Decide on interface for Renumerator

[krother]

[cosi1]

Maybe something like that would do the job?

__init__(structure, alignment = False)

When alignment is given, the constructor automatically inserts required gaps, basing on that alignment. If not, it is assumed that nothing will be inserted unless the user invokes insert_gap() manually.

insert_gap(position, length)

Inserts a gap at a given position.

renumber()

Applies all the insertions to the structure passed to the constructor.

[krother]

Would the structure be the template or the model? Can I use it for both (e.g. when modeling multiple templates or fragments?

I would like to have a method that renumbers a small section:

def renumber_section(index_start, index_end)

E.g. for renumbering a fragment at a specific location. If no alignment is given, the indices can be interpreted as residue numbers directly.

[cosi1]

Would the structure be the template or the model? Can I use it for both (e.g. when modeling multiple templates or fragments?

I think that it would be best to operate on both template and model (since they are both descendants of ModernaStructure).

def renumber_section(index_start, index_end)

Could you explain that?

[krother]

The idea was to use Renumerator to renumber a fragment before inserting it. For that, Renumerator needs to know which part of the model it belongs to. Or would we create a proxy alignment for each fragment?

I agree that Renumerator could operate on both templates and models.

[cosi1]

The idea was to use Renumerator to renumber a fragment before inserting it. For that, Renumerator needs to know which part of the model it belongs to. Or would we create a proxy alignment for each fragment?

Hmm... I didn't think of it that way... I always thought of the renumerator as a tool to insert gaps into structures (templates and models). Maybe we might need to rethink the idea of the renumerator to be more versatile.

[krother]

OK now I understand better. For that the interface you propose is very sound. I think this part is ready to be implemented. No need to mix responsibilities.

We also need to figure out where to put the renumeration code from Fragments. Could be a separate place.

[cosi1]

Ok, so let's wait for Lena's opinion. When we reach consensus, I'll start implementing the logic (basically copypasting from renumber_template()).

[lenarother]

OK, I agree that there can be one class for renumbering Template and Model and separate for renumbering Fragment.

[lenarother]

Some comments on renumeration from Asia in #30.