BcForms documentation

BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models (see https://wholecell.org).

BcForms includes a grammar for describing forms of macromolecular complexes composed of DNA, RNA, protein, and small molecular subunits and crosslinks between the subunits. The DNA, RNA, and protein subunits can be described using BpForms and the small molecule subunits can be described using SMILES. BcForms also includes four software tools for verifying descriptions of complexes and calculating physical properties of complexes such as their molecular structure, formula, molecular weight, and charge: this website, a JSON REST API, a command line interface, and a Python API. BcForms is available open-source under the MIT license.

Contents

• 1. Installation
  • 1.1. Prerequisites
  • 1.2. Latest release From PyPI
  • 1.3. Latest revision from GitHub
  • 1.4. Installing the optional features
• 2. Command line interface
• 3. API documentation
  • 3.1. bcforms package
    • 3.1.1. Submodules
    • 3.1.2. bcforms.__main__ module
    • 3.1.3. bcforms._version module
    • 3.1.4. bcforms.core module
    • 3.1.5. bcforms.rest module
    • 3.1.6. Module contents
• 4. About
  • 4.1. License
  • 4.2. Development team
  • 4.3. Acknowledgements
  • 4.4. Questions and comments
• 5. References