# Find the alignments we want to use rm -rf ../findalignments/best rm -rf ../findalignments/t06 rm -rf ../findalignments/templates.dat cp /projects/compbio/experiments/protein-predict/casp7/T0289/T0289.best-scores.rdb ../findalignments/best cp /projects/compbio/experiments/protein-predict/casp7/T0289/T0289.t06-w0.5-scores.rdb ../findalignments/t06 ls -l /projects/compbio/experiments/protein-predict/casp7/T0289/ | gawk '{if (substr($1, 0, 1) == "d") print $9}' > ../findalignments/templates.dat cd ../findalignments ./go.sh cd ../T0289 # Extract the constraints from the alignments rm -rf out rm -rf constraints.under cp ../findalignments/manyalignments.under . ~palu/karplus/undertaker/undertaker < getconstraints.under > out cat out|grep Constraint|gawk -f ../scripts/normalize.awk > constraints.under cat out|grep RES2ATOM > res2cbatom.dat rm -rf out # Extract the best constraints (new method) rmdir -rf getbest mkdir getbest cp constraints.under getbest cp res2cbatom.dat getbest cp /projects/compbio/experiments/protein-predict/casp7/T0289/T0289.t06.CB8-sep9.rdb getbest cd getbest cat T0289.t06.CB8-sep9.rdb|gawk -f ~palu/test/scripts/cleanprobabilities.awk > probabilities.dat ~palu/predict/src/main probabilities.dat res2cbatom.dat constraints.under bestconstraints.under 0 cp bestconstraints.under temp echo "SetCost constraints 1" >> temp cp temp /projects/compbio/experiments/protein-predict/casp7/T0289/constraint.costfcn cp bestconstraints.under .. cd .. #cat constraints.under|gawk '{if ($7>0) print $0}' > bestconstraints.under #cp bestconstraints.under temp #echo "SetCost constraints 1" >> temp #cp temp /projects/compbio/experiments/protein-predict/casp7/T0289/constraint.costfcn # Evaluate the constraints by comparing with the real structure rm -rf constraint.weights.costs.dat ~palu/karplus/undertaker/undertaker < evaluate.constraints.under > out cat out | grep "(weighted)" > constraint.weights.costs.dat rm out rm -rf bestconstraint.weights.costs.dat ~palu/karplus/undertaker/undertaker < evaluate.bestconstraints.under > out cat out | grep "(weighted)" > bestconstraint.weights.costs.dat rm out # compute errors #rm -rf temp #mkdir temp #cp constraint.weights.costs.dat temp #cd temp #cat constraint.weights.costs.dat | gawk -f ../../scripts/extract.awk > constraints.dat #rm -rf ../../plot/error-plot/errors.dat #cat constraints.dat | sort -n -k 3 |gawk -f ../../scripts/calc-error.awk >> ../../plot/error-plot/errors.dat #cp ../plottitle ../../plot/error-plot/ #cd ../../plot/error-plot/ #./plot.sh #mkdir ../../T0289/plots #cp errorplot.pdf ../../T0289/plots #cat errors.dat|gawk 'BEGIN{best=100000;}{l[a]=$1; if ($4 < best) {bestindex=a; best=$4;} a++; }END{print l[bestindex]}' > bestfraction #cp bestfraction ../../T0289 #cd ../.. # plot mkdir plots rm -rf ../plot/constraintweights/weightdist.pdf cp constraint.weights.costs.dat ../plot/constraintweights cp bestconstraint.weights.costs.dat ../plot/constraintweights cp bestconstraints.under ../plot/constraintweights cp plottitle ../plot/constraintweights cd ../plot/constraintweights ./plot.sh cp weightdist.pdf ../../T0289/plots cd ../../T0289 rm -rf ../plot/locationplot/plot.pdf rm -rf plots/locationplot.pdf rm -rf plots/locationplot-diff.pdf rm -rf ../plot/locationplots/bestconstraints.under cp constraint.weights.costs.dat ../plot/locationplots cp bestconstraints.under ../plot/locationplots cp plottitle ../plot/locationplots cd ../plot/locationplots ./plot.sh cp plot.pdf ../../T0289/plots/locationplot.pdf cp plot-diff.pdf ../../T0289/plots/locationplot-diff.pdf cd ../../T0289 # test against servers echo "InfilePrefix /projects/compbio/experiments/protein-predict/casp7/T0289/decoys/" > servers.no-scwrl.under cat /projects/compbio/experiments/protein-predict/casp7/T0289/decoys/read-pdb+servers.under|grep -i -v scwrl >> servers.no-scwrl.under ~palu/karplus/undertaker/undertaker < evaluate.constraints.servers.under rm -rf ../plot/server.decoys/servers.pdf rm -rf plots/servers.pdf cp decoys/evaluate.constraints.rdb ../plot/server.decoys cp plottitle ../plot/server.decoys cd ../plot/server.decoys ./plot.sh cp servers.pdf ../../T0289/plots cp bestservers.pdf ../../T0289/plots cp histogram.pdf ../../T0289/plots cd ../../