enable missing residues at the interface in the rmsd calc

[manonreau]

Computes the irmsd and lrmsd despite missing atoms/residues at the interface. A warning is raised instead of an error.

[NicoRenaud]

I'm afraid one test is failing :(

[manonreau]

I'm afraid one test is failing :(

This is the test that checks if an error is raised if 2 interfaces are not strictly identical. Pretty logical !

[NicoRenaud]

Well I'm thinking those tests were here for a reason. We do use pdb2sql in a few projects so I don't really want to modify the default behavior of the methods. What we could do is to make the error raising optional. For example with a keyword argument of the routines or an attribute of the class.

Class StructureSimilarity(self, decoy, ref, verbose=False, enforce_residue_matching=True):
           ...
          self.enforce_residue_matching = enfore_residue_matching

and in the methods

if self.enforce_residue_mathcing:
    raise ValueError(....)

That way you can in your case turn the residue matching option off but the default behaviour doesn't change. Of course we introduce one argument in a bit of a adhoc fashion but I would prefer that at the moment

[manonreau]

now:

• if self.enforce_residue_matching == True: an error is raised if the residues from the ref differ from those of the decoy (no matter the value of check)
• if check == True: checks if residues ref == residues decoys, if not, raises an error (self.enforce_residue_matching == True) or a warning (self.enforce_residue_matching == False)

I would delete the check, is that dangerous ?