readalphabet /projects/compbio/lib/alphabet/alpha.alphabet
readalphabet /projects/compbio/lib/alphabet/bystroff.alphabet
readalphabet /projects/compbio/lib/alphabet/str.alphabet
readalphabet /projects/compbio/lib/alphabet/tco.alphabet

readalphabet /projects/compbio/lib/alphabet/burial.alphabet
readalphabet /projects/compbio/lib/alphabet/abs_sa.alphabet
readalphabet /projects/compbio/lib/alphabet/rel_sa.alphabet
readalphabet /projects/compbio/lib/alphabet/two-spot-burial.alphabet

readalphabet /projects/compbio/lib/alphabet/chi.alphabet

# readbackgroundprobs /projects/compbio/lib/alphabet/dunbrack-in-scop.backgrounds



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

ReadNeuralNet dssp/networks/t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net
# NameNet t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net

ReadParams params/16-dec-01-anneal
SetOverhang


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

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include t2k-11-apr-2002-dssp.t2k-thin90-dssp

ReportNetQualityForTestTo quality-reports/t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.test
ReportQvsPhatTo quality-reports/t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.q_vs_phat
ReportTestByChain quality-reports/t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.by-chain
ReportUnitUsageTo quality-reports/t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.unit-usage


# Include test2.t2k-thin90-dssp
# ReportNetQualityForTestTo quality-reports/test2-t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.test
# ReportQvsPhatTo quality-reports/test2-t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.q_vs_phat
# ReportTestByChain quality-reports/test2-t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.by-chain
# ReportUnitUsageTo quality-reports/test2-t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.unit-usage

TestNet

ReportTestByChain
ReportQvsPhatTo 
ReportUnitUsageTo