# DO NOT EDIT THIS FILE.
# IT WAS CREATED BY VARIABLE SUBSTITUTION FROM A TEMPLATE FILE IN
# ../../run-scripts  (i.e. from the parent directory of all the alphabets directories)
# IF YOU WANT ANOTHER VERSION, RUN 'make trAB.scripts' or 'make tAcB.scripts'
# WITH THE DESIRED Make.main MACROS

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

ReadAlphabet /projects/compbio/lib/alphabet/ALPHALIBFILE
ReadBackgroundProbs /projects/compbio/lib/alphabet/dunbrack-in-scop.backgrounds

ReadNeuralNet       networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net

ReadParams /projects/compbio/experiments/protein-predict/predict-2nd/testing/params/PARAMFILE
SetOverhang
time

# Note: the following includes read the training set(s),
# and, in doing so, reset the InFilePrefix

ReadToSet train
InFilePrefix  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/
Include DATASET-THIRDSA.TXXALIGN-ALPHANAME
ReadToSet train
InFilePrefix  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/
Include DATASET-THIRDSB.TXXALIGN-ALPHANAME

time


ReportNetQualityForTrainTo quality-reports/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-mult250-from-empty.train

CenterWeights
Equilibrate
TrainNet 100
ReportNeuralNet networks/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.net
time