function[Max,k,BestSolutions] = RunOffLineProtein(Fibbonacci_n,PopSize,T,CantGen,Elitism)% RunOffLineProtein. Calls the  Gaussian UMDA to find the HP model with minimum energy in an offline lattice% The sequence is the Fibbonacci sequence built from the input parameter      % For reference on the Offline HP model see:%-- H. P. Hsu, V. Mehra and  P. Grassberger (2003)  Structure optimization in an off-lattice protein model.%-- Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Sep;68(3 Pt 2):037703. Epub 2003 Sep 30. %-- http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000068000003037703000001&idtype=cvips&gifs=yes         % INPUTS% Fibbonacci_n: Value n for the construction of the Fibbonacci sequence. NumbVar = F(n)% PopSize: Population size% T: Truncation parameter (when T=0, proportional selection is used)% CantGen: Maximum number of generations% Elitism: Number of the current population individuals that pass to the next one.  %---Elistism=-1: The whole selected population (only for truncation) passes to the next generation   % OUTPUTS% Max: Maximum value found by the algorithm at each generation% k: Generation where the maximum was found, case it were known in advance% BestSolutions: Matrix with the best solution at each generation% EXAMPLE% [Max,k,BestSolutions] = RunOffLineProtein(6,100,0.5,500,1); % In this example the Gaussian UMDA will search for the optimal  position  of a chain with 13 residues (F(6) = 13).global InitConf;% The sequence of residues is initializedInitConf = CreateFibbInitConf(Fibbonacci_n);NumbVar = size(InitConf,2);% Gaussian UMDA search the set of angles that determines the best optimal energetic configuration of the sequence in the lattice% Each continuous variable takes values in the interval [0,2*pi].% The MaximumValue for the algorithm is arbitrarily set.[Max,k,BestSolutions] = RunGaussianEDA(PopSize,NumbVar,T,'OffEvalProtein',CantGen,NumbVar,[zeros(1,NumbVar);2*pi*ones(1,NumbVar)],0,0,Elitism); % The best solution found is printed OffPrintProtein(BestSolutions(k-1,:));% Last version 10/09/2005. Roberto Santana (rsantana@si.ehu.es)