Adding charge tracking

[irudayaf]

Gianni,

I had the idea to include charge as a function of the pore profile averaged over the trajectory. This will actually be a feature useful for pores with a charge filters. All it would entitle is keeping track of the sum of partial charges in each bin, which is already part of the topology.
Let me know what you think, I would be happy to make these additions.

Best
Jerome

[Inniag]

I think this would be a nice feature to have, but I'm not quite clear on how this would be implemented.

CHAP operates on a per-residue basis for creating hydrophobicity profiles, so when talking about partial charges, which ones would you include? All atoms within a cutoff distance, all atoms within residues within a cutoff distance, something else? I'd prefer to keep it simple and consistent.

Also, are partial charges really needed or would it be sufficient to consider only charged residues? In principle you could already do this by hijacking the hydrophobicity profile calculation and replacing the residue hydrophobicity values by residue charges. This would not change the colour scale though.

(PS: I will be very busy until about mid-October and I doubt that I can make any major changes or perform code review until then. Please be patient.)

[irudayaf]

I guess the partial charges will indeed even out over time, so tracking the total charges might suffice (I will have think). I can use try the hydrophobicity calculation and see how that fares.

[Inniag]

Great, let me know how that works and we can think of a more permanent solution after.