# This script must be run from the directory which has the
# subdirectories: networks,quality-reports
InFilePrefix
OutFilePrefix

#ReadAlphabet /projects/compbio/lib/alphabet/DSSP.alphabet

ReadNeuralNet   networks/dunbrack-1795-1+3-IDaaHr-5-15-7-15-9-15-13-ebghstl-from-empty.net
NameNet                           t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net

ReadParams /cse/faculty/karplus/dna/predict-2nd/testing/params/16-dec-01-anneal
SetOverhang
time

# THIS training uses the t04-2621 id set, not holding out
#  anything for testing.

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include t04-2621.t04-thin90-dssp
time

ReportNetQualityForCrossTrainTo quality-reports/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.train

TrainNet 5
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.net
time

ReportTrainByChain quality-reports/t04-2621-IDaaHr-5-15-7-15-9-15-13-ebghstl-dssp-seeded.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time