# 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/IDGaaH13-5-15-7-15-9-15-13-bys-empty.net
NameNet dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net

ReadParams /cse/faculty/karplus/dna/predict-2nd/testing/params/16-dec-01-anneal
SetOverhang
# check time after read-net and read-params
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-in-scop-2.t2k-thin90-bys
# check time after read-train
time
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-in-scop-3.t2k-thin90-bys
# check time after read-train
time

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-in-scop-1.t2k-thin90-bys
# check time after read-test
time


# ReportNetQualityForTrainTo quality-reports/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.train
ReportNetQualityForCrossTrainTo quality-reports/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.train

TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 5
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 5
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 5
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 5
time

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 50
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 50
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 50
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 50
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 50
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.net
# check time after train 50
time


ReportNetQualityForTestTo quality-reports/dunbrack-in-scop-2+3-IDGaaH13-5-15-7-15-9-15-13-bys-from-empty.test
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
# check time after reports
time