SetSeed
ReadAlphabet /projects/compbio/lib/alphabet/burial.alphabet

InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/
OutFilePrefix /cse/faculty/karplus/dna/predict-2nd/testing/burial/

#start with best fold from cross-validation nets
ReadNeuralNet burial/networks/dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net
NameNet t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

ReadParams params/16-dec-01-anneal
SetOverhang

# THIS training uses the t2k-5631 id set, not holding out
#  anything for testing.


# 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 t2k-5631.t2k-thin90-CA-burial-10-7

ReportNetQualityForCrossTrainTo quality-reports/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.train

TrainNet 5
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net

CenterWeights
TrainNet 50
ReportNeuralNet networks/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.net


ReportTrainByChain quality-reports/t2k-5631-IDaaHr-5-15-7-15-9-15-13-CA-burial-10-7-from-empty.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo