Your question is far too generic to be able to give a precise answer.
The first mistake people do is operate on an array one element at a time instead of operating on the whole array at once. Other than the fact that you constantly overwrite A, this appears to be the mistake you've made in your example.
%assuming array is a row vector
v = ind1:ind2; %make a vector of the values i iterates over
A = (array .* (v + ind2) + array .*(v + ind1)) ./ hypot(ind2 - v, ind1 - v);
A = cos(pi*A);
For more complicated stuff, bsxfun, repmat, ndgrid, etc. may be useful indeed.
