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Salts and other disconnected structures
In the Section 4.3 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 14.1.
Salts
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 = new AtomContainer();
sodium = new Atom("Na");
sodium.setFormalCharge(+1);
chloride = new Atom("Cl");
chloride.setFormalCharge(-1);
salt.addAtom(sodium);
salt.addAtom(chloride);
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 14.1.
Figure 6.1: The ICrystal interface extends the IAtomContainer interface.
Crystals
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 6.1):
Script 5.2 code/SaltCrystal.groovy
salt = new Crystal();
sodium = new Atom("Na");
sodium.setFormalCharge(+1);
chloride = new Atom("Cl");
chloride.setFormalCharge(-1);
salt.addAtom(sodium);
salt.addAtom(chloride);
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):
Script 5.3 code/SaltCrystalParam.groovy
salt = new Crystal();
salt.setA(new Vector3d(5.6402, 0, 0));
salt.setB(new Vector3d(0, 5.6402, 0));
salt.setC(new Vector3d(0, 0, 5.6402));
salt.setZ(4);
sodium = new Atom("Na");
sodium.setFormalCharge(+1);
sodium.setFractionalPoint3d(
new Point3d(0, 0, 0)
);
chloride = new Atom("Cl");
chloride.setFormalCharge(-1);
chloride.setFractionalPoint3d(
new Point3d(0.5, 0.5, 0.5)
);
salt.addAtom(sodium);
salt.addAtom(chloride);