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

ReadNeuralNet networks/dunbrack-395-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded2.net
NameNet test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.net

ReadParams params/29-dec-99

# 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 test.t99-read-read

SetOverhang

ReportNeuralNet networks/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.net

# ReportTrainByChain quality-reports/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.by-chain
# TestNet


ReportNetQualityForTrainTo quality-reports/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-t.quality
ReportNetQualityForCrossTrainTo quality-reports/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded.quality

freeze 0
freeze 1
freeze 2
freeze 3
unfreeze 4

TrainNet 10
ReportNeuralNet networks/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.net

freeze 0
freeze 1
freeze 2
unfreeze 3
unfreeze 4

TrainNet 10
ReportNeuralNet networks/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.net

unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3
unfreeze 4

TrainNet 10
ReportNeuralNet networks/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.net

ReportTrainByChain quality-reports/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.by-chain

ReportQvsPhatTo quality-reports/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.q-vs-phat

ReportUnitUsageTo quality-reports/test-IDaa13-5-8-7-10-5-9-9-ehl3-3-ehl-seeded-trained.unit-usage

TestNet