Insertion codes not preserved in addMissingAtoms

[zhang-ivy]

This issue is related to @peastman 's fix: #184

While findMissingResidues can now handle PDBs with residue insertion codes, in addMissingAtoms (which calls _addAtomsToTopology), the new topology with the missing atoms added does not maintain residue insertion codes.

This should be a simple fix: change this line newResidue = newTopology.addResidue(residue.name, newChain, residue.id) (https://github.com/pandegroup/pdbfixer/blob/master/pdbfixer/pdbfixer.py#L401)
to newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)

[peastman]

A PR would be welcome!

[zhang-ivy]

Sorry for the delay, I'm trying to create the PR now, but I get the following error when I try to push to my newly created insertion-codes branch:

fatal: unable to access 'https://github.com/pandegroup/pdbfixer.git/': The requested URL returned error: 403

Can you add me as a contributor to this repo?

[jchodera]

@ivyzhang999 : You should be able to create your own fork of the repo and then contribute the PO from your fork!

We typically don't do that for projects that involve encrypted environment variables because travis does not encrypt them in PRs from forks for security reasons, but that isn't an issue here!