If you have multiple 1s in a row of your B matrix, then creating variable names like C, D, .. is not advisible: https://www.mathworks.com/matlabcentral/answers/304528-tutorial-why-variables-should-not-be-named-dynamically-eval. It is better to use cell arry.
Try the following code
A = [1 2 3 4 5; 1 2 3 4 5; 1 2 3 4 5; 1 2 3 4 5; 1 2 3 4 5];
B = [1 0 1 0 0; 1 0 1 0 0; 1 0 1 0 0; 1 0 1 0 0; 1 0 1 0 0];
grps = cumsum(B, 2);
C = cell(size(A,1),1);
for i = 1:numel(C)
C{i} = splitapply(@(x) {x}, A(i,:), grps(i,:));
end
If number of 1s are equal in each row then you can also run the following
C = reshape([C{:}], [], numel(C)).';
