# 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/IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-empty.net
NameNet dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net

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

# 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-1795-2.t2k-thin90-dssp
time

ReadToSet cross-train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-1795-3.t2k-thin90-dssp
time

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-1795-1.t2k-thin90-dssp
time


#    ReportNetQualityForTrainTo quality-reports/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.train
ReportNetQualityForCrossTrainTo quality-reports/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.train

TrainNet 5
ReportNeuralNet networks/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.net
time

ReportNetQualityForTestTo quality-reports/dunbrack-1795-2t3c-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-from-empty.test
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time