Necessary enhancements of ParmEd to suit BAC requirements

[dww100]

We need to decide if we can build on Parmed or need to roll our own tools.

I'll develop a list of target proteins and their issues on the wiki

[dww100]

Required enhancements to Parmed:

1. Read additional metadata from PDB/cif (sequence, BIOMT, SSBOND) [Moved to Obtain information for building from PDB header #65]
2. Add insertion code to dataframe created from structure
3. Convenience functions for chain/segid selections

[dww100]

Add to create_dataframe in https://github.com/ParmEd/ParmEd/blob/master/parmed/utils/pandautils.py:
ret['insertion'] = [atom.residue.insertion_code for atom in atoms]

Now available in:
https://github.com/UCL-CCS/ParmEd/tree/bacbuilder

[dww100]

Edit parse in https://github.com/ParmEd/ParmEd/blob/master/parmed/formats/pdb.py to add metadata

[dww100]

My idea is to use this thread to discuss changes needed and whether to add to code in Parmed or in BAC2.

All new additions to dataframe output should be added to UCL-CCS/ParmEd#5

[dww100]

Header information separated into #65
Convenience functions into #66