to_xyzr.sh 1A01compares converter outputs.
If you use these tools in your research, cite:
- Neil R. Voss, Mark Gerstein. 3V: cavity, channel, and cleft volume calculator and extractor. Nucleic Acids Res. 2010. DOI. See publications/ for PDFs.
- Additional references are listed in publications/.
- Neil Voss on neilvosslab on Bluesky.