docs/limitations.rst
Limitations and alternatives
----------------------------
`BpForms` has a few known limitations. Here we describe these limitations and, where possible suggest alternative solutions.
* `BpForms` cannot represent the secondary structure (e.g., base pairing) of biopolymers. Extending `BpForms` to represent secondary structure would enable `BpForms` to represent more DNA forms involved in DNA damage and repair.
* `BpForms` cannot represent branched biopolymers such as carbohydrates. Other formats such as WURCS are better suited for this purpose. See `Glycopedia <https://glycopedia.eu/e-chapters/a-traveler-s-guide-to-complex-carbohydrates-in-the-cyber-space/article/representations>`_ for more information.
* `BpForms` cannot represent the three-dimensional structure of a polymer. The `PDB format <http://www.wwpdb.org/documentation/file-format>`_ is better suited for this purpose.