calculateFragments calculates too much fragments

[sgibb]

calculateFragments calculates fragments for all n amino acids in a sequence but only n - 1 bonds are present, so just n - 1 fragments are valid.

E.g. this peptide with 4 amino acids has 3 bonds and valid fragments from a1 to a3 (same for b, c, x, y, z):

Current output:

calculateFragments("ACE", type="b")
         mz ion type pos z seq
# 1  72.04439  b1    b   1 1   A
# 2 232.07504  b2    b   2 1  AC
# 3 361.11763  b3    b   3 1 ACE

but correct output would be:

calculateFragments("ACE", type="b")
         mz ion type pos z seq
# 1  72.04439  b1    b   1 1   A
# 2 232.07504  b2    b   2 1  AC