# DO NOT EDIT THIS FILE.
# IT WAS CREATED BY VARIABLE SUBSTITUTION FROM A TEMPLATE FILE IN
# ../../run-scripts  (i.e. from the parent directory of all the alphabets directories)
# IF YOU WANT ANOTHER VERSION, RUN 'make trAB-mult50.scripts' 
# WITH THE DESIRED Make.main MACROS

# This script must be run from the directory which has the
# subdirectories: networks,quality-reports
InFilePrefix
OutFilePrefix

SetSeed		# Start from a random starting point.
		# Set the seed to a specific value if you need
		# deterministic behavior for debugging.

ReadAlphabet /projects/compbio/lib/alphabet/featurecenter.alphabet
ReadBackgroundProbs /projects/compbio/lib/alphabet/dunbrack-in-scop.backgrounds

ReadNeuralNet       ../networks/Gpb-5-20-5-20-5-aa-empty.net
NameNet dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-from-empty.net

ReadParams /projects/compbio/experiments/protein-predict/predict-2nd/testing/params/7-jul-05.params
SetOverhang
time

# Note: the following includes read the training set(s),
# and, in doing so, reset the InFilePrefix

ReadToSet train
InFilePrefix  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/
Include dunbrack-30pc-1763-THIRDSA.pb-aa
ReadToSet train
InFilePrefix  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/
Include dunbrack-30pc-1763-THIRDSB.pb-aa
time


ReportNetQualityForTrainTo quality-reports/dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-mult50-from-empty.train

TrainNet 5
ReportNeuralNet networks/dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-mult50-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-mult50-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-mult50-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-mult50-from-empty.net

CenterWeights
Equilibrate
TrainNet 30
ReportNeuralNet networks/dunbrack-30pc-1763-pb-Gpb-5-20-5-20-5-THIRDSNAME-aa-mult50-from-empty.net

time