Add support for custom alignment file in [caprieval]

[AnnaKravchenko]

When aligning a short reference DNA to a longer DNA model, the current capri alignement gives poor results:

• Structural alignment fails; (btw this leads to a python error instead of a ‘readable' one);
• Sequential alignment returns very large lrmsd values. At the same time, manual alignment (in pymol) shows some models are pretty accurate, which means that at least some 'large lrmsd values’ are incorrect.
  In sequential alignement, alignement file for DNA chain also shows that alignement is incorrect.

What wouls slove my problem is if caprieval would accept a user-supplied alignment file for evaluation.

I intend to add an new option align_fname to alignment_method parameter of caprieval module.

Not sure yet how to deal with multiple docking partners and multiple chains. Will start with solving my current issues - a single-chain receptor alignement - and we’ll see where it goes.

[VGPReys]

I would advise to add a new parameter and not an option in the alignment method, otherwise you cannot supply the path to the file you want to use.

[AnnaKravchenko]

Good point indeed!