TARGET= t82

default: ${TARGET}.blast-all ${TARGET}.all  
# ${TARGET}.remote-all 

joints:
	-make -k PRED=1bol PRED2=1b joint
#	-make -k PRED=1aie PRED2=1a joint
#	-make -k PRED=1olgA PRED2=1o joint
#	-make -k PRED=2bbkL PRED2=2b joint
#	-make -k PRED=1eceA PRED2=1e joint
#	-make -k PRED=1bebA PRED2=1b joint
#	-make -k PRED=1neq PRED2=1n joint
#	# Try the known ribonucleases
#	-make -k PRED=1eriA PRED2=1e joint
#	-make -k PRED=1rgeA PRED2=1r joint
#	-make -k PRED=1rthA PRED2=1r joint
#	-make -k PRED=2rn2 PRED2=2r joint
#	-make -k PRED=3dni PRED2=3d joint
#	-make -k PRED=7rsa PRED2=7r joint
#	-make -k PRED=9rnt PRED2=9r joint

# Which target alignment to use in building joint models
A2M = t98_6.a2m.gz

TARGET-A2M = ${TARGET}.${A2M}

# directories
PCEM-SCRIPTS = /projects/compbio/experiments/models.97/scripts
MOTIF-SCRIPTS = /projects/compbio/experiments/motif-models/scripts
CASP3-SCRIPTS = /projects/compbio/experiments/casp3/scripts

PCEM-INDEXES = /projects/compbio/experiments/models.97/indexes
PCEM-PDB = /projects/compbio/experiments/models.97/pdb
LIB= /projects/compbio/lib

NEW-SAM = /projects/compbio/bin/alpha/new


# programs in non-standard places
PHYTREE = /projects/compbio/usr/karplus/src/phytree/phytree
DG = /projects/compbio/usr/karplus/src/phytree/dg
PREDICT-2ND-DIR = /projects/compbio/usr/karplus/predict-2nd
PREDICT-2ND = ${PREDICT-2ND-DIR}/predict-2nd

# libraries and data files
NR= /projects/compbio/data/nrp/nr
NRP= /projects/compbio/data/nrp/NRP_ALL.PDB
PDB= /projects/compbio/data/pdb/all-protein
MIXTURE = ${LIB}/recode2.20comp
TRANS-REG = ${LIB}/fssp-trained.regularizer
NEURAL-NET= ${CASP3-SCRIPTS}/../networks-used/fssp-12345-IDaa1-9-6-11-9-3-8-7-ehl-seeded6-trained.net



CASP3-2D-ID =1751-3146-3362

# change the following two lines (or redefine when calling make)
# to use a different chain as a template.
PRED=1xxx
PRED2=1x


# source directory and files for template
PRED-DIR = ${PCEM-PDB}/${PRED2}/${PRED}
PRED-SEQ = ${PRED-DIR}/info/${PRED}.dssp.seq
PRED-A2M = ${PRED-DIR}/nostruct-align/${PRED}.target98-pdb.a2m.gz 
PRED-FSSP-A2M = ${PRED-DIR}/struct-align/${PRED}.fssp.a2m.gz 
PRED-FSSPT98-A2M = ${PRED-DIR}/struct-align/${PRED}.fssp-t98.a2m.gz 
PRED-CONST-A2M = ${PRED-DIR}/struct-align/${PRED}.constr-t98-pdb.a2m.gz 
PRED-2D = ${PRED-DIR}/info/${PRED}.hssp.2d

# destination directory for alignments
PRED-DEST= ${PRED}

#destination file prefixes for joint alignments
PT = ${PRED-DEST}/${PRED}-${TARGET}
TP = ${PRED-DEST}/${TARGET}-${PRED}

joint: ${TP}-vit.pw.a2m.gz ${PT}-vit.pw.a2m.gz \
	${TP}-post.pw.a2m.gz ${PT}-post.pw.a2m.gz \
	${TP}-global.pw.a2m.gz 	${PT}-global.pw.a2m.gz \
	${PT}-fssp-global.pw.a2m.gz \
	${PT}-fsspt98-global.pw.a2m.gz \
	${PT}-const-global.pw.a2m.gz

#	${TP}-joint.pw.a2m.gz ${PT}-joint.pw.a2m.gz 
#	${TP}--0.7.pw.a2m.gz ${PT}--0.7.pw.a2m.gz \
#	${TP}--0.85.pw.a2m.gz ${PT}--0.85.pw.a2m.gz \


.PRECIOUS: \
%.gz %.t98.a2m.gz %.t98_4.a2m.gz .t98_5.a2m.gz .t98_6.a2m.gz \
	%.dist %-varh50-pdb.rdb %-t98.rdb %-fssp-t98.rdb \
	%.tree %_sorted.a2m.gz %_sorted.ids %.tree.ps \
	%.nrp-ids 




%.all:
	-make -k $*.${A2M}	\
		$*.${A2M:a2m.gz=2d} \
		$*.${A2M:.a2m.gz=-varh50-pdb.rdb} \
		$*-t98.rdb \
		$*-sum98.rdb \
		$*-fssp-vit.rdb \
		$*-t98-mixed.rdb \
		$*-t98-vit.rdb \
		$*.${A2M:a2m.gz=tree} 


%.blast-all:
	-make -k $*-blast.rdb $*-double-blast.rdb

%.remote-all:
	-make -k $*.remote_4.a2m.gz \
		$*.remote_4.2d \
		$*.remote_4-varh50-pdb.rdb \
		$*.remote_4.tree 

%.gz: %
	gzip -f $^

%.pa: %.a2m.gz
	prettyalign $^ -m5 -l120 -i -n > $@

# fimstrength for target98 (but not for joint models)
FIMSTR = 1.0

%.t98_4.a2m.gz %.t98_5.a2m.gz %.t98_6.a2m.gz: %.seq
	${PCEM-SCRIPTS}/target98-with-param \
		 -out $*.t98 \
		 -seed $^ \
		 -new_sam \
		 -iter 6 -all \
		 -thresholds -50,-40,-30,-22,-16,-14 \
		 -build varh50 \
		 -weight_dist \
		 -fimstrength ${FIMSTR}
	gzip -f $*.t98_*.a2m

	
%.remote_4.a2m.gz: %.seq
	${PCEM-SCRIPTS}/target98-with-param \
		 -out $*.remote \
		 -new_sam \
		 -seed $^ \
		 -iter 4 -all \
		 -thresholds -12,-10,-9,-8 \
		 -build varh50 \
		 -weight_dist \
		 -fimstrength ${FIMSTR}
	gzip -f $*.remote_*.a2m


%-t98.rdb: %.seq
	${PCEM-SCRIPTS}/score-lib \
		-chains ${PCEM-INDEXES}/target98.ids \
		-lib pdb -lib domains -a2m target98 \
		-build varh50 -db $^ \
		-NLLminusNULL -4 \
		-NLLreverse 1.0 \
		-viterbi 0 -sw_score 2 \
		-output $@

%-t98-vit.rdb: %.seq
	${PCEM-SCRIPTS}/score-lib \
		-chains ${PCEM-INDEXES}/target98.ids \
		-lib pdb -lib domains -a2m target98 \
		-build varh50 -db $^ \
		-NLLminusNULL -4 \
		-NLLreverse 1.0 \
		-viterbi 1 -sw_score 2 \
		-output $@

%-t98-mixed.rdb: %.seq
	${PCEM-SCRIPTS}/score-lib \
		-chains ${PCEM-INDEXES}/target98-mixed.ids \
		-lib pdb -lib domains -a2m target98-mixed \
		-build w0.5 -db $^ \
		-NLLminusNULL -4 \
		-NLLreverse 1.0 \
		-viterbi 0 -sw_score 2 \
		-output $@

%-fssp-vit.rdb: %.seq
	${PCEM-SCRIPTS}/score-lib \
		-chains ${PCEM-INDEXES}/fssp.ids \
		-lib pdb -lib domains -a2m fssp \
		-build varh50 -db $^ \
		-NLLminusNULL -4 \
		-NLLreverse 1.0 \
		-viterbi 1 -sw_score 2 \
		-output $@

%-fssp-t98.rdb: %.seq
	${PCEM-SCRIPTS}/score-lib \
		-chains ${PCEM-INDEXES}/fssp-t98.ids \
		-lib pdb -lib domains -a2m fssp-t98 \
		-build varh50 -db $^ \
		-NLLminusNULL -4 \
		-NLLreverse 1.0 \
		-viterbi 0 -sw_score 2 \
		-output $@

%-sum98.rdb:  %.${A2M:.a2m.gz=-varh50-pdb.rdb} %-t98.rdb
	${CASP3-SCRIPTS}/sum-both-ways $^ > $@

${PRED-DEST}:
	-mkdir ${PRED-DEST}
	-fixmode ${PRED-DEST}

${TP}-joint.pw.a2m.gz: ${TARGET-A2M} \
	${PRED-SEQ} ${PRED-A2M} 
	make ${PRED-DEST}
	${PCEM-SCRIPTS}/build-joint98 \
		-thresholds -9,-6,-2 \
		-seqA ${TARGET}.seq \
		-seqB ${PRED-SEQ} \
		-a2mA $< -a2mB ${PRED-A2M} \
		-mult ${TP}-joint.mult \
		-dist ${TP}-joint.dist \
		> ${TP}-joint.pw.a2m
	gzip -f ${TP}-joint.*

${PT}-joint.pw.a2m.gz: ${TARGET-A2M} \
	${PRED-SEQ} ${PRED-A2M} 
	make ${PRED-DEST}
	${PCEM-SCRIPTS}/build-joint98 \
		-useB \
		-thresholds -9,-6,-2 \
		-seqA ${TARGET}.seq \
		-seqB ${PRED-SEQ} \
		-a2mA $< -a2mB ${PRED-A2M} \
		-mult ${PT}-joint.mult \
		-dist ${PT}-joint.dist \
		> ${PT}-joint.pw.a2m
	gzip -f ${PT}-joint.*
	
${TP}-joint-%.pw.a2m.gz: ${TARGET-A2M} \
	${PRED-SEQ} ${PRED-A2M} 
	make ${PRED-DEST}
	${PCEM-SCRIPTS}/build-joint98 \
		-thresholds -9,-6,-2 \
		-seqA ${TARGET}.seq \
		-seqB ${PRED-SEQ} \
		-a2mA $< -a2mB ${PRED-A2M} \
		-mult ${TP}-$*.mult \
		-dist ${TP}-$*.dist \
		-fimstrength $* \
		> ${TP}-joint-$*.pw.a2m
	gzip -f ${TP}-joint-$*.*

${PT}-joint-%.pw.a2m.gz: ${TARGET-A2M} \
	${PRED-SEQ} ${PRED-A2M} 
	make ${PRED-DEST}
	${PCEM-SCRIPTS}/build-joint98 \
		-useB \
		-thresholds -9,-6,-2 \
		-seqA ${TARGET}.seq \
		-seqB ${PRED-SEQ} \
		-a2mA $< -a2mB ${PRED-A2M} \
		-mult ${PT}-$*.mult \
		-dist ${PT}-$*.dist \
		-fimstrength $* \
		> ${PT}-joint-$*.pw.a2m
	gzip -f ${PT}-joint-$*.*

${TP}-vit.pw.a2m.gz : ${TARGET-A2M:.a2m.gz=-varh50.mod} ${PRED-SEQ} 
	make ${PRED-DEST}
	${NEW-SAM}/hmmscore ${TP}-vit.pw \
		 -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 1 -sw 2 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${TP}-vit.pw.a2m

${PT}-vit.pw.a2m.gz : ${PRED-A2M:.a2m.gz=-varh50.mod} 
	make ${PRED-DEST}
	${NEW-SAM}/hmmscore ${PT}-vit.pw \
		-i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 1 -sw 2 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${PT}-vit.pw.a2m

${TP}-post.pw.a2m.gz : ${TARGET-A2M:.a2m.gz=-varh50.mod} ${PRED-SEQ} 
	make ${PRED-DEST}
	${NEW-SAM}/hmmscore ${TP}-post.pw \
		 -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-dpstyle 4 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${TP}-post.pw.a2m

${PT}-post.pw.a2m.gz : ${PRED-A2M:.a2m.gz=-varh50.mod} 
	make ${PRED-DEST}
	${NEW-SAM}/hmmscore ${PT}-post.pw \
		-i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-dpstyle 4 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${PT}-post.pw.a2m


${TP}-global.pw.a2m.gz : ${TARGET-A2M:.a2m.gz=-varh50.mod} ${PRED-SEQ} 
	make ${PRED-DEST}
	hmmscore ${TP}-global.pw -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 0 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${TP}-global.pw.a2m

${PT}-global.pw.a2m.gz : ${PRED-A2M:.a2m.gz=-varh50.mod} 
	make ${PRED-DEST}
	hmmscore ${PT}-global.pw -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 0 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${PT}-global.pw.a2m

${PT}-fssp-global.pw.a2m.gz : ${PRED-FSSP-A2M:.a2m.gz=-varh50.mod} 
	make ${PRED-DEST}
	hmmscore ${PT}-fssp-global.pw -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 0 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${PT}-fssp-global.pw.a2m
	
${PT}-fsspt98-global.pw.a2m.gz : ${PRED-FSSPT98-A2M:.a2m.gz=-varh50.mod} 
	make ${PRED-DEST}
	hmmscore ${PT}-fsspt98-global.pw -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 0 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${PT}-fsspt98-global.pw.a2m
	
${PT}-const-global.pw.a2m.gz : ${PRED-CONST-A2M:.a2m.gz=-varh50.mod} 
	make ${PRED-DEST}
	hmmscore ${PT}-const-global.pw -i $< -db ${TARGET}.seq -db ${PRED-SEQ} \
		-viterbi 0 \
		-subtract_null 4 -simplethreshold 1 \
		-select_align 8
	gzip -f ${PT}-const-global.pw.a2m
	
%.dist: %.mod ${TRAIN_SET}
	hmmscore $* -i $*.mod -db ${TRAIN_SET} -sw 2 \
		-subtract_null 4 -simplethreshold 1 -sort 2 \
		-fimstrength ${FIMSTR}

%-varh50-pdb.rdb: %.a2m.gz
	${PCEM-SCRIPTS}/score-target -alignment $^ -build varh50 \
		-db ${PDB} \
		-NLLminusNULL	-5.0 -NLLreverse -1.0 \
		-viterbi 0 -sw_score 2 \
		-output $@

%-pdb.dist %-pdb.a2m: %.mod ${PDB}
	hmmscore $*-pdb -i $*.mod -db ${PDB} -sw 2 \
		-subtract_null 4 -simplethreshold 1 -sort 2 \
		-select_align 2 \
		-fimstrength ${FIMSTR}
	gzip -f $*-pdb.a2m


%-h0.5.mod: %.a2m.gz
	${PCEM-SCRIPTS}/h0.5 $^ $@

%-varh50.mod: %.a2m.gz
	${PCEM-SCRIPTS}/varh50 $^ $@
%.h1.0.mod: %.a2m.gz
	${PCEM-SCRIPTS}/h1.0 $^ $@
	
%_sorted.ids %.tree %_sorted.a2m.gz %.phytrace: %.a2m.gz
	gunzip $^
	${PHYTREE} -o -i -r flat $* $*.a2m ${LIB}/recode2.20comp
	-gzip -f $*.a2m
	-gzip -f $*_sorted.a2m
	-rm $*.phytrace $*.tree_weight

%.tree.ps: %.tree
	${DG} $^


%.ids: %.a2m.gz
	zcat $^ \
	| ids-from-fasta > $@

# make id list for sequences from nrp, stripping off multdomain range info
# (Assumes that a colon in a name indicates an NRP name).
%.nrp-ids: %.a2m.gz
	zcat $^ \
	| ids-from-fasta -nodom \
	| egrep ":" \
	> $@

%.seq.gz: %.ids
	extract-from-fasta $^ < ${NRP} > $*.seq
	gzip -f $*.seq


%.2d : %.a2m.gz
	echo ReadNeuralNet ${NEURAL-NET} > tmp.script
	echo InFilePrefix /projects/compbio/lib/ >> tmp.script
	echo WeightingRegularizer recode3.20comp >> tmp.script
	echo SequenceWeight HenikoffWeight 1.0 0.5 >> tmp.script
	echo InFilePrefix  >> tmp.script
	echo ReadA2M $^ >> tmp.script
	echo PrintPrediction $@ ${CASP3-2D-ID} >> tmp.script
	echo PrintPredictionFasta $@.seq >> tmp.script
	${PREDICT-2ND} < tmp.script

%-blast.rdb:	%.seq
	${CASP3-SCRIPTS}/single-blast -q $^ -interdb ${NR} -db ${PDB} > $@

%-double-blast.rdb:	%.seq
	${CASP3-SCRIPTS}/double-blast -q $^ -interdb ${NR} -db ${PDB} > $@