%
% theory_settings.txt 
% Loaded automatically when running HCA_theory.m
%
% TODO: check which ones are necessary and comment everything
%
promptfortheory = 1;         % ask user for theories
promptforsavetheory = 1;
savetxts = 1;
resultsDir = 'theoryData';
fastas = 'fastas_2020-03-13_13_46_06_.txt';
% Theory generation
skipBarcodeGenSettings = 0;  % whether to skip barcode generatoin settings   
skipChangeBpNmRatio = 0;

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

% parameters
[theoryGen]
precision=5;
meanBpExt_nm = 0.34;
pixelWidth_nm= 110;
psfSigmaWidth_nm = 300;
concN=6;
concY=0.02;
concDNA = 0.2;
isLinearTF = 1;
deltaCut = 3;
widthSigmasFromMean = 4;
yoyo1BindingConstant = 26; % yoyo binding constant
computeFreeConcentrations = 1;
computeBitmask = 0; % whether to compute bitmask
method = 'literature';      % method    
k = 2^16;                   % k has to be k=m*2^d. k should be longer than smallest experiment size
m = 2^14;                   % harcoded parameters for literature, can be changed here by the user
[model]
pattern = 'CB';
