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

ReadAlphabet /projects/compbio/lib/alphabet/hbonds.alphabet

ReadNeuralNet   networks/dunbrack-30pc-1763-t06-thin90-IDGaaH13-3-13-7-13-9-13-11-tr12-str2uc-from-empty.net
NameNet                  t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.net

ReadParams /projects/compbio/experiments/protein-predict/predict-2nd/testing/params/7-jul-05.params
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 t06.ALIGN-str2uc
time

ReportNetQualityForCrossTrainTo quality-reports/t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.train

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.net
time

TrainNet 50
ReportNeuralNet networks/t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.net
time

TrainNet 50
ReportNeuralNet networks/t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.net
time

TrainNet 50
ReportNeuralNet networks/t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.net
time

ReportTrainByChain quality-reports/t06-ALIGN-IDGaaH13-3-13-7-13-9-13-11-str2uc-seeded.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time