%Team Blue Genes
%Jiayi Liang, Steven Hahn, William Schuppert, Runkun Jiang
%BioMOD competition 2011
%This file calculates the fluctuations of the synthetic DNA structures and
%outputs the diagonal of the Kirchhoff matrix (the fluctuations). 

function syntheticDNA
% Size of matrix/number of atoms 
m_size = 3066;
% Cutoff distance
cutoff = 13;
% Specific DNA data of coordinates, can be extracted from PDB files
fileName = 'FILENAME.xlsx'; 

fprintf('Loading...');

readXL = xlsread(fileName);
A = zeros(m_size, m_size);
G = zeros(m_size, 1);
for i = 1 : m_size
    compareRow = readXL(i, 5:7);
    
    %compareRow
    for j = 1 : m_size
        if i == j
            continue;
        end
        compareAltRow = readXL(j, 5:7);
        %compareAltRow
        compDist = vertcat(compareRow, compareAltRow);
        distance = pdist(compDist);
        %distance
        if distance < cutoff
            A(i, j) = -1;
        else
            A(i, j) = 0;
        end
    end
    rowSum = -1 * sum(A(i, :));
    A(i, i) = rowSum;
end
% Kirchhoff Matrix

% Node Number
for i = 1 : m_size
    G (i, 1) = readXL(i, 1);
end

B = pinv (A);
% Inverse Kirchhoff Matrix

diagonal = diag (B);
diagonal
% Diagonal elements output

plot (G, diagonal);
% Plot of flexibility data to node number

end