The PDB constructor has now changed (for the better). Related packages will need to be fixed since my refactoring. The constructor now only accepts the content of a PDB file which matches the FASTA object constructor. Calling functions should use one of:  - clone (copy lines from an existing object)  - from_filepath (read a file from the disk and create a PDB object)  - from_lines (use the list of PDB file lines to create a PDB object)  - retrieve (new: read a PDB file from the RCSB or a cached copy and create a PDB object)
The PDB constructor has now changed (for the better).
Related packages will need to be fixed since my refactoring.
The constructor now only accepts the content of a PDB file which matches the FASTA object constructor.
Calling functions should use one of:
 - clone (copy lines from an existing object)
 - from_filepath (read a file from the disk and create a PDB object)
 - from_lines (use the list of PDB file lines to create a PDB object)
 - retrieve (new: read a PDB file from the RCSB or a cached copy and create a PDB object)

Removed PDB.read function
Used existing code to neaten the PDB.write function

Kortemme-Lab/klab,Kortemme-Lab/klab,Kortemme-Lab/klab,Kortemme-Lab/klab