modifications

Summary of a discussion we had at the Bioc2014 conference.

A infrastructure package with:

• parsing unimod
• definition of modification: mod with slots type, theoretical mass difference, support for arbitrary modifications.
• assigning modifications to actual positions in peptides/proteins: aamod with a pointer to a mod and a position, probability/score
• Multiple aamod should be able to point to the same mod and all position should be reachable from any position or the mod itself

Given a Pbase::Proteins instance, a modification in a peptide/protein would be annotation with an aamod.