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

ReadAlphabet /projects/compbio/lib/alphabet/ALPHALIBFILE

ReadNeuralNet   networks/dunbrack-30pc-1763-TXXALIGN-ARCHITECTURE-TRAINSET-ALPHANAME-from-empty.net
NameNet                  DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.net

ReadParams /projects/compbio/experiments/protein-predict/predict-2nd/testing/params/PARAMFILE
SetOverhang
time

# THIS training uses the t06 id set, not holding out
#  anything for testing.

ReadToSet train
InFilePrefix  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/
Include DATASET.ALIGN-ALPHANAME
time

ReportNetQualityForCrossTrainTo quality-reports/DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.train

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.net
time

TrainNet 50
ReportNeuralNet networks/DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.net
time

TrainNet 50
ReportNeuralNet networks/DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.net
time

TrainNet 50
ReportNeuralNet networks/DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.net
time

ReportTrainByChain quality-reports/DATASET-ALIGN-ARCHITECTURE-ALPHANAME-seeded.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time