Families of Equivalent, Interconvertible Representations

Klotho computes with several informationally equivalent representations :

• an edge description, where each term describes two atoms and the bond between them, equivalent to describing the edges in a connected graph;

• a key-pair description, equivalent to the edge description but organized slightly differently to exploit some sorting predicates built into Prolog;

• and a terminal form (``term form''), which is a completely determined adjacency list of atoms, bonds, stereochemistry, and associated information for the molecule. This was the representation we started with, inspired by an idea of David Searls; it was the need to avoid coding such a long representation for many molecules that led us to develop Klotho.

Notice that certain information is implicit in the first three representations, and is inserted into the terminal form by the action of the grammar . For example, only a few atom numbers are indicated in the configuration rule (just enough to insure the resulting compound is definitely numbered the way biochemists do), and no isotope; complete enumeration of the atoms occurs in the edge and key-pair descriptions; and isotope and most charge information is inserted in the terminal form. The isotope is something of a relic from the days when we thought we would trace the atoms computationally the way one does experimentally, by labelling the compound with a different isotope. In fact since all the atom numbers are distinct, all that is required is to map atom numbers from one compound to another through the reactions, and tabulate the mappings. Because we use substituent groups to make even larger molecules , we explicitly generate all hydrogens not already indicated in the configuration rule in the other three representations.

So that we can check the configuration rules for the compounds, Klotho also generates isomeric SMILES strings; we sometimes call these representations ``external'' to distinguish them from those of Klotho proper. These, and the PDB files resulting from passing the strings through CONCORD , are not informationally equivalent to Klotho's representations, though some of the information is intensionally coded by CONCORD and by the conventions with which we view three-dimensional structures.

Back to Klotho's home page.