y1zhou / arpeggia

Calculation of interatomic interactions in molecular structures

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