tests: Atom, Molecule and Cluster class with rdkit

[AndyDanian]

Check testing of Atom, Molecule and Cluster class.

Add the tests necessaries for those classes.

[AndyDanian]

All Conflicts due RDKit integration in the test of Atom, Molecule and Cluster classes were fixed

• The Atom class have 100% of coverage

• The Molecule class have 81% of coverage
  missing lines: 134-135, 143-154, 161-181, 189, 194-197, 206, 238, 292, 378, 387, 436, 438, 460, 462

• The Cluster class have 95% of coverage
  missing lines: 88, 190, 229, 440, 583-588, 690-696

[AndyDanian]

Recheck the testing because the atom, classes and cluster classes were refectory!