fFRI algorithm.

Input: atoms(N)	▷ XYZ coordinates from PDB file
mincoor ← minval(atoms)	▷ Compute dimensions of bounding box
maxcoor ← maxval(atoms)
R ← boxsize	▷ Set size of grid
Nbox ← ceiling((maxcoor − mincoor)/R)	▷ Compute number of boxes in each direction
for ii ← 1, Natoms do
i, j, k ← ceiling((atoms(ii) − mincoor)/R)	▷ Count the number of atoms in each box
Natoms(i, j, k) ← Natoms(i, j, k) + 1
end for
for k ← 1, Nbox[3] do
for j ← 1, Nbox[2] do
for i ← 1, Nbox[1] do
allocate(box(i, j, k))	▷ Allocate space for each box
end for
end for
end for
for ii ← 1, Natoms do	▷ Copy coordinates to appropriate box based on 3D coordinates
i, j, k ← ceiling((atoms(ii) − mincoor)/R)
box(i, j, k) ← atoms(ii)
end for
for k ← 1, Nbox[3] do	▷ Iterate over boxes
for j ← 1, Nbox[2] do
for i ← 1, Nbox[1] do
for na ← 1, Natoms(i, j, k) do	▷ Iterate over atoms in current box
for n ← k − 1, k + 1 do	▷ Iterate over adjacent boxes
for m ← j − 1, j + 1 do
for l ← i − 1, i + 1 do
for nb ← 1, Natoms(l, m, n) do	▷ Iterate over atoms in adjacent boxes
dist ← distance(box(i, j, k)(na), box(l, m, n)(nb))
FRI(na) ← kernel(dist)
end for
end for
end for
end for
end for
end for
end for
end for