SingleMoleculeAnalysisScripts/formatEBAcceptorQuench.m at main · NilsSomm/SingleMoleculeAnalysisScripts · GitHub

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function [ EB_format ] = formatEBAcceptorQuench(fn,savename)
%This script takes in a .mat traces file and formats it for .dat import to
%ebFRET such that the FRET values are the same as the normalized Acceptor
%values

file = load(fn);
disp('file name is')
disp(file)


traces= file.traces;
len = length(traces);

acptr= {traces(:).acptr};
donr= {traces(:).donr};


for i = 1:len;
    trace_length = length(traces(i).acptr);
    %twos = 2.* ones(length(x),1)
    %A(1:trace_length,1:1) = i;
    s(i).frame = i*ones(trace_length,1);

%     %try the normalization here
%     s(i).donr = (traces(i).donr)/(min(traces(i).donr))-0.95;
%     s(i).acptr= traces(i).acptr/(min(traces(i).acptr))-0.95;

    accMax = max(traces(i).acptr);
    accMin = min(traces(i).acptr);

    s(i).acptr= (traces(i).acptr - accMin)/(accMax - accMin);
    s(i).donr = 1 - s(i).acptr;


    %s(i).acptr = i;
end

%don't know a good way to do this
frame_all= {s(:).frame};
frame_all= transpose(frame_all);
frame_all = cell2mat(frame_all);

acptr_all= {s(:).acptr};
acptr_all= transpose(acptr_all);
acptr_all = cell2mat(acptr_all);

donr_all= {s(:).donr};
donr_all= transpose(donr_all);
donr_all = cell2mat(donr_all);


EB_format = [frame_all,donr_all,acptr_all];
assignin('base','EB_format',EB_format);
assignin('base','s',s);

%filename = [fn,'forEB.txt']
%save(filename, EB_format)
save(savename,'EB_format','-ascii');

%assignin('base','donr',donr);
%{
B = struct2table(s);
assignin('base','B',B);


C =table2array(B);
assignin('base','C',C);
%}
%}
%}
end