Implement membrane protein belt simulations

[ninamiolane]

Implementations should model the belt analytically

When computing the integral, one needs to subtract the protein in the center:

• subtract the individual contributions of the atoms
• width of the belt
• location of the belt
• density of the belt is two-folds:
  • internally: carbons
  • externally: other atoms

[geoffwoollard]

Helena is working on adding a lipid belt to a membrane protein. The forward model has just a few simple geometric parameters in it.

By "model the belt analytically" do you mean

1. adding in atoms based on some geometric parameters
2. going from parameters directly to the signal they contribute to the projection based on analytical equations and doing the integral sum

OF course, it can be both... but they will be distinct code

[kdd-ubc]

The way we are currently implementing it is by putting atoms within an ellipsoid defined by the geometric parameters, and subtract the protein in the center (to be done this week by Helena). The model will then be converted into a pdb file that can be passed to the TEM simulator