InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/
OutFilePrefix /cse/faculty/karplus/dna/predict-2nd/testing/aa/

ReadNeuralNet aa/networks/IDaaHr-5-15-7-15-9-15-20-aa-empty.net
NameNet dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

ReadParams params/16-dec-01-anneal
SetOverhang


# 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 dunbrack-in-scop-1.t2k-thin90-aa
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-in-scop-2.t2k-thin90-aa

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-in-scop-3.t2k-thin90-aa


# ReportNetQualityForTrainTo quality-reports/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.train
ReportNetQualityForCrossTrainTo quality-reports/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.train

TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.net


ReportNetQualityForTestTo quality-reports/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-20-aa-from-empty.test
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo