Atom and Bond

Atoms and bonds are the foundation of varies of molecules. They are represented as objects in Kekule.js.

Working with Atom

To create an atom:

var atom = new Kekule.Atom('atom1');  // create an atom with an id

Atom can be modified by its properties:

Property	Value Type	Description
atomicNumber	int	Atomic number of atom, e.g. 6 for carbon. It will be automatically changed when property symbol is set.
symbol	string	Symbol of atom, e.g., ‘C’ for carbon. It will be automatically changed when property atomicNumber is set.
massNumber	int	Mass number of the isotope.
isotopeId	string	A shortcut property to set atomic number and mass number all at once, e.g. ‘13C’ or ‘C13’.
charge	float	Charge on this atom. Partial charge (e.g. +0.5) is allowed.

// set atom to represent C13
atom.setSymbol('C').setMassNumber(13);  // note that the property can be set cascadedly
// same effect as the previous line
atom.setIsotopeId('C13');
// atom O2-
atom.setAtomicNumber(8).setCharge(-2);

Some property values can be set during the creation of atom:

var atom = new Kekule.Atom('atom1', 'C', 13);   // create C13 atom

Working with Bond

To create a bond:

var bond = new Kekule.Bond('bond1');  // create a bond with an id

Two of the most important properties of bond is its type and order:

Property	Value Type	Description
bondType	string	Type of bond, can be set to Kekule.BondType.COVALENT/IONIC/COORDINATE/METALLIC/HYDROGEN.
bondOrder	int	Order of covalence bond, can be set to Kekule.BondOrder.SINGLE/DOUBLE/TRIPLE and so on.

// create a double covalent bond
bond.setBondType(Kekule.BondType.COVALENT).setBondOrder(2);

If bondType or bondOrder property is not set, the bond will be considered as a single covalent bond by default.

Atoms can be connected together by bonds, thus a molecule is created. This will be discussed in the next part of this tutorial.