Fix PDBFixer dependencies

[jchodera]

Ensembler apparently uses some undocumented parts of the PDBFixer internals---specifically PDBFixer.structure, which no longer exists---to do loop modeling. This currently causes tests to fail:

nsembler.tests.test_loopmodel.test_pdbfix_KC1D_HUMAN_D0_4KB8_D ... MPI rank 0 pdbfixer error for template KC1D_HUMAN_D0_4KB8_D - see logfile
'PDBFixer' object has no attribute 'structure'
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/ensembler/modeling.py", line 138, in pdbfix_template
    chainid = next(fixer.structure.iter_chains()).chain_id
AttributeError: 'PDBFixer' object has no attribute 'structure'
ERROR

We need to update this for whatever PDBFixer does now.

[jchodera]

Ideally, we can just use the public API.

[sonyahanson]

Hmmmm.

[jchodera]

Hmmm?

[jchodera]

I don't think we had noticed this because (1) we were using Rosetta for loop modeling, and (2) we were using the released pdbfixer from a long time ago in the dependencies. Now we have updated to pdbfixer-dev to catch these issues.

[jchodera]

We've also added nightli.es nightly builds so we get an alert when something breaks.