Molecular Volume and Solvent Analysis Tools

This repository provides a set of command-line tools for analyzing molecular structures, focusing on extracting channels, cavities, calculating solvent-excluded volumes, and analyzing ribosomal tunnels. These tools are invaluable for researchers in structural biology and molecular biophysics.

Documentation

• docs/AUTHORS.md: maintainers and contributor credits.
• docs/CHANGELOG.md: chronological record of changes.
• docs/CODE_ARCHITECTURE.md: high-level system design and data flow.
• docs/INSTALL.md: setup steps and build requirements.
• docs/FILE_STRUCTURE.md: directory map and generated assets.
• docs/MARKDOWN_STYLE.md: documentation formatting rules.
• docs/QUICKSTART.md: end-to-end usage walkthrough.
• docs/RELEASE_HISTORY.md: released versions and highlights.
• docs/REPO_STYLE.md: repo organization and naming conventions.
• docs/TODO.md: backlog items and legacy work notes.
• docs/UTILS.md: reference for src/lib/utils-main.cpp helpers.

Citation

If you use these tools in your research, please cite:

• Neil R. Voss, Mark Gerstein.
  3V: cavity, channel, and cleft volume calculator and extractor.
  Nucleic Acids Res. 2010 Jul;38(Web Server issue):W555-62.
  • DOI: 10.1093/nar/gkq395
  • PubMed: 20478824
  • PubMed Central: PMC2896178
  • Download Pre-print PDF: 3V_cavity_channel_and_cleft_volume_calculator_and_extractor.pdf

Secondary References

• Voss NR.
  Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization.
  Doctoral Dissertation. Yale University; November 2006. Dissertation Director: Prof. Peter B. Moore.

  • Download PDF: NR_Voss-thesis-Geometric_Studies_of_RNA_and_Ribosomes.pdf

• Voss NR, et al.
  The Geometry of the Ribosomal Polypeptide Exit Tunnel.
  J Mol Biol. 2006 Jul 21;360(4):893-906.

  • DOI: 10.1016/j.jmb.2006.05.023
  • PubMed: 16784753
  • Download Pre-print PDF: Geometry_of_the_Ribosomal_Polypeptide_Exit_Tunnel.pdf

• Contact: Mark Gerstein <[email protected]> or Neil Voss <[email protected]>

Getting started

• Install and build: docs/INSTALL.md
• Quickstart walkthrough: docs/QUICKSTART.md
• Command help: run ./bin/<tool>.exe --help

Testing

• Regression harnesses live in tests/ (see tests/test_suite.py and tests/test_volumes.py).
• YAML scenarios are defined in tests/test_suite.yml.

Release notes

• Release highlights: docs/RELEASE_HISTORY.md
• Detailed change log: docs/CHANGELOG.md

Utilities

• Helper catalog and grid utilities: docs/UTILS.md

Tools

Common executables: Volume.exe, Channel.exe, Cavities.exe, Solvent.exe, Tunnel.exe, VDW.exe, VolumeNoCav.exe, AllChannel.exe, AllChannelExc.exe, FsvCalc.exe, FracDim.exe, TwoVol.exe, ProteinRNAVolume.exe.