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

ReadNeuralNet networks/aa-1-10-1-aa-t2k-kidera.net
NameNet test-aa-1-10-1-aa-t2k-trained2.net

ReadParams params/2-feb-00-fast
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 test.guide-t2k-thin90

ReportNetQualityForCrossTrainTo quality-reports/test-aa-1-10-1-aa-t2k-trained2.quality

freeze 0
unfreeze 1

TrainNet 20
ReportNeuralNet networks/test-aa-1-10-1-aa-t2k-trained2.net

unfreeze 0
unfreeze 1

TrainNet 30
ReportNeuralNet networks/test-aa-1-10-1-aa-t2k-trained2.net

TrainNet 20
ReportNeuralNet networks/test-aa-1-10-1-aa-t2k-trained2.net


ReportQvsPhatTo quality-reports/test-aa-1-10-1-aa-t2k-trained2.q-vs-phat
ReportUnitUsageTo quality-reports/test-aa-1-10-1-aa-t2k-trained2.unit-usage
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo