Molecular volume and solvent analysis tools

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.

Documentation

Getting started

• 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.

Reference

• docs/CODE_ARCHITECTURE.md: system design and data flow.
• docs/FILE_STRUCTURE.md: directory map and generated assets.

Project records

• 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.

Quick start

Build the executables:

cd src
make
cd ..

Confirm the CLI is available:

./bin/Volume.exe -h

See docs/USAGE.md for workflows and examples.

Testing

• ./tests/test_volume.sh runs the volume regression check.
• ./tests/test_pdb_to_xyzr.sh 1A01 compares converter outputs.

Citation

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/.

Contact

• Neil Voss on neilvosslab on Bluesky.