# 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-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-n_notor2-from-empty.net
NameNet                  t06-IDGaaH13-3-13-7-13-9-13-11-n_notor2-seeded.net

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

# THIS training uses the t06-2621 id set, not holding out
#  anything for testing.

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include t06.t06-n_notor2
time

ReportNetQualityForCrossTrainTo quality-reports/t06-IDGaaH13-3-13-7-13-9-13-11-n_notor2-seeded.train

TrainNet 50
ReportNeuralNet networks/t06-IDGaaH13-3-13-7-13-9-13-11-n_notor2-seeded.net
time

TrainNet 50
ReportNeuralNet networks/t06-IDGaaH13-3-13-7-13-9-13-11-n_notor2-seeded.net
time

ReportTrainByChain quality-reports/t06-IDGaaH13-3-13-7-13-9-13-11-n_notor2-seeded.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time