CASPDIR=/projects/compbio/experiments/protein-predict/casp7 T0ID=T0332 H=${HOST} manyalignments.under: cp -r ../findalignments . cp ${CASPDIR}/${T0ID}/${T0ID}.best-scores.rdb findalignments/best cp ${CASPDIR}/${T0ID}/${T0ID}.t06-w0.5-scores.rdb findalignments/t06 #NOTE: this gives all directories, but that is no problem for the following script that only looks for merged-a2m files ls -l ${CASPDIR}/${T0ID}/ | gawk '{if (substr($$1, 0, 1) == "d") print $$9}' > findalignments/templates.dat cd findalignments;./go.sh cp findalignments/manyalignments.under . manyalignments-good-all.under: manyalignments.under cp manyalignments.under manyalignments-good-all.under perl -pi -e "s/merged-a2m/merged-good-all-a2m/g" manyalignments-good-all.under alignment_constraints-good-all-%.under: manyalignments-good-all.under cp ../template_files/getconstraints.under . perl -pi -e "s/T0ID/${T0ID}/g" getconstraints.under perl -pi -e "s/MANY/manyalignments-good-all/g" getconstraints.under perl -pi -e "s/RADIUS/$*/g" getconstraints.under ../programs/undertaker < getconstraints.under >& out cat allconstraints.under|grep Constraint|gawk -f ../scripts/normalize.awk > alignment_constraints-good-all-$*.under cp out makingconstraints-good-all-$*.log rm -rf out cp alignment_constraints-good-all-$*.under current.under constraint-all-radius-%.costfcn: alignment_constraints-good-all-%.under cat alignment_constraints-good-all-$*.under > constraint-all-radius-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-all-radius-$*.costfcn cp constraint-all-radius-$*.costfcn ${CASPDIR}/${T0ID} #Using radius 8 fraction%.under: alignment_constraints-good-all-8.under cat alignment_constraints-good-all-8.under|sort -g -k 7 -r|gawk -f ../scripts/bestfraction.awk -v F=$* > fraction$*.under fraction%.costfcn: fraction%.under cat fraction$*.under > constraint-fraction$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-fraction$*.costfcn cp constraint-fraction$*.costfcn ${CASPDIR}/${T0ID} length_fraction%.under: alignment_constraints-good-all-8.under cat makingconstraints.log | grep "Making conformation" | gawk '{print "SIZE ", ($$11-$$9)+1}' > temp123 cat alignment_constraints-good-all-8.under|sort -g -k 7 -r >> temp123 cat temp123|gawk -f ../scripts/bestlengthfraction.awk -v F=$* > length_fraction$*.under rm temp123 length_fraction%.costfcn: length_fraction%.under cat length_fraction$*.under > constraint-length_fraction$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-length_fraction$*.costfcn cp constraint-length_fraction$*.costfcn ${CASPDIR}/${T0ID} init_opt: rm -rf optimize-${H} mkdir optimize-${H} cp ../programs/optimize optimize-${H} cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb optimize-${H} cp optimize-${H}/${T0ID}.t06.CB8-sep9.rdb optimize-${H}/probabilities.dat cat current.under|gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > optimize-${H}/current.under optimized.under: init_opt cd optimize-${H};./optimize probabilities.dat current.under 1 copycostfcn8: cat optimize-${H}/optimized > ${CASPDIR}/${T0ID}/align.constraints cat optimize-${H}/optimized_bonus > ${CASPDIR}/${T0ID}/align_bonus.constraints cat optimize-${H}/rejected > ${CASPDIR}/${T0ID}/rejected.constraints cat optimize-${H}/rejected_bonus > ${CASPDIR}/${T0ID}/rejected_bonus.constraints cat optimize-${H}/nonc > ${CASPDIR}/${T0ID}/non_contacts.constraints cat optimize-${H}/nonc_bonus > ${CASPDIR}/${T0ID}/non_contacts_bonus.constraints cat optimize-${H}/all > align_all.costfcn echo "SetCost align_constraints 1 rejected_constraints 1 non_contacts 1 backbone_only 0" >> align_all.costfcn cat align_all.costfcn|gawk -f ../scripts/adjust_weights.awk > ${CASPDIR}/${T0ID}/align_combined.costfcn rm -rf optimize-${H} copytocurrent%: cp alignment_constraints-good-all-$*.under current.under optimized8.costfcn: alignment_constraints-good-all-8.under copytocurrent8 optimized.under copycostfcn8 echo "done" REAL_PDB: cat ${CASPDIR}/${T0ID}/Makefile | grep REAL_PDB | gawk '{m = match($$0,"="); print substr($$0, m+1)}' > REAL_PDB %.weights.costs.dat: REAL_PDB cp ../template_files/evaluate.constraints.under . PDBNATIVE=(`cat REAL_PDB`);perl -pi -e "s/T0ID/${T0ID}/g" evaluate.constraints.under;perl -pi -e "s/NATIVE/$$PDBNATIVE/g" evaluate.constraints.under perl -pi -e "s/ALLCONSTRAINTS/$*/g" evaluate.constraints.under ../programs/undertaker < evaluate.constraints.under > out cat out | grep "(weighted)" > constraint.weights.costs.dat cp ../template_files/evaluate.constraints.under . rm out weight-plot-%: %.weights.costs.dat mkdir -p plots rm -rf temp mkdir temp cp -r ../plot/constraintweights/* temp cp constraint.weights.costs.dat temp echo ${T0ID}" "$* > temp/plottitle cd temp;./plot.sh;cp weightdist.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots/weightdist-$*.pdf server-plot-%: REAL_PDB mkdir -p plots rm -rf temp mkdir temp echo "InfilePrefix ${CASPDIR}/${T0ID}/decoys/" > servers.no-scwrl.under cat ${CASPDIR}/${T0ID}/decoys/read-pdb+servers.under|grep -i -v scwrl >> servers.no-scwrl.under cp ../template_files/evaluate.constraints.servers.under . perl -pi -e "s/T0ID/${T0ID}/g" evaluate.constraints.servers.under PDBNATIVE=(`cat REAL_PDB`);perl -pi -e "s/NATIVE/$$PDBNATIVE/g" evaluate.constraints.servers.under perl -pi -e "s/ALLCONSTRAINTS/$*/g" evaluate.constraints.servers.under rm -rf decoys mkdir decoys cp ${CASPDIR}/${T0ID}/$* . /projects/compbio/programs/undertaker/undertaker < evaluate.constraints.servers.under cp -r ../plot/server.decoys/* temp cp decoys/evaluate.constraints.rdb temp echo ${T0ID}" "$* > temp/plottitle cd temp;./plot.sh;cp servers.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots;cp histogram.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots;cp bestservers.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots