CASPDIR=/projects/compbio/experiments/protein-predict/casp7 T0ID=T0360 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 alignconstraints_v3: manyalignments-good-all.under cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb probabilities.dat cp ../template_files/getconstraints.under . perl -pi -e "s/T0ID/${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 cp out makingconstraints.log cp align.constraints_v3 ${CASPDIR}/${T0ID}/align.constraints_v3 cp align_bonus.constraints_v3 ${CASPDIR}/${T0ID}/align_bonus.constraints_v3 cp all.constraints_v3 ${CASPDIR}/${T0ID}/all.constraints_v3 cp non_contacts.constraints_v3 ${CASPDIR}/${T0ID}/non_contacts.constraints_v3 cp non_contacts_bonus.constraints_v3 ${CASPDIR}/${T0ID}/non_contacts_bonus.constraints_v3 cp rejected.constraints_v3 ${CASPDIR}/${T0ID}/rejected.constraints_v3 cp rejected_bonus.constraints_v3 ${CASPDIR}/${T0ID}/rejected_bonus.constraints_v3 rm -rf out servermodelslist: 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 all.constraints_meta: manyalignments-good-all.under cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb probabilities.dat cp ../template_files/getmetaconstraints.under . perl -pi -e "s/T0ID/${T0ID}/g" getmetaconstraints.under perl -pi -e "s/MANY/manyalignments-good-all/g" getmetaconstraints.under perl -pi -e "s/RADIUS/$*/g" getmetaconstraints.under ../programs/undertaker < getmetaconstraints.under >& out cp out makingmetaconstraints.log cp align.constraints_meta01 ${CASPDIR}/${T0ID}/ cp align_bonus.constraints_meta01 ${CASPDIR}/${T0ID}/ cp all.constraints_meta01 ${CASPDIR}/${T0ID}/ cp non_contacts.constraints_meta01 ${CASPDIR}/${T0ID}/ cp non_contacts_bonus.constraints_meta01 ${CASPDIR}/${T0ID}/ cp rejected.constraints_meta01 ${CASPDIR}/${T0ID}/ cp rejected_bonus.constraints_meta01 ${CASPDIR}/${T0ID}/ rm -rf out all.constraints_meta02-: manyalignments-good-all.under cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb probabilities.dat cp ../template_files/getmeta_weighted_constraints.under . perl -pi -e "s/T0ID/${T0ID}/g" getmeta_weighted_constraints.under perl -pi -e "s/MANY/manyalignments-good-all/g" getmeta_weighted_constraints.under perl -pi -e "s/RADIUS/$*/g" getmeta_weighted_constraints.under ../programs/undertaker < getmeta_weighted_constraints.under >& out cp out makingmeta_weighted_constraints.log cp align.constraints_meta02 ${CASPDIR}/${T0ID}/ cp align_bonus.constraints_meta02 ${CASPDIR}/${T0ID}/ cp all.constraints_meta02 ${CASPDIR}/${T0ID}/ cp non_contacts.constraints_meta02 ${CASPDIR}/${T0ID}/ cp non_contacts_bonus.constraints_meta02 ${CASPDIR}/${T0ID}/ cp rejected.constraints_meta02 ${CASPDIR}/${T0ID}/ cp rejected_bonus.constraints_meta02 ${CASPDIR}/${T0ID}/ rm -rf out all.constraints_meta03-: manyalignments-good-all.under cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb probabilities.dat cp ../template_files/getmeta_both_constraints.under . perl -pi -e "s/T0ID/${T0ID}/g" getmeta_both_constraints.under perl -pi -e "s/MANY/manyalignments-good-all/g" getmeta_both_constraints.under perl -pi -e "s/RADIUS/$*/g" getmeta_both_constraints.under ../programs/undertaker < getmeta_both_constraints.under >& out cp out makingmeta_both_constraints.log cp align.constraints_meta03 ${CASPDIR}/${T0ID}/ cp align_bonus.constraints_meta03 ${CASPDIR}/${T0ID}/ cp all.constraints_meta03 ${CASPDIR}/${T0ID}/ cp non_contacts.constraints_meta03 ${CASPDIR}/${T0ID}/ cp non_contacts_bonus.constraints_meta03 ${CASPDIR}/${T0ID}/ cp rejected.constraints_meta03 ${CASPDIR}/${T0ID}/ cp rejected_bonus.constraints_meta03 ${CASPDIR}/${T0ID}/ rm -rf out 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} optimized8.costfcn: alignment_constraints-good-all-8.under cp ${CASPDIR}/${T0ID}/${T0ID}.t06.CB8-sep9.rdb probabilities.dat cp ../template_files/optimize.under . perl -pi -e "s/T0ID/${T0ID}/g" optimize.under ../programs/undertaker < optimize.under > optimizing.log cat optimized |gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > ${CASPDIR}/${T0ID}/align.constraints_v2 cat optimized_bonus|gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > ${CASPDIR}/${T0ID}/align_bonus.constraints_v2 cat rejected |gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > ${CASPDIR}/${T0ID}/rejected.constraints_v2 cat rejected_bonus |gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > ${CASPDIR}/${T0ID}/rejected_bonus.constraints_v2 cat nonc |gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > ${CASPDIR}/${T0ID}/non_contacts.constraints_v2 cat nonc_bonus |gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > ${CASPDIR}/${T0ID}/non_contacts_bonus.constraints_v2 cat all |gawk '{T = $$0; gsub("\\([A-Za-z0-9]*\\)", "", T); print T}' > align_all.costfcn echo "SetCost align_constraints 1 rejected_constraints 1 non_contacts 1 backbone_only 0" >> align_all.costfcn cat align_all.costfcn|gawk -f ../scripts/adjust_weights.awk > ${CASPDIR}/${T0ID}/align_combined.costfcn_v2 REAL_PDB: cat ${CASPDIR}/${T0ID}/Makefile | grep REAL_PDB | gawk '{m = match($$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