CASPDIR="/projects/compbio/experiments/protein-predict/casp7" # Find the alignments we want to use cp -r ../findalignments . cp $CASPDIR/T0318/T0318.best-scores.rdb findalignments/best cp $CASPDIR/T0318/T0318.t06-w0.5-scores.rdb findalignments/t06 ls -l $CASPDIR/T0318/ | gawk '{if (substr($1, 0, 1) == "d") print $9}' > findalignments/templates.dat cd findalignments ./go.sh cd .. # Extract the constraints from the alignments cp findalignments/manyalignments.under . ../programs/undertaker < getconstraints.under > out cat out|grep Constraint|gawk -f ../scripts/normalize.awk > constraints.under cat out|grep RES2ATOM > res2cbatom.dat cp out makingconstraints.log rm -rf out # Extract the best constraints (new method) rmdir -rf getbest mkdir getbest cp constraints.under getbest cp res2cbatom.dat getbest cp $CASPDIR/T0318/T0318.t06.CB8-sep9.rdb getbest cd getbest cat T0318.t06.CB8-sep9.rdb|gawk -f $CASPDIR/constraints/scripts/cleanprobabilities.awk > probabilities.dat ../../programs/main probabilities.dat res2cbatom.dat constraints.under 0.5 cp optimized temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-50opt.costfcn cp random temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-50ran.costfcn cp topweight temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-50tw.costfcn ../../programs/main probabilities.dat res2cbatom.dat constraints.under 0.8 cp optimized temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-80opt.costfcn cp random temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-80ran.costfcn cp topweight temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-80tw.costfcn ../../programs/main probabilities.dat res2cbatom.dat constraints.under 0.9 cp optimized temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-90opt.costfcn cp random temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-90ran.costfcn cp topweight temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-90tw.costfcn ../../programs/main probabilities.dat res2cbatom.dat constraints.under 0.95 cp optimized temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-95opt.costfcn cp random temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-95ran.costfcn cp topweight temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-95tw.costfcn ../../programs/main probabilities.dat res2cbatom.dat constraints.under 1.0 cp optimized temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-100opt.costfcn cp random temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-100ran.costfcn cp topweight temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-100tw.costfcn cp scaled temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-scaled.costfcn cd .. cat constraints.under|gawk '{if ($7>0) print $0}' > bestconstraints-all.under cp bestconstraints-all.under temp echo "SetCost constraints 1" >> temp cp temp $CASPDIR/T0318/constraint-all.costfcn