Substitution score from or to Z is 0

[jbarnoud]

As noted in a comment to #56, the substitution score from and to the Z dummy block is always 0. This is used in PBclust to build the distance matrix, and to compare sequences with the --compare option.

To this, @pierrepo commented:

We should not have to compare "z" to a PB since "z" is not a PB. It just means that a PB cannot be assigned to this residue.
So maybe we should rise an error as this point.

How to we want to handle substitution from and to the Z dummy block ? The obvious way, as suggested by @pierrepo is to raise an exception. Yet, this means that we cannot do a clustering when some information is missing, or that we need to find tricks.

Bare in mind that this will affect how we calculate distance matrices. See #62 for more about distance matrix calculations.

cc @pierrepo @alexdb27

[alexdb27]

I think we can use the "gapopen" value used for structural alignement if a real PB is in front of Z, while it is zero if Z in front of Z. cc @pierrepo @jbarnoud

[pierrepo]

OK. How much is a gapopen value ?

[alexdb27]

-600 !!!
Ok, it is x 100 ...