New class iterator in the module `structure` to work with trajectories.

[dprada]

In my opinion, the only important functionality left to implement before publishing this is something to work with trajectories. We could probably discuss here how this tool could be shaped.

I would like to avoid additional auxiliary classes as most of the libraries have (mdtraj or MDAnalysis). In my opinion the power of the tool should be in a unique place, a iterator.

¿What do we need? We need a tool to extract frames (step, time, coordinates, and boxes) in a smart and simple way when these structures are stored in a trajectory file. However, their use should not be restricted to trajectory files.

As user, I would like to do something like this:

import molsysmt as msm

iterator = msm.structure.iterator('traj.h5', start=100, interval=10, stop=200, selection='atom_name=="CA"')

for step, time, coordinates, box in iterator:
     print(step, time, coordinates, box)

iterator.close()

or

import molsysmt as msm

iterator = msm.structure.iterator(['traj.gro', 'traj.xtc'], indices=[10, 22, 30, 78, 145], selection=[10, 11, 12])

for step, time, coordinates, box in iterator:
     print(step, time, coordinates, box)

iterator.close()

or

import molsysmt as msm

iterator = msm.structure.iterator('traj.dcd', start=1, interval=10, stop=1000, chunk_size=20)

for _, chunk_times, chunk_coordinates, _ in iterator:
     print(chunk_times, chunk_coordinates)

iterator.close()

This iterator could have the following instatation arguments:

• molecular_system: The standard molecular system input.
• start: first structure index of the trajectory to start with. [default: 0]
• interval: number of structure indices to be skipt in each iteration. [default: 1]
• stop: the iteration finishes if the current structure index is larger than or equal to this integer. [default: None]
• chunk_size: amount of structures in the output of each iteration [default: 1]
• selection: atoms selection [default: 'all']
• syntaxis: syntaxis used in selection [default: 'MolSysMT']

I am not sure if to do this iterator method, we need to define a specific structures_iterator in the module item for each form (trajectory file or form with structures in general).

@Daniel-Ibarrola: What do you think? Do you have an alternative proposal?

[dprada]

This issue was fixed with #86 by @Daniel-Ibarrola.