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

ReadNeuralNet networks/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded.net
NameNet dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2-trained.net

ReadParams params/21-nov-99
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-395.t99-read

ReportNetQualityForTrainTo quality-reports/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2-t.quality
ReportNetQualityForCrossTrainTo quality-reports/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2.quality


freeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 10
Equilibrate
TrainNet 20

unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3
TrainNet 100


freeze 0
freeze 1
unfreeze 2
freeze 3
TrainNet 30

freeze 0
freeze 1
freeze 2
unfreeze 3
TrainNet 30

unfreeze 0
freeze 1
freeze 2
freeze 3
TrainNet 50

freeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 40

unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3
TrainNet 100

unfreeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 50

ReportNeuralNet networks/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2-trained.net

ReportTrainByChain quality-reports/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2-trained.by-chain

ReportQvsPhatTo quality-reports/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2-trained.q-vs-phat

ReportUnitUsageTo quality-reports/dunbrack-395-IDaa13-5-8-5-10-5-9-7-ehl-seeded2-trained.unit-usage

TestNet