EvalChainFunctional

 Given a chain of molecules, calculates the numer of Collisions with 
 neighboring same sign molecules, and the number of Overlappings molecules.
 HPInitConf is the configuration of the Chain of molecules
 vector is the set of moves for all

0001 function[Collisions,Overlappings,Pos] =  EvalChainFunctional(vector)
0002 % Given a chain of molecules, calculates the numer of Collisions with
0003 % neighboring same sign molecules, and the number of Overlappings molecules.
0004 % HPInitConf is the configuration of the Chain of molecules
0005 % vector is the set of moves for all
0006 
0007 global HPInitConf;
0008 sizeChain = size(vector,2);
0009 
0010 Collisions = 0;
0011 Overlappings = 0;
0012 
0013 
0014 Pos = zeros(sizeChain,2);
0015 
0016 Pos(1,1) = 0;  %Position for the initial molecule
0017 Pos(1,2) = 0;
0018  
0019 Pos(2,1) = 1;  %Position for the second molecule
0020 Pos(2,2) = 0;
0021 
0022  for i=3:sizeChain
0023 
0024  if(Pos(i-1,2)==Pos(i-2,2))
0025   if (vector(i)==0)            %UP MOVE
0026    Pos(i,1) = Pos(i-1,1);  
0027    Pos(i,2) = Pos(i-1,2) + (Pos(i-1,1)-Pos(i-2,1));
0028   elseif (vector(i)==1)        %FORWARD MOVE
0029    Pos(i,1) = Pos(i-1,1) + (Pos(i-1,1)-Pos(i-2,1));  
0030    Pos(i,2) = Pos(i-1,2);
0031   else                         %DOWN MOVE
0032    Pos(i,1) = Pos(i-1,1);  
0033    Pos(i,2) = Pos(i-1,2) - (Pos(i-1,1)-Pos(i-2,1));
0034   end
0035   end
0036 if (Pos(i-1,1)==Pos(i-2,1))
0037   if (vector(i)==0)            %UP MOVE
0038     Pos(i,2) = Pos(i-1,2);  
0039     Pos(i,1) = Pos(i-1,1) -  (Pos(i-1,2)-Pos(i-2,2));  
0040   elseif (vector(i)==1)        %FORWARD MOVE
0041     Pos(i,2) = Pos(i-1,2) +  (Pos(i-1,2)-Pos(i-2,2));  
0042     Pos(i,1) = Pos(i-1,1);
0043   else                         %DOWN MOVE
0044     Pos(i,2) = Pos(i-1,2);  
0045     Pos(i,1) = Pos(i-1,1) + (Pos(i-1,2)-Pos(i-2,2));
0046   end
0047  end
0048 
0049    for j=1:i-2,   % Check for Overlappings and Collissions in all the    molecules except the previous one
0050     if(Pos(i,1)==Pos(j,1) & Pos(i,2)==Pos(j,2))
0051       Overlappings = Overlappings + 1;
0052     elseif (HPInitConf(i)==0  & HPInitConf(j)==0) 
0053      if (Pos(i,1)==Pos(j,1) & Pos(i,2)==Pos(j,2)-1)
0054         Collisions =   Collisions + 2;
0055      end
0056      if (Pos(i,1)==Pos(j,1)+1 & Pos(i,2)==Pos(j,2))
0057         Collisions =   Collisions + 2;
0058      end
0059      if (Pos(i,1)==Pos(j,1) & Pos(i,2)==Pos(j,2)+1)
0060         Collisions =   Collisions + 2;
0061      end
0062      if (Pos(i,1)==Pos(j,1)-1 & Pos(i,2)==Pos(j,2))
0063         Collisions =   Collisions + 2;
0064      end
0065     elseif (HPInitConf(i)+HPInitConf(j)>0)    
0066      if (Pos(i,1)==Pos(j,1) & Pos(i,2)==Pos(j,2)-1)
0067         Collisions =   Collisions - 1;
0068      end
0069      if (Pos(i,1)==Pos(j,1)+1 & Pos(i,2)==Pos(j,2))
0070         Collisions =   Collisions - 1;
0071      end
0072      if (Pos(i,1)==Pos(j,1) & Pos(i,2)==Pos(j,2)+1)
0073         Collisions =   Collisions - 1;
0074      end
0075      if (Pos(i,1)==Pos(j,1)-1 & Pos(i,2)==Pos(j,2))
0076         Collisions =   Collisions - 1;
0077      end
0078     end 
0079  end 
0080 end 
0081 
0082 %HPInitConf =  [zeros(1,12),1,0,1,0,1,1,0,0,1,1,0,0,1,1,0,1,1,0,0,1,1,0,0,1,1,0,1,1,0,0,1,1,0,0,1,1,0,1,0,1,zeros(1,12)];
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