%%% --- Biophysics of Macromolecules --- %%%
%%% --- LMU - Sommersemester 2020    --- %%%
%%% --- Prof. Lipfert                --- %%%
%%%
%%% Solutions to 
%%% Problem set 3, Problem 1
%%% Two-state protein folding

clc; clear;

%%% Define thermal energy
RT = 0.6; % Thermal energy in kcal/mol

%%% Load data
temp = load('FractionFolded_GuHCl_Tthermophilus_BLACK.txt');
GdnHCl_Tt = temp(:,1);
f_U_Tt = temp(:,2);
f_U_Tt = f_U_Tt/100; % Convert from % to fraction

temp = load('FractionFolded_GuHCl_yeast_BLACK.txt');
GdnHCl_yeast = temp(:,1);
f_U_yeast = temp(:,2);
f_U_yeast = f_U_yeast/100; % Convert from % to fraction


figure(1); clf; hold on; box on;
%%% Plot data for T. Thermophilus PGK
p1 = plot(GdnHCl_Tt, f_U_Tt, 'ro', 'linewidth', 2, 'markersize', 15, 'markerfacecolor', [0 0 0])

%%% Plot data for yeast PGK
p2 = plot(GdnHCl_yeast, f_U_yeast, 'bo', 'linewidth', 2, 'markersize', 15, 'markerfacecolor', [0 0 0])

set(gca,'LineWidth', 1,'FontSize', 25, 'FontWeight', 'bold', 'TickLength',[0.02 0.02])
ylabel('Fraction unfolded');
xlabel('[GdnHCl] (M)');
axis([-0.2 5.2 -0.1 1.1])

%%% Fit the data for T. Thermophilus PGK
[param residual exitflag] = fminsearch(@(param) norm(f_U_Tt - (1./(1+exp(-(param(1) + param(2).*GdnHCl_Tt)./RT))) ), [-5 1])
dG_0 = param(1);
m = param(2);
xfit = 0:0.01:5;
yfit = (1./(1+exp(-(param(1) + param(2).*xfit)./RT)));

%%% Co-plot the fit
plot(xfit, yfit, 'r-', 'linewidth', 2)
display(['Fitted DeltaG_0 = ' num2str(dG_0,3) ' kcal/mol;  m =' num2str(m,3) ...
    ' kcal/mol/M;  [GdnHCl]_1/2 = ' num2str(-dG_0/m,3) ' M' ])

%%% Fit the data for T. Thermophilus PGK
[param residual exitflag] = fminsearch(@(param) norm(f_U_yeast - (1./(1+exp(-(param(1) + param(2).*GdnHCl_yeast)./RT))) ), [-2 1])
dG_0 = param(1);
m = param(2);
%xfit = 0:0.01:3;
yfit = (1./(1+exp(-(param(1) + param(2).*xfit)./RT)));


%%% Co-plot the fit
plot(xfit, yfit, 'b-', 'linewidth', 2)
display(['Fitted DeltaG_0 = ' num2str(dG_0,3) ' kcal/mol;  m =' num2str(m,3) ...
    ' kcal/mol/M;  [GdnHCl]_1/2 = ' num2str(-dG_0/m,3) ' M' ])

%%% Add legend
legend([p1 p2], {'T. thermophilus', 'yeast'}, 'location', 'southeast')

%%% Export plot to png
print(figure(1),'-r300','-dpng', 'FractionUnfoldedFit.png')