Meta Atoms

An important concept within JTHERGAS is that of a meta-atom. This is where the basic atom node information (in the graphical representation) is extended beyond the 'normal' molecular atom representation mentioned previously. Meta-atoms are used at many levels within JTHERGAS. All meta-atoms within JTHERGAS are defined through the database and is one of the keys to JTHERGAS's flexibility.

Two examples of meta atoms are the extended atom definitions of the atoms in the definition of a Benson rule and the Nancy linear forms. More complex meta-atoms exist within JTHERGAS such as one more a methyl (CH₃) or a phenyl (aromatic ring) group which can be used to simplify molecular matching.

One of the flexibilities within the JTHERGAS system is that all the meta-atoms are not hard-coded within the library, but are defined within the extendable database. With each meta-atom there is associated a complete molecular structure. This means that any new meta atom can be defined when needed without modifying the base code.

There are two types of meta-atoms:

• Benson Rule: The Benson group additivity rules are defined making distinctions between, the different valences of the specific atoms, such as single, double, triple, aromatic, etc., and even for defining whole functional groups, such as CO, CN, NO2, to name a few.

• Linear Atoms: Within the symmetry recognition, some symmetries depend on whether the connection group is linear or not. During the recognition process, these meta-atoms are substituted into the structure.