## Note: dunbrack-395 means that training is done on 395 high-resolution
## sequence files, leaving little for testing

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

ReadNeuralNet networks/dunbrack-395-IDaa12-9-6-11-9-3-8-7-ehl-seeded-trained.net
NameNet dunbrack-395-IDaa13-9-6-11-9-3-8-7-ehl-seeded3-trained.net

SetOverhang	// turn ON overhangs (max width)
SequenceWeight EntropyWeight 1.3 10	// change sequence weighting method


ReadParams params/9-nov-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 dunbrack-395.t99-read

ReportNetQualityForTrainTo quality-reports/dunbrack-395-IDaa13-9-6-11-9-3-8-7-ehl-seeded3-t.quality
ReportNetQualityForCrossTrainTo quality-reports/dunbrack-395-IDaa13-9-6-11-9-3-8-7-ehl-seeded3.quality


unfreeze 0
freeze 1
freeze 2
freeze 3
TrainNet 40

freeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 40

freeze 0
freeze 1
unfreeze 2
freeze 3
TrainNet 40

freeze 0
freeze 1
freeze 2
unfreeze 3
TrainNet 40

unfreeze 0
freeze 1
freeze 2
freeze 3
TrainNet 40

freeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 40

ReportNeuralNet networks/dunbrack-395-IDaa13-9-6-11-9-3-8-7-ehl-seeded3-trained.net