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

ReadNeuralNet networks/dunbrack-395-IDaa13-5-7-9-9-5-8-9-ehl-seeded-trained.net
NameNet dunbrack-395-IDaa13-5-7-9-9-5-8-9-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 /projects/compbio/experiments/models.97/pdb/11/119l/
ReadTrain nostruct-align/119l.t99.a2m info/119l.dssp.2d

InFilePrefix /projects/compbio/experiments/models.97/pdb/15/153l/
ReadTrain nostruct-align/153l.t99.a2m info/153l.dssp.2d

InFilePrefix /projects/compbio/experiments/models.97/pdb/16/16pk/
ReadTrain nostruct-align/16pk.t99.a2m info/16pk.dssp.2d

ReportNetQualityForTrainTo quality-reports/test-equilibrate-t.quality
ReportNetQualityForCrossTrainTo quality-reports/test-equilibrate.quality

unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3
equilibrate

ReportNeuralNet networks/test-equilibrated.net

TrainNet 5

unfreeze 0
freeze 1
freeze 2
freeze 3
TrainNet 40

freeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 40

ReportNeuralNet networks/test-equilibrate-trained.net

ReportTrainByChain quality-reports/test-equilibrate-trained.by-chain

ReportQvsPhatTo quality-reports/test-equilibrate-trained.q-vs-phat

ReportUnitUsageTo quality-reports/test-equilibrate-trained.unit-usage

TestNet