Improve `pdb_mkensemble` to work as lib

[joaomcteixeira]

Currently, pdb_mkensemble requires file paths to work, which means the pdb_mkensemble.run function cannot take a list of lists (or similar iterators) to make an ensemble. This makes the tool not fully compatible with the lib mode.

To do: improve the pdb_mkensemble.run function to accept a list of lists (of lines) at the same time it can accept file paths.