CASPDIR=/projects/compbio/experiments/protein-predict/casp7
T0ID=T0283
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-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.under:	manyalignments.under
	cp ../template_files/getconstraints.under .
	perl -pi -e "s/T0ID/${T0ID}/g" getconstraints.under 
	perl -pi -e "s/MANY/manyalignments/g" getconstraints.under	 
	../programs/undertaker < getconstraints.under >& out
	cat out|grep Constraint|gawk -f ../scripts/normalize.awk > alignment_constraints.under
	cat out|grep RES2ATOM > res2cbatom.dat
	cp out makingconstraints.log
	rm -rf out

alignment_constraints-local.under:	manyalignments-local.under
	cp ../template_files/getconstraints.under .
	perl -pi -e "s/T0ID/${T0ID}/g" getconstraints.under
	perl -pi -e "s/MANY/manyalignments-local/g" getconstraints.under	 
	../programs/undertaker < getconstraints.under >& out
	cat out|grep Constraint|gawk -f ../scripts/normalize.awk > alignment_constraints-local.under
	cat out|grep RES2ATOM > res2cbatom-local.dat
	cp out makingconstraints-local.log
	rm -rf out

alignment_constraints-good.under:	manyalignments-good.under
	cp ../template_files/getconstraints.under .
	perl -pi -e "s/T0ID/${T0ID}/g" getconstraints.under
	perl -pi -e "s/MANY/manyalignments-good/g" getconstraints.under	 
	../programs/undertaker < getconstraints.under >& out
	cat out|grep Constraint|gawk -f ../scripts/normalize.awk > alignment_constraints-good.under
	cat out|grep RES2ATOM > res2cbatom-good.dat
	cp out makingconstraints-good.log
	rm -rf out

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	 
	../programs/undertaker < getconstraints.under >& out
	cat out|grep Constraint|gawk -f ../scripts/normalize.awk > alignment_constraints-good-all.under
	cat out|grep RES2ATOM > res2cbatom-good-all.dat
	cp out makingconstraints-good-all.log
	rm -rf out

fraction-local%.under:	alignment_constraints-local.under
	cat alignment_constraints-local.under|sort -g -k 7 -r|gawk -f ../scripts/bestfraction.awk -v F=$* > fraction-local$*.under

fraction-local%.costfcn:	fraction-local%.under
	cat fraction-local$*.under > constraint-fraction-local$*.costfcn	
	echo "SetCost constraints 1" >> constraint-fraction-local$*.costfcn
	cp constraint-fraction-local$*.costfcn ${CASPDIR}/${T0ID}

fraction-good-all%.under:	alignment_constraints-good-all.under
	cat alignment_constraints-good-all.under|sort -g -k 7 -r|gawk -f ../scripts/bestfraction.awk -v F=$* > fraction-good-all$*.under

fraction-good-all%.costfcn:	fraction-good-all%.under
	cat fraction-good-all$*.under > constraint-fraction-good-all$*.costfcn	
	echo "SetCost constraints 1" >> constraint-fraction-good-all$*.costfcn
	cp constraint-fraction-good-all$*.costfcn ${CASPDIR}/${T0ID}

fraction-good%.under:	alignment_constraints-good.under
	cat alignment_constraints-good.under|sort -g -k 7 -r|gawk -f ../scripts/bestfraction.awk -v F=$* > fraction-good$*.under

fraction-good%.costfcn:	fraction-good%.under
	cat fraction-good$*.under > constraint-fraction-good$*.costfcn	
	echo "SetCost constraints 1" >> constraint-fraction-good$*.costfcn
	cp constraint-fraction-good$*.costfcn ${CASPDIR}/${T0ID}


fraction%.under:	alignment_constraints.under
	cat alignment_constraints.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" >> constraint-fraction$*.costfcn
	cp constraint-fraction$*.costfcn ${CASPDIR}/${T0ID}


length_fraction%.under:	alignment_constraints.under
	cat makingconstraints.log | grep "Making conformation" | gawk '{print "SIZE ", ($$11-$$9)+1}' > temp
	cat alignment_constraints.under|sort -g -k 7 -r >> temp
	cat temp|gawk -f ../scripts/bestlengthfraction.awk -v F=$* > length_fraction$*.under
	rm temp

length_fraction%.costfcn:	length_fraction%.under
	cat length_fraction$*.under > constraint-length_fraction$*.costfcn	
	echo "SetCost constraints 1" >> 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}$*
	cat optimize-${H}$*/${T0ID}.t06.CB8-sep9.rdb|gawk -f ${CASPDIR}/constraints_v2/scripts/cleanprobabilities.awk > optimize-${H}$*/probabilities.dat
	cp res2cbatom.dat optimize-${H}$*
	cp alignment_constraints-local.under optimize-${H}$*

optimized90-%.under:	alignment_constraints-local.under init_opt90%
	cd optimize-${H}90$*;./main probabilities.dat res2cbatom.dat alignment_constraints-local.under 0.90 $*

optimized90-%.costfcn:	optimized90-%.under
	cat optimize-${H}90$*/optimized > constraint-optimized90-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-optimized90-$*.costfcn
	cp constraint-optimized90-$*.costfcn ${CASPDIR}/${T0ID}
	cat optimize-${H}90$*/topweight > constraint-tw90-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-tw90-$*.costfcn
	cp constraint-tw90-$*.costfcn ${CASPDIR}/${T0ID}

optimized95-%.under:	alignment_constraints-local.under init_opt95%
	cd optimize-${H}95$*;./main probabilities.dat res2cbatom.dat alignment_constraints-local.under 0.95 $*

optimized95-%.costfcn:	optimized95-%.under
	cat optimize-${H}95$*/optimized > constraint-optimized95-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-optimized95-$*.costfcn
	cp constraint-optimized95-$*.costfcn ${CASPDIR}/${T0ID}
	cat optimize-${H}95$*/topweight > constraint-tw95-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-tw95-$*.costfcn
	cp constraint-tw95-$*.costfcn ${CASPDIR}/${T0ID}

optimized99-%.under:	alignment_constraints-local.under init_opt99%
	cd optimize-${H}99$*;./main probabilities.dat res2cbatom.dat alignment_constraints-local.under 0.99 $*

optimized99-%.costfcn:	optimized99-%.under
	cat optimize-${H}99$*/optimized > constraint-optimized99-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-optimized99-$*.costfcn
	cp constraint-optimized99-$*.costfcn ${CASPDIR}/${T0ID}
	cat optimize-${H}99$*/topweight > constraint-tw99-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-tw99-$*.costfcn
	cp constraint-tw99-$*.costfcn ${CASPDIR}/${T0ID}

optimized999-%.under:	alignment_constraints-local.under init_opt999%
	cd optimize-${H}999$*;./main probabilities.dat res2cbatom.dat alignment_constraints-local.under 0.999 $*

optimized999-%.costfcn:	optimized999-%.under
	cat optimize-${H}999$*/optimized > constraint-optimized999-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-optimized999-$*.costfcn
	cp constraint-optimized999-$*.costfcn ${CASPDIR}/${T0ID}
	cat optimize-${H}999$*/topweight > constraint-tw999-$*.costfcn	
	echo "SetCost constraints 1" >> constraint-tw999-$*.costfcn
	cp constraint-tw999-$*.costfcn ${CASPDIR}/${T0ID}

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/$$PDBNATIVE/g" evaluate.constraints.under 
	perl -pi -e "s/ALLCONSTRAINTS/alignment_constraints.under/g" evaluate.constraints.under
	../programs/undertaker < evaluate.constraints.under > out
	cat out | grep "(weighted)" > constraint.weights.costs.dat
	cp ../template_files/evaluate.constraints.under .
	perl -pi -e "s/ALLCONSTRAINTS/$*/g" evaluate.constraints.under
	PDBNATIVE=(`cat REAL_PDB`);perl -pi -e "s/T0ID/${T0ID}/g" evaluate.constraints.under;perl -pi -e "s/NATIVE/$$PDBNATIVE/g" evaluate.constraints.under 
	../programs/undertaker < evaluate.constraints.under > out
	cat out | grep "(weighted)" > bestconstraint.weights.costs.dat
	rm out

weight-plot-%:	alignment_constraints.under %.weights.costs.dat
	mkdir -p plots
	rm -rf temp
	mkdir temp
	cp -r ../plot/constraintweights/* temp
	cp constraint.weights.costs.dat temp
	cp bestconstraint.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
	../programs/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" >> 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-20
	cp meta.old meta.under
	make metahelper-30
	cp meta.old meta.under
	make metahelper-40
	cp meta.old meta.under
	make metahelper-50
	cp meta.old meta.under
	make metahelper-60
	cp meta.old meta.under
	make metahelper-70


combine-constraints:
	rm -rf temp
	cat constraints-meta.costfcn > temp
	cat alignment_constraints.under >> temp
	cat temp|gawk -f ../scripts/combineconstraints.awk|gawk -f ../scripts/normalize.awk > constraints-combined.under


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}
	cat optimize-${H}/${T0ID}.t06.CB8-sep9.rdb|gawk -f ${CASPDIR}/constraints_v2/scripts/cleanprobabilities.awk > optimize/probabilities.dat
	cp metares2cbatom.dat optimize-${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" >> constraint-meta-combined95-$*.costfcn
	cp constraint-meta-combined95-$*.costfcn ${CASPDIR}/${T0ID}