In the Section molecules we saw how atoms and bonds are contained in
the IAtomContainer data model. It was mentioned that
it is a general container, and this is exactly what we need for disconnected
structures like salts and molecular crystal structures.
Functionality to determine if the content of an IAtomContainer is connected, you can use the ConnectivityChecker, as explained in Section partitioning.
Salts are one of the most common disconnected structures found in compound databases: a salt is a combination of two or more connected molecules bound to each other by coulombic interactions. These may be solids.
A common kitchen example is the table salt sodium chloride. We can represent this using the following model:
Salt
If you prefer a single IAtomContainer to only contain connected
atoms, instead of unbound atoms as in this salt example, you can
partition them into two or more new containers, as explained in
Section partitioning.
Of course, the representation given in the previous section
is a very basic model for sodium chloride. A crystal
structure would perhaps be a more accurate description of what you
like to represent. In this case, the ICrystal subclass of
the IAtomContainer can be used (see Figure crystalInheritance):
SaltCrystal
If we want to add the crystal structure parameters and crystal structure coordinates of the atoms, we add can add them too (data taken from this webpage):
SaltCrystalParam