3. Tutorial

This section contains tutorials for the grammar, web application, REST API, command line interface, and Python API. Additional interactive tutorials for the Python API are available as Jupyter notebooks at https://sandbox.karrlab.org.

Table of contents

• 3.1. BpForms grammar
  • 3.1.1. Grammar
• 3.2. Graphical web interface
• 3.3. REST API
• 3.4. Command line interface
• 3.5. Python API
  • 3.5.1. Importing BpForms
  • 3.5.2. Creating biopolymer forms
  • 3.5.3. Getting and setting monomeric forms
  • 3.5.4. Getting and setting the base of a monomeric form
  • 3.5.5. Protonation and tautomerization
  • 3.5.6. Calculation of physical properties
  • 3.5.7. Generating IUPAC/IUBMB sequences for BpForms
  • 3.5.8. Determine if two biopolymers describe the same structure