write PDB conect records for S-S bridges and HETATM

[Valdes-Tresanco-MS]

Sorry, I had to delete the repository and it automatically closed the PR. I include previous code for testing

Here is a well-resolved structure with disulfide bonds. It also has a phosphate ion that serves for heteroatoms
Test code.
Save conect records by default:

import parmed

s = parmed.load_file('3m7q_test.pdb')
s.save('3m7q_parmed.pdb', format='pdb', renumber=False, overwrite=True)

Don't save conect records:

import parmed

s = parmed.load_file('3m7q_test.pdb')
s.save('3m7q_parmed.pdb', format='pdb', renumber=False, overwrite=True, conect=False)

This file contains 3m7q.pdb (Original PDB), 3m7q_test.pdb (PDB without CONECT records) and 3m7q_parmed.pdb (Saved pdb with CONECT records using this PR)
parmed_conect_test.zip

I look forward to your comments
Mario S.

[swails]

Sorry it took me so long to get to this. It looks great! Can you add a test case and then I'll get it merged.

[Valdes-Tresanco-MS]

I am not sure if this test is enough. This test fails with PDBs that have the CONECT record for coordination bonds. We can implement it later if necessary