Arpeggia

This is a port of the Arpeggio library to Rust, with a focus on identifying certain protein-protein interactions in PDB and mmCIF files.

Features

• Parse PDB and mmCIF files
• Parse user selection of chain groups
• Extract protein chains and residues
• Calculate distances between residues
• Identify protein-protein interactions
  • Steric clashes
  • VdW interactions
  • Hydrophobic interactions
  • Aromatic interactions
  • Cation-pi interactions
  • Ionic interactions
  • Hydrogen bonds
  • Weak hydrogen bonds
  • Disulfide bonds
  • Covalent bonds
• Output results in various formats (e.g., JSON, CSV)
• Bundle into a PyO3 extension module
• Add hydrogens to the structure model

Installation

Cargo install

TODO: publish to crates.io

Pre-built binaries

Binaries for tagged releases can be found at the GitHub Releases page.

Build from source

1. Clone the repository:

   git clone https://github.com/y1zhou/arpeggia.git
   cd arpeggia

2. Build and install using Cargo:

   cargo install --path .

This will install the arpeggia binary to your Cargo binary directory (usually ~/.cargo/bin).

Usage

To see all available commands and options:

arpeggia help

TODO: document how the contacts, sasa, and seq commands can be used.