Meta Atom Data

An important concept within JThermodynamicsCloud 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. Figure 2 shows the meta atom structures in the database for a doubly bonded carbon and a carboxyl group. The structure on the right is used to describe the doubly bonded carbon, which can have the meta atom name Cd, and the structure on the left describes a multi-atom carbonyl (ketone) meta-atom, co.