CASPDIR=/projects/compbio/experiments/protein-predict/casp7 T0ID=XTARGET H=${HOST} .SECONDARY: alignment_constraints-good-all-6.under alignment_constraints-good-all-8.under alignment_constraints-good-all-9.under alignment_constraints-good-all-10.under alignment_constraints-good-all-12.under alignment_constraints-good-all-16.under alignment_constraints-good-all-23.under 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-local.under: manyalignments.under cp manyalignments.under manyalignments-local.under perl -pi -e "s/merged-a2m/merged-local-a2m/g" manyalignments-local.under manyalignments-good.under: manyalignments.under cp manyalignments.under manyalignments-good.under perl -pi -e "s/merged-a2m/merged-good-a2m/g" manyalignments-good.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 out|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/main 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}$*;./main probabilities.dat current.under $* copycostfcn6-%: cat optimize-${H}$*/optimized > constraint-optimized6-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized6-$*.costfcn cp constraint-optimized6-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus > constraint-optimized6_bonus-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized6_bonus-$*.costfcn cp constraint-optimized6_bonus-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized6_bonus_nonc-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized6_bonus_nonc-$*.costfcn cp constraint-optimized6_bonus_nonc-$*.costfcn ${CASPDIR}/${T0ID} rm -rf optimize-${H}$* copycostfcn8-%: cat optimize-${H}$*/optimized > constraint-optimized8-$*.costfcn echo "SetCost align_constraints 1 rejected_constraints 1 non_contacts 1 backbone_only 0" >> constraint-optimized8-$*.costfcn cat constraint-optimized8-$*.costfcn|gawk -f ../scripts/adjust_weights.awk > ${CASPDIR}/${T0ID}/constraint-optimized8-$*.costfcn cat optimize-${H}$*/optimized_bonus > constraint-optimized8_bonus-$*.costfcn echo "SetCost align_constraints 1 rejected_constraints 1 non_contacts 1 backbone_only 0" >> constraint-optimized8_bonus-$*.costfcn cat constraint-optimized8_bonus-$*.costfcn|gawk -f ../scripts/adjust_weights.awk > ${CASPDIR}/${T0ID}/constraint-optimized8_bonus-$*.costfcn cat optimize-${H}$*/optimized_nonc > constraint-optimized8_nonc-$*.costfcn echo "SetCost align_constraints 1 rejected_constraints 1 non_contacts 1 backbone_only 0" >> constraint-optimized8_nonc-$*.costfcn cat constraint-optimized8_nonc-$*.costfcn|gawk -f ../scripts/adjust_weights.awk > ${CASPDIR}/${T0ID}/constraint-optimized8_nonc-$*.costfcn cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized8_bonus_nonc-$*.costfcn echo "SetCost align_constraints 1 rejected_constraints 1 non_contacts 1 backbone_only 0" >> constraint-optimized8_bonus_nonc-$*.costfcn cat constraint-optimized8_bonus_nonc-$*.costfcn|gawk -f ../scripts/adjust_weights.awk > ${CASPDIR}/${T0ID}/constraint-optimized8_bonus_nonc-$*.costfcn rm -rf optimize-${H}$* copycostfcn9-%: cat optimize-${H}$*/optimized > constraint-optimized9-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized9-$*.costfcn cp constraint-optimized9-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus > constraint-optimized9_bonus-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized9_bonus-$*.costfcn cp constraint-optimized9_bonus-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized9_bonus_nonc-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized9_bonus_nonc-$*.costfcn cp constraint-optimized9_bonus_nonc-$*.costfcn ${CASPDIR}/${T0ID} rm -rf optimize-${H}$* copycostfcn10-%: cat optimize-${H}$*/optimized > constraint-optimized10-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized10-$*.costfcn cp constraint-optimized10-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus > constraint-optimized10_bonus-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized10_bonus-$*.costfcn cp constraint-optimized10_bonus-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized10_bonus_nonc-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized10_bonus_nonc-$*.costfcn cp constraint-optimized10_bonus_nonc-$*.costfcn ${CASPDIR}/${T0ID} rm -rf optimize-${H}$* copycostfcn12-%: cat optimize-${H}$*/optimized > constraint-optimized12-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized12-$*.costfcn cp constraint-optimized12-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus > constraint-optimized12_bonus-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized12_bonus-$*.costfcn cp constraint-optimized12_bonus-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized12_bonus_nonc-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized12_bonus_nonc-$*.costfcn cp constraint-optimized12_bonus_nonc-$*.costfcn ${CASPDIR}/${T0ID} rm -rf optimize-${H}$* copycostfcn16-%: cat optimize-${H}$*/optimized > constraint-optimized16-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized16-$*.costfcn cp constraint-optimized16-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus > constraint-optimized16_bonus-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized16_bonus-$*.costfcn cp constraint-optimized16_bonus-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized16_bonus_nonc-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized16_bonus_nonc-$*.costfcn cp constraint-optimized16_bonus_nonc-$*.costfcn ${CASPDIR}/${T0ID} rm -rf optimize-${H}$* copycostfcn23-%: cat optimize-${H}$*/optimized > constraint-optimized23-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized23-$*.costfcn cp constraint-optimized23-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus > constraint-optimized23_bonus-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized23_bonus-$*.costfcn cp constraint-optimized23_bonus-$*.costfcn ${CASPDIR}/${T0ID} cat optimize-${H}$*/optimized_bonus_nonc > constraint-optimized23_bonus_nonc-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-optimized23_bonus_nonc-$*.costfcn cp constraint-optimized23_bonus_nonc-$*.costfcn ${CASPDIR}/${T0ID} rm -rf optimize-${H}$* copytocurrent%: cp alignment_constraints-good-all-$*.under current.under copytocurrent_comb: cp constraint-combined.under current.under optimized6-%.costfcn: alignment_constraints-good-all-6.under copytocurrent6 optimized-%.under copycostfcn6-% echo "here" optimized8-%.costfcn: alignment_constraints-good-all-8.under copytocurrent8 optimized-%.under copycostfcn8-% echo "here" optimized8_comb-%.costfcn: constraint-combined.under copytocurrent_comb optimized-%.under copycostfcn8-% echo "here" optimized9-%.costfcn: alignment_constraints-good-all-9.under copytocurrent9 optimized-%.under copycostfcn9-% echo "here" optimized10-%.costfcn: alignment_constraints-good-all-10.under copytocurrent10 optimized-%.under copycostfcn10-% echo "here" optimized12-%.costfcn: alignment_constraints-good-all-12.under copytocurrent12 optimized-%.under copycostfcn12-% echo "here" optimized16-%.costfcn: alignment_constraints-good-all-16.under copytocurrent16 optimized-%.under copycostfcn16-% echo "here" optimized23-%.costfcn: alignment_constraints-good-all-23.under copytocurrent23 optimized-%.under copycostfcn23-% echo "here" 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/$$PDBNATIVE/g" evaluate.constraints.servers.under perl -pi -e "s/ALLCONSTRAINTS/$*/g" evaluate.constraints.servers.under rm -rf decoys mkdir decoys cp ${CASPDIR}/${T0ID}/$* . /projects/compbio/programs/undertaker/undertaker < evaluate.constraints.servers.under cp -r ../plot/server.decoys/* temp cp decoys/evaluate.constraints.rdb temp echo ${T0ID}" "$* > temp/plottitle cd temp;./plot.sh;cp servers.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots;cp histogram.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots;cp bestservers.pdf ${CASPDIR}/constraints_v2/${T0ID}/plots metahelper-%: perl -pi -e "s/ALPHA/$*/g" meta.under ../programs/undertaker < meta.under >& out cp out makingmetaconstraints.log cat makingmetaconstraints.log|grep -a Constraint|grep -v "#"|gawk -f ../scripts/normalize.awk > metaconstraint-$*.under cat makingmetaconstraints.log|grep RES2ATOM > metares2cbatom-$*.dat rm -rf out rm -rf temp cp metaconstraint-$*.under temp echo "SetCost constraints 1 backbone_only 0" >> temp cp temp constraint-meta-$*.costfcn cp temp ${CASPDIR}/${T0ID}/constraint-meta-$*.costfcn constraints-meta-%: echo "InFilePrefix ${CASPDIR}/${T0ID}/decoys/" > servers-clean.under cat ${CASPDIR}/${T0ID}/decoys/read-pdb+servers.under | grep -i -v scwrl | grep -v try | grep -v submitted >> servers-clean.under cp ../template_files/meta.under . perl -pi -e "s/T0ID/${T0ID}/g" meta.under perl -pi -e "s/USECONSTRAINTS/$*/g" meta.under cp meta.under meta.old make metahelper-0 cp meta.old meta.under make metahelper-10 cp meta.old meta.under make metahelper-15 cp meta.old meta.under make metahelper-20 cp meta.old meta.under make metahelper-25 cp meta.old meta.under make metahelper-30 combine-constraints: rm -rf temp3 rm -rf temp2 rm -rf temp1 cp ${CASPDIR}/${T0ID}/${T0ID}.647_47_75_01.rr.constraints temp1 BESTEVALUE=(`cat ../best_evalues.dat|grep ${T0ID}|gawk '{print $$2}'`);cat temp1|gawk -f ../scripts/normalize-E.awk -v E=$$BESTEVALUE > temp2 cat alignment_constraints-good-all-8.under >> temp2 cat temp2|gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}'> temp3 cat temp3|gawk -f ../scripts/combineconstraints.awk|gawk -f ../scripts/normalize.awk|sort -g -k 7 -r > constraint-combined.under constraint-combined.costfcn: combine-constraints cat constraint-combined.under > constraint-combined.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-combined.costfcn cp constraint-combined.costfcn ${CASPDIR}/${T0ID} meta-combined-optimized95-%.under: cd optimize-${H};./main probabilities.dat metares2cbatom.dat constraints-combined.under 0.95 $* meta-init_opt: rm -rf optimize-${H} mkdir optimize-${H} cp ../programs/main optimize-${H} cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb optimize-${H} cp optimize-${H}/${T0ID}.t06.CB8-sep9.rdb optimize/probabilities.dat cp metares2cbatom.dat optimize-${H} cp constraints-combined.under optimize-${H} meta-combined-optimized95-%.costfcn: meta-init_opt meta-combined-optimized95-%.under cat optimize-${H}/optimized > constraint-meta-combined95-$*.costfcn echo "SetCost constraints 1 backbone_only 0" >> constraint-meta-combined95-$*.costfcn cp constraint-meta-combined95-$*.costfcn ${CASPDIR}/${T0ID}