# 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.scripts' or 'make tAcB.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/ALPHALIBFILE
ReadBackgroundProbs /projects/compbio/lib/alphabet/dunbrack-in-scop.backgrounds

ReadNeuralNet       networks/ARCHITECTURE-ALPHANAME-empty.net
NameNet DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net

ReadParams /cse/faculty/karplus/dna/predict-2nd/testing/params/PARAMFILE
SetOverhang
time

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

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include DATASET-THIRDSA.TXXALIGN-ALPHANAME
time

ReadToSet TRAINORCROSS
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include DATASET-THIRDSB.TXXALIGN-ALPHANAME
time

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include DATASET-THIRDSC.TXXALIGN-ALPHANAME
time


#    ReportNetQualityForTrainTo quality-reports/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.train
ReportNetQualityForCrossTrainTo quality-reports/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.train

TrainNet 5
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

ReportNetQualityForTestTo quality-reports/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.120.test
TestNet

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

ReportNetQualityForTestTo quality-reports/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.220.test
TestNet

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time

ReportNetQualityForTestTo quality-reports/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.test
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time