[Optimization] Compute sin/cos outside for-loop

[discoleo]

Optimization of turn3d

The following code appears in function turn3d:

theta <- seq(0, 2*pi, length.out = n + 1)[-(n + 1)]
for (i in inds) {
    vb <- cbind(vb, rbind(x[i], sin(theta)*y[i], cos(theta)*y[i], 1))

The sin(theta) and cos(theta) are computed during each iteration inside the for-loop. Furthermore, theta is a vector with 12 values: the repeated evaluation may become sufficiently expensive.

[dmurdoch]

Show me the timings for this and your proposed improvement.

[discoleo]

I was looking for a simple solution to rotate a protein (e.g. a ion channel monomer) around its central pore and generate the surface around the pore. The monomer may have hundreds of amino acids.

Using turn3d seemed a sufficiently simple hack. I do not have yet a functional code: but I have to think if it will work with 100 * (10 to 20 atoms) > 1000 atoms.

[dmurdoch]

Don't worry about optimization yet. Keep your code simple, and get it to work. If it's fast enough, move on to the next task. If not, then worry about optimization.