# 1 level Makefile

#
# this is makefile for processing of triple resonance spectra from an FID recorded in the nonlinear sampling mode (NLS) in Vnmr (Varian Inc.)
#

#
# installations:  'nmrPipe' is assumed to be preinstalled separately, 
#                 'bin' (with programs'mddnmr1.2c' and 'pros') must be also in the path 

#
# for each spectrum make a working directory, where you copy this 'Makefile'  from bin directory
# set range in direct dimension 1HN in ppm
RANGEH = 8.82 9.57
# the FIDDIR directory is assumed to be in the upper dirrectory, e.g. '../fid'
# then command 'make data' processes '$FIDDIR/fid' with '$FIDDIR/proc/fidSP.com' (calling nmrPipe) and result put into $DATDIR/F???.DAT
# below specify paths to these two dirs  $FIDDIR $DATDIR  (change fidSP.com if these directories are not in the upper directory)
# 
#
# below are 5 names to be specified by the user, most other options could be left as defaults 
# EXPNAME is the common name of the fid and data directories
EXPNAME = ubi_ghnco_3d_600Y
FIDDIR = ../$(EXPNAME).fid
DATDIR = ../$(EXPNAME).data
# ROOT is common name of files *.in and *.hdr_3
ROOT =  ghnco
INFILE =     ${FIDDIR}/$(ROOT).in
INDEXFILE =  ${FIDDIR}/$(ROOT).hdr_3

TABFILE = ../ubi_nhsqc_600Y.fid/hsqc2d.tab
# TABFILE  contains name of the ipeak list file with HN peaks, which are used for estimation of number of components in all triple-resonance experiments.
# it is assumed to be supplied by the user and can be any file with HN ppm values in the specified colomn . 
# in this example it is nmrDraw generated tab file of 2D HSQC-TROSY. 
# below set are the number of colomns for the amide proton ppm values, and the number of lines to skip in the file (7 and 6 in the usual nmrDraw file) before first peak line. 
TABCOLOMN= 7
TABLINESKIP=6
# usable are 3d or 2d peak lists, or a constant (below)
# TABFILE = 30
# uncomment this line, in this case colomn and skip are any (in many cases it could be adequate approximation, but it is recommended to use the peak list; otherwise the constant must be the max number for all regions.)
# So, this 'Makefile', plus $INFILE about sparse sampling indices and optional $TABFILE with some peaks, are all what is needed to do 'make all' command;
# this can be done already at this point.



# General comments: 
# this makefile will call several shell scripts , which contain a number of default parameters in them, which should work for most cases as is. 
# (optionally any of the *.sh files could be copyed into the working directory if any user modification or non-default behavior is needed.)
# 
# For example, to change default nmrPipe processing : 
# after MDD reconstructions are done , pipe processing script 'conv_yz.com' is called from 'process.sh' (making FT in two indirect dimensions) 
# the default scripts (from the path) are used if no 'conv_yz.com' is found in the current dir
# in the latter ('conv_yz.com') 
# default pipe processing is:  SP=sine2, zero filling to twice,FT, 0 0 indirect phases 1,2 with 1st point c=0.5 for f180=n,  and -90 180 with 1st point 1.0 for f180=y
# (optionally: copy both 'process.sh' and 'conv_yz.com' to the current dir and modify these two for specific processing)


# 
# This are for files other than HNCO : set multiplier for peaks counting in relation to 1 HN peak in HNCO  (e.g. 2 for HNCA, 4 for HNCACB ...)
HNSTRIP =  1
# Below are if several intermediate steps (here called TA) are needed, to use all sparse data set 1 and 1. 
# optional: number of TA calculation steps
NTASTEPS = 1
# optional: number of TA processing steps
NTALAST =  1


###############################################################################################
# END OF Header section (do not have to make changes below)
#

# these are fixed (for now) working dir names for intermediate files
CURDIR = `pwd`
# mdds  - for mdd files
# proc  - for processed spectra in nmrpipe format, they are numbered by ta steps
# ress  - for results of mdd calculations
# runs  - for regions mddcalcs shell files 
# tabs  - for peak tables
# temp  - for all other temporary files
# logs  - for logs

SUBDIRS =  mdds proc ress runs tabs temp logs 
# optional: it is usually  Y  
OPTION =   Y




# this make "all" can work fine in easy cases (on a single CPU)

all: infiles calcs runmdds specs 

# at this point, with only the Makefile in the current dir you can type 'make all' and after some time (from minutes to a few hours) there should be processed spectra in the 'proc' directory . 


# if the mdd processing is done on a cluster use make-target "allcluster" , here instead of 'calcruns' it makes 'pack'
allcluster: infiles calcs pack
	echo "after all 'runs/run???.sh' completed, import back all the dirs that were exported (now with completed results and logs), untar them in the current directory and type 'make process' "



infiles: $(INFILE) ${FIDDIR}/$(ROOT).hdr_1 data

calcs: maketempdirs calchdrs calcruns calcmdds 


#pack4cluster
pack: runs/run001.sh mdds/ae001.mdd 
	tar cvf $(EXPNAME).tar runs mdds ress logs; compress $(EXPNAME).tar ; ls -la $(EXPNAME).tar.Z; \
	echo "copy this tar to the cluster and  run the shells 'runs/run???.sh' in parallel on a cluster ";


# $INFILE is created before in vnmr sparse expt  
# it and its files containing sparse indices should be in $FIDDIR
# note that in the $INFILE the dimension order is for example "C,N,Hdir" (i.e. Hdir is last), the other two dims: fast experiment dim is first, in this case "C"

${FIDDIR}/$(ROOT).hdr_1: $(INFILE) ${FIDDIR}/$(ROOT).hdr_3
	cd $(FIDDIR); runspheader.sh $(INFILE) ${FIDDIR}/$(ROOT).hdr_3; cd $(CURDIR);

refdata:
	echo " " >> $(FIDDIR)/proc/fidSP.com; 
	$(FIDDIR)/proc/fidSP.com 6.0 10.5 $(EXPNAME) R 0.0  
	conv_yz.com  $(DATDIR) R R    0.5  32 64  0 0   0.5 64 128  0 0;
	dat2pipe.com  $(DATDIR)  tRR
	rm $(DATDIR)/*R???.DAT 

# $DATDIR/F???.DAT are transposed so that direct dimension is in Z; only direct dim is FT-ed, the other two dims are in time domain
data: $(DATDIR)/F001.DAT
	echo " " >> $(FIDDIR)/proc/fidSP.com;


$(DATDIR)/F001.DAT: $(FIDDIR)/fid
	$(FIDDIR)/proc/fidSP.com $(RANGEH) $(EXPNAME) F 0.0


# this could be done once or every time
maketempdirs: 
	for i in $(SUBDIRS); do \
	if [ -e $$i ]; then echo  "exists " $$i ; else echo "making " $$i ; mkdir $$i; fi; \
	done; \
	echo "options:  $(DATDIR) $(FIDDIR) $(INFILE) $(NTASTEPS) $(NTALAST) $(OPTION) $(HNSTRIP) $(TABFILE)"; \
	echo "Initialization complete "


calchdrs:  $(INFILE) 
	processNall.sh "calcHDRs" $(DATDIR) $(FIDDIR) $(INFILE) $(NTASTEPS) $(NTALAST) $(OPTION) $(HNSTRIP) $(TABFILE) $(TABCOLOMN) $(TABLINESKIP)

calcmdds:  $(INFILE) data
	processNall.sh "calcMDDs" $(DATDIR) $(FIDDIR) $(INFILE) $(NTASTEPS) $(NTALAST) $(OPTION) $(HNSTRIP) $(TABFILE) $(TABCOLOMN) $(TABLINESKIP)

calcruns:  $(INFILE) data
	processNall.sh "calcRUNs" $(DATDIR) $(FIDDIR) $(INFILE) $(NTASTEPS) $(NTALAST) $(OPTION) $(HNSTRIP) $(TABFILE) $(TABCOLOMN) $(TABLINESKIP)


runmdds: runmdds.sh
	echo "start MDD calculation for all $$nregs regions; ...."; cat runs/nreg_pk_comp.txt; 
	runmdds.sh
	echo "finished MDD calculation for all regions";

specs:  $(INFILE) ress/res001001.dat
	process.sh    "procSpecs" $(DATDIR) $(FIDDIR) $(INFILE) $(NTASTEPS) $(NTALAST) $(OPTION) $(HNSTRIP) $(TABFILE)


# optional: sometimes used to make intermediate reconstruction to 3dims
calcres3: ress/res001001.dat
	processNall.sh "calcRes3" $(DATDIR) $(FIDDIR) $(INFILE) $(NTASTEPS) $(NTALAST) $(OPTION) $(HNSTRIP) $(TABFILE) $(TABCOLOMN) $(TABLINESKIP)


#mddnmr: main.c
#	g77 main.c -LLIB -lutils -lalapack -lablas -o mddnmr

.c.o:
	$(CC) -c $<


clean: 
	rm -f tmp?*  _*.gawk temp/[rnbtTS]???*
	echo "clean complete " 

purge:  clean
	rm -f temp/* tmp* ; echo "ok"