Welcome to BINANA’s documentation!

BINANA background

• Introduction
• Citation
• License
• Description of select directories and files
• Locations of BINANA tutorials
  • Command-line use
  • Python library
  • JavaScript library
  • Web-browser app

Interactions

• Close contacts
• Electrostatic interactions
• Binding-pocket flexibility
• Hydrophobic contacts
• Hydrogen bonds
• Halogen bonds
• Salt bridges
• pi interactions
• Metal coordination bonds
• Ligand atom types and rotatable bonds
• Summary of parameter values
• Comments on protonation

Command-line use: documentation

• Suggested commmand-line use
• Alternative methods of use
• Specifying custom parameters

Python library: documentation

• binana

Python library: examples of use

• Load the BINANA module
• Load optional visualization module for this demo
• Load in a receptor and ligand
• Get information about the hydrogen bonds (example)
• Get information about the cation-pi interactions (example)
• Other interactions are also available
• Get and display PDB-formatted text
• Get the interactions as a dictionary for easier big-data analysis
• Some prefer CSV-formatted data
• Get all the interactions at once
• Get and display PDB-formatted text containing all interactions
• Get all interactions as a single dictionary

Indices and tables

• Index

• Module Index

• Search Page