Section 3.2.4.2.2. Chemical connectivity

The data items in these categories are as follows:

(a) CHEMICAL_CONN_ATOM

(b) CHEMICAL_CONN_BOND

The bullet () indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow () is a reference to a parent data item.

The CHEMICAL_CONN_ATOM category labels the chemical atoms in a connected representation of the molecular species and can also give the coordinates for the atoms in a two-dimensional chemical diagram (Example 3.2.4.7). Each atom may also carry an indication of the number of connected non-hydrogen atoms (*_NCA) and the number of hydrogen atoms (*_NH) to which it is connected. Together with the CHEMICAL_CONN_BOND category, the data items in the CHEMICAL_CONN_ATOM category provide a basic description of the chemical structure. Although the description of the chemical structure provided in these two categories is not as extensive as the information that may be conveyed in a molecular information file (Chapter 2.4 ), it should allow a substructure to be searched for in a suitable database.

The CHEMICAL_CONN_BOND category lists pairs of atoms that contribute to chemical bonds and describes the nature of the bond between them (Example 3.2.4.8). Taken with data items in the CHEMICAL_CONN_ATOM category, data items in this category complete the basic description of a molecular entity.

Bond types are assigned from a list that specifies single, double, triple, quadruple, aromatic, polymeric, delocalized double and π bonds. These are not intended to cover all possible cases, but to characterize a molecular model suitable for database substructure searching.