# Copyright Mirela Andronescu 2008
# Sample options file for CGlearn.pl
# Comments are lines starting with #

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# Most important input options
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Executable that creates the training and test data sets: tools/add_initial_predictions_simfold
# The name of the executable that can be used to obtain the training and test data sets
# none if no such executable is provided, in which case training set (and optionally test set)
#   have to be provided.

Training file: data/TRA_StructFull-max500-fold1.txt
# Other examples: data/TRA_151Rfam_Tco_MFE_fm363.txt
# must contain predictions with the initial parameter set

Training filename: TRA-SF1
# Other examples: TRA-151Rfam
# the "Training filename" is a friendly short name used for the new directory name only

Number of iterations {50|100|...}: 2
# the number of CG iterations

Bounds parameter B {1K|10K|0.8%|inf|...}: 1K
# lower and upper bound on the parameters
# if you don't want any bounds, type inf (for infinity)

Thermo file: data/all_thermodynamic_constraints_fm363_l2norm.lp
# The file with the thermodynamic constraints

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
# the recommended value is 0.995

Test file: data/TES_StructFull-max500-fold1.txt
# the file I test on at the end of the iterations
# must be in the same format as the training file
# can be none

Initial params file: data/turner_parameters_fm363_constrdangles.txt
# The file with the initial parameters

Fixparams file: data/params_fix_205_259.txt
# A file which contains fixed values for some parameters, or the word 
#   "variable" for the non-fixed parameters. 
# For example data/params_fix_fitted_thermo_l2norm.txt contains values
#   obtained by doing linear regression on the thermodynamic set only.
# Another example is when we want to fix the dangling end parameters
#   to the Turner99 values or to 0.
# type none if no parameters are fixed

Fixparams filename: FIX-205-259
# a friendly name used for the new directory name only

Additional constraints file: data/constraints_dangling_ends_fm363.txt
# A file which contains general constraints.
# For example, in the 363-parameters model, we want the 3' dangling ends
#   to be less than the 5' dangling ends.
# Specific bounds on the parameters can be given here too.
#   for example the dangling ends have to be negative
# Example of such file: data/constraints_dangling_ends_fm363.txt
# type none if no additional constraints are given

Additional constraints filename: CON-DL
# A friendly name used for the new directory name only

Executable that creates the structural constraints: tools/create_structural_constraints_simfold
# The name of the executable that creates the structural constraints

Executable that predicts and analyses results: tools/predict_and_analyse_results_simfold
# The name of the executable that predicts and analyses the results of the new parameters

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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)

Do perturbation {0|1}: 0
# 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.