Add basic examples for Molecule class

doc/source/code-examples/index.rst

@@ -8,4 +8,4 @@ This section provides examples of how to use Qibochem.
 .. toctree::
     :maxdepth: 2
 
-    examples
+    molecule

doc/source/code-examples/molecule.rst

@@ -0,0 +1,60 @@
+Building a Molecule
+===================
+
+To get started with Qibochem, the molecular system of interest is first defined:
+
+Molecular geometry input
+------------------------
+
+A ``Molecule`` can be defined either inline, or using an ``.xyz`` file. An example for a H2 molecule:
+
+.. code-block::
+
+    from qibochem.driver.molecule import Molecule
+    
+    # Inline definition
+    h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))])
+
+    # From an .xyz file
+    # h2 = Molecule(xyz_file='h2.xyz')
+
+Note that the comment line in the ``.xyz`` file can be used to define the electronic charge and spin multiplicity of the molecule.
+If it is not given, it defaults to 0 and 1, respectively.
+
+
+Obtaining the molecular Hamiltonian
+-----------------------------------
+
+After defining the molecular coordinates, the next step is to obtain the molecular integrals.
+Qibochem offers the functionality to interface with either `PySCF`_ or `PSI4`_ towards that end:
+
+.. _PySCF: https://pyscf.org/
+.. _PSI4: https://psicode.org/
+
+.. code-block::
+
+    from qibochem.driver.molecule import Molecule
+    
+    # Inline definition of H2
+    h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))])
+
+    # Using PySCF
+    h2.run_pyscf()
+    # Using PSI4
+    # h2.run_psi4()
+
+After the molecular integrals have been calculated, molecular Hamiltonian can then be constructed in the form of a Qibo ``SymbolicHamiltonian``:
+
+.. code-block::
+
+    from qibochem.driver.molecule import Molecule
+    
+    # Inline definition of H2
+    h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))])
+
+    # Calculate molecular integrals
+    h2.run_pyscf()
+
+    # Get molecular Hamiltonian
+    hamiltonian = h2.hamiltonian()
+