# Sample options file for CGlearn.pl

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# Most important input options
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Training file: data/TRA_151Rfam_Tco_MFE_fm363.txt
# must contain predictions with the initial parameter set

Number of iterations {50|100|...}: 50
# the number of CG iterations

Bounds parameter B {1K|10K|0.8%|...}: 10K
# lower and upper bound on the parameters

Weight of the thermodynamic set lambda {0|1|0.9|0.995}: 0.995
# it is in [0,1]. It is 0 if no thermodynamic set is included

Test file: data/TES_S-Processed33_MFE_fm363.txt
# the file I test on at teh end of the iterations 
# must be in the same format as the training file 


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# Other options, I suggest you leave these unchanged 
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L norm used for the objective function {1|2}: 2
# default is 2

Normalisation criterion {n1|n2}: n2
# n1: 1/D, n2 = 1/N*1/numstr (in the ISMB paper it's n2)

Model is simplified {1|0}: 0
# 1 if we don't consider internal loops 1x1, 1x2 and 2x2 separately
# 0 if we consider the model described in the ISMB paper (363 parameters)

Initial parameter set {Tco|P1|P2}: Tco
# Tco = Turner99 constrained dangles, P1 = perturbed1, P2 = perturbed2

Do perturbation {0|1}: 1
# 0 means the algorithm stops if no more constraints can be generated
# 1 means the latest parameters are randomly perturbed by at most 1kcal/mol, 
#      and then the iterations continue.

Dangling ends are fixed to the initial values {0|1}: 0
# 1 means the 48 dangling end parameters are fixed to the initial values
# 0 means they are not fixed.

