refactoring of pair_cores.py * add pdb-markup reading (user can provide pdb markup or alignment) * add CachedDownloadPdb as pdb_getter and allow change chache_dir * drop useless removing of monomers without structure (it should be already done by previous steps) * add messages to exceptions and documentation * rename run() to homology_from_3d() * hardening: raise if a structure at least one of sequences can't be loaded see #86 It seems not to work with markups (returns no blocks)