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

ReadAlphabet /projects/compbio/lib/alphabet/two-spot-burial.alphabet

ReadNeuralNet   networks/dunbrack-in-scop-1+2-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-from-empty.net
NameNet                              t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-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-near-backbone-11
time

ReportNetQualityForCrossTrainTo quality-reports/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.train

TrainNet 5
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.net
time

ReportTrainByChain quality-reports/t04-2621-IDGaaH13-3-13-7-13-9-13-11-near-backbone-11-seeded.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time