Quick fix for updating RCA4 and TORC after reorder

[arosale4]

After any renumbering of any of the atoms, the RCA4 and TORC values need to be corrected to the new atom index value. These are a quick fix, that just gets the job done. This problem goes back to using numbers instead of atom objects for these bond properties, which is found in issue #42.

[ericchansen]

This has a lot of bugs that need to be worked out before I can run tests.

• 609 - PEP8 comment syntax (space between # and comment)
• 615 - for i,atom_index == atom_index maybe should be for i, atom_index in enumerate(atom_index)? Also, you shouldn't name the iterator variable the same as the variable you're looping over.
• 626 - PEP8
• 627 - Variable typo
• 628 - PEP8 for arithmatic
• 629 - Variable typo?
• 631 - Not sure what's up with this. Should it be a loop or a relationship? Also spacing of variables doesn't follow PEP8.
• 635 - elif without an if

That's all I noticed.