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

ReadAlphabet /projects/compbio/lib/alphabet/bystroff.alphabet

ReadNeuralNet       networks/IDaaHr-5-15-7-15-9-15-13-bys-empty.net
NameNet dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

ReadParams /cse/faculty/karplus/dna/predict-2nd/testing/params/16-dec-01-anneal
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 dunbrack-in-scop-1.t2k-thin90-bys
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-in-scop-3.t2k-thin90-bys

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-in-scop-2.t2k-thin90-bys


# ReportNetQualityForTrainTo    quality-reports/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.train
ReportNetQualityForCrossTrainTo quality-reports/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.train

TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.net


ReportNetQualityForTestTo quality-reports/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-bys-from-empty.test
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo