Everything else is opinion. The foundation of a chemical information system is its ability to represent molecules in a computer, and to communicate a molecule's structure from one place to another. This can seem like a simple problem at first glance, and easy solutions are often proposed and implemented. But a close examination of the problem reveals that several subtle traps await the unwary, and methods of avoiding them must be considered before an effective computer representation of a molecule can be designed. When using such models, we must always avoid the trap of arguing that a particular model is right rather than arguing that it is useful .
Models are just that - models.
Daylight's system represents molecules using a fairly standard valence model. For example, the Daylight system understands the normal valences of organic compounds, and by counting the bonding electrons in a molecule, can fill in unspecified hydrogens, detect aromatic and anti-aromatic ring systems, and issue warnings when unlikely or impossible molecules are specified. The Daylight system represents a molecule as a graph in which the nodes are atoms and the edges are bonds. Each atom has a several properties, including its atomic number, atomic weight, charge, and the number of attached hydrogens. If the atom is a chiral center, it can also have chiral specifications.