Most output formats destroy non-standard bond information

[avirshup]

mol = mdt.from_smiles('CCCC')
print mol.write('pdb')

Gives

HETATM    1  C0  UNL     1       0.928  -0.017  -0.007  0.00  0.00           C  
[...]
HETATM   14  H9  UNL     1       0.809   2.183   1.709  0.00  0.00           H  
END                                                                             

But we expect a CONECT section ... at least for the HETATMs

[avirshup]

Implemented moldesign._tests.test_topology_preserved_in_serialization, which for now only has SDF bonds working correctly ...