main_demo4.m

% Init

	clear;
	addpath('./model');
	addpath('./funcs');
	addpath('./funcs2');

	init_font;


%
	pm = [-0.12, 1];
	targs_plot  = {'DA','DA_D2R', ...
		'Gi_GTP','Gi_GDP','AC1_Gi_GDP','AC1_Gi_GTP','Gi_Gbc', 'Gbc', 'ACprimed'};
	yranges  = {pm*1.4, pm*0.02,  ...
		 pm*0.5, pm*0.5, pm*0.12,  pm*0.12, pm*15, pm*15, pm};

	targs = {{}};
	colors  = {[1 1 1]*0 };
	linew   = {2};
	mults   = {1};
%
	flag_competitive 		= 0;
	flag_Gi_sequestrated_AC = 1;
	flag_optoDA 			= 1; % 0 or 1;
	flag_duration 			= 1;
	stop_time  = 6;
	Toffset_DA = 3;

%%%
	stop_time  = 30;
	Toffset_DA = 10;
%%%

	[model, species, params, container] = ...
	msn_setup(flag_competitive, flag_Gi_sequestrated_AC, flag_optoDA, flag_duration, stop_time, Toffset_DA);
	trange   = [-1,3];
	ylegend  = '(uM)';



%% 5/25 AC1 

%%%%%%
%{
	targ = 'AC1';
	species{ targ,'Obj'}.InitialAmount = 9; % 0.9*8;
	targ = 'RGS';
	species{ targ,'Obj'}.InitialAmount = 0.9/50 * 32 *0.2;
	targ = 'D2R';
	species{ targ,'Obj'}.InitialAmount = 0.18 * 16 *4;
%}
%%%%%%


% Prep. figures

	a = {};
	fig     = figure;
	for i = 1:numel(targs_plot);
		a{i} = plot_prep(fig, trange, targs_plot{i}, 'Time (s)', ylegend, i);
		ylim(yranges{i});
		hold on;
		plot(a{i}, trange, [0 0], 'k:');
	end
	% yticks(a{1},[0 0.5]);

% Run & Plot
%{
	targ = 'Golf';
	init_conc = species{ targ,'Obj'}.InitialAmount;
	fprintf('%s, init conc: %g\n', targ, init_conc);
	species{ targ,'Obj'}.InitialAmount = init_conc * 10;
%}
	for j = 1:numel(targs);
		sd = run_sbiosimulate(model, species, targs{j}, mults{j})
		for i = 1:numel(targs_plot);
			[T, DATA] = obtain_profile(targs_plot{i}, sd, Toffset_DA);
			% ymax = max(DATA);
			% yr   = [-0.1*ymax, 1.1*ymax];
			% ylim(yr);
			yr = yranges{i};
			plot(a{i}, T, DATA, '-', 'LineWidth', linew{j}, 'Color', colors{j});
			plot(a{i}, [0 0], [yr(2), yr(2)*0.8 - yr(1)*0.2], 'r-','LineWidth',1);
			% plot(a{i}, [0 0], [yr(2), yr(2)*0.8], 'r-','LineWidth',1);
		end
	end

%

function sd = run_sbiosimulate(model, species, targ, mult)
	reservs = change_conc(targ, species, mult);
	sd = sbiosimulate(model);
	restore_conc(targ, species, reservs);
end


function reservs = change_conc(targ, species, mult)
	reservs = {};
	for k = 1: numel(targ)
		reservs{k} = species{targ{k},'Obj'}.InitialAmount;
		species{targ{k},'Obj'}.InitialAmount = reservs{k} * mult(k);
	end
end


function restore_conc(targ, species, reservs)
	for k = 1: numel(targ)
		species{targ{k},'Obj'}.InitialAmount = reservs{k};
	end
end


function ax = plot_prep(fig, xx, titl, xtitle, ytitle, i)
	ii = i - 1;
	col = floor(ii / 3);
	row = mod(ii, 3);
	ax = axes(fig, 'Position',[(0.08+col*0.3), (0.75 - row*0.33),  0.15*1.5,  0.2]); %%

	ax.ActivePositionProperty = 'Position';

	title(titl,'interpreter','none');
	box off;
	set(ax,'TickDir','out');
	hold on;
	xlabel( xtitle, 'Interpreter', 'none');
	ylabel( ytitle );
	xlim(xx);
end