%
% theory_settings.txt 
% Loaded automatically when running HCA_theory.m
%
% TODO: check which ones are necessary and comment everything
%
promptfortheory = 0;         % ask user for theories
promptforsavetheory = 0;
savetxts = 1;
resultsDir = 'theoryData';
fastas = 'theories_parallel.txt';
% Theory generation
skipBarcodeGenSettings = 1;  % whether to skip barcode generatoin settings   
skipChangeBpNmRatio = 0;

% lambda folder
[lambda]
fold =''
name = 'sequence.fasta';

% parameters
[theoryGen]
precision = 5;  %default is 5;
meanBpExt_nm = 0.3;
pixelWidth_nm= 130;
psfSigmaWidth_nm = 300;
concN=6;
concY=0.02;
concDNA = 0.2;
isLinearTF = 1;
deltaCut = 3;
widthSigmasFromMean = 4;
yoyo1BindingConstant = 26; % yoyo binding constant
computeFreeConcentrations = 1;
method = 'literature';      % method    
k = 2^15;                   % k has to be k=m*2^d. k should be longer than smallest experiment size
m = 2^11;                   % harcoded parameters for literature, can be changed here by the user

