Other Representations of Three-Dimensional Molecular Structure

9 Other Representations of Three-Dimensional Molecular Structure 

While atomic coordinates form the fundamental structure of a molecule, many methods prefer to represent a three-dimensional structure as a surface or a shape. Of course, these are ultimately computed from the atomic coordinates and perhaps atomic partial charges. It may be possible to represent these molecular surfaces or shapes as an array of three-dimensional coordinates. These could be stored as a column in the database analogous to the array of atomic coordinates. It might be necessary to create another data type, perhaps a composite data type, to store molecular surfaces or shapes. Once these representations are stored, they can be used in new SQL functions to assist in searching based on molecular surface or shape. 

O Donnell, T.J., Rao, S.N., Koehler, K., Martin, Y.C., and Eccles, B. 1990. A general approach for atom-type assignment and the interconversion of molecular structure files. /. Comp. Chem. 12(2) 209-214. 

OpenBabel. http //openbabel.sourceforge.net/ (accessed April 18,2008). 

---