function[eval] =  OffEvalProtein(vector)% OffEvalProtein evaluates calculate the energy corresponding to the sequence lattice configuration determined by the lattice in vector.% Fixing the lengths of the edges, each angle defines the position of the next residue respective the two previous ones.  % From the residues positions, the interaction energies are calculated by the energy function    % 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% vector: Sequence of residues ( (H)ydrophobic or (P)olar, respectively represented by zero and one)% OUTPUTS% eval: Energy evaluation.% InitConf has been initialized with a Fibbonacci sequence by the RunOffLineProtein.m routine global InitConf;% The position of the sequence in the latticce are calculated[Pos] =  OffFindPos(vector);  sizeChain = size(InitConf,2);% See reference for the calculation of the energy functiontotcos = 0;% Cosine part of the evaluationfor i=1:sizeChain-1, totcos = totcos + (1-cos(vector(i)));end% Distance part of the evaluationtotAB = 0;for i=1:sizeChain-2, for j=i+2:sizeChain,  dist = sqrt ((Pos(i,1) - Pos(j,1))^2 +  (Pos(i,2) - Pos(j,2))^2);  if (InitConf(i)==1 & InitConf(j)==1)        ABeffect = 1;  elseif (InitConf(i)==0 & InitConf(j)==0)        ABeffect = 0.5;  else       ABeffect = -0.5;  end  totAB = totAB + (1/(dist^12) - ABeffect/(dist^6)); endendeval = -1.0*(totcos*0.25 + totAB*4); % Last version 10/09/2005. Roberto Santana (rsantana@si.ehu.es)