Charles Karney: Publication 85/85, Karney(2007)

C. F. F. Karney.
Quaternions in molecular modeling.
J. Mol. Graph. Mod., 25(5):595–604, January 2007.
E-print: arXiv:physics/0506177 (Mirror).
Reprint: jmgm07
DOI: 10.1016/j.jmgm.2006.04.002
BibTeX Entry

Quaternions are an important tool to describe the orientation of a molecule. This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational data, in the random sampling of rotations, and in establishing grids in orientation space. These examples show that many of the rotational problems that arise in molecular modeling may be handled simply and efficiently using quaternions.

Note 1: A collection of orientation sets based on the 600-cell and 48-cell as described in section 8 of this paper is available at http://charles.karney.info/orientation/.

Note 2: a facsimile of

J. E. Keat,
Analysis of least-squares attitude determination routine DOAOP,
Technical Report CSC/TM-77/6034, Computer Sciences Corp. (Feb. 1977).

is available at keat77.