######################################################################## # # # USER DEFINITIONS FOR CIF2PDB INSTALLATION # # # ######################################################################## # In the m4 document Makefile.m4 (NOT Makefile), # define values for: # # expand -- A directory in which to expand compressed files # The default is `/var/tmp'. On some systems `/tmp' # may be preferable. If expanded files are to be # kept long term, then holding the expanded file in # the current directory `.' may be preferable. # The directory used must allow for at least 40 # megabytes of files for a full build and test. # decomp -- The httpd virtual path to the cgi-bin script # `decomp'.cgi. This is a special script which # decompresses files on the fly. If this script is # not available on your system, define `decomp' as # `NODECOMP' # vpath -- The httpd virtual path to the directory holding # this version of the directory, i.e. containing # the cif2pdb_n.n.n directory. If `decomp' is # defined as `NODECOMP' then `vpath' may simply # be set to `..' MANIFEST.html and # README.cif2pdb.html must be rebuilt if `vpath' # changes. # binpath -- The path to utility programs such as sed # # # ######################################################################## # Directory for uncompressed files, EXPAND = /var/tmp # Path to decomp.cgi, DECOMP = NODECOMP # Path to program directory, VPATH = .. # Path to utilities such as sed, BINPATH = /usr/bin/ ######################################################################## # # # END OF USER DEFINITIONS # # # ######################################################################## ######################################################################## # # # SPECIAL DEFINITIONS FOR CIF2PDB INSTALLATION # # # ######################################################################## # The following definitions may need to be modified at # some sites, but most often are best left alone. # Make changes in the m4 document Makefile.m4 # (NOT Makefile) # # There is a strong assumption that the name of the directory # within which this build is being made is cif2pdb_n.n.n # where n.n.n is the current version, and that ciftbx.src is # installed on the same level. # # This is the path to the CIFtbx2 directory TBXPATH = ../ciftbx.src # # # This is a path to cif_mm.dic # MMDICPATH = ../dictionaries/cif_mm_cif2pdb.dic # # provide a path to the shell sh here SHELL = /bin/sh # # Add any necessary compilation flags on the next line FFLAGS = -g # # On some systems, csh is broken, and tcsh should be used. In # that case, uncomment the next line #CSHELL = tcsh # # In can be useful to time the performance of the package # # If no timer is desired, comment out the next line and uncomment # the one after TIMER = time #TIMER = ######################################################################## # # # NO CHANGES SHOULD BE NEEDED BELOW THIS LINE # # # ######################################################################## # # # Makefile built for SITE = LOCAL # # Makefile for cif2pdb 2.0.1 # Version of 1 August 2005 # # # # H. J. Bernstein, Bernstein+Sons # yaya@bernstein-plus-sons.com # # # make clean Cleans up the installation directory # make distclean Restore the installation directory to # distribution state # make Makefile_local Builds Makefile_local AND # Makefile from Makefile.m4 # make (or make all) Compiles cif2pdb # make tests Tests the compilation of cif2pdb # # The following calls are used in building release kits # # make README.cif2pdb.html Builds README.cif2pdb.html # from README.cif2pdb.html.m4 # make MANIFEST.html Builds MANIFEST.html from # MANIFEST.html.m4 # make expanded Creates local expanded files # make postshar Compresses files after unpacking # cif2pdb.cshar or cif2pdb.shar # make Makefile_expanded # make Makefile_sdsc # make Makefile_ndb # make Makefile_pdb # Make special versions of Makefile, # but do not replace the default # Makefile. The expanded version is # similar to the default local version, # but expands in the current directory. # in order to use one of the special # versions, make -f Makefile_... # make shars Builds cif2pdb.cshar.Z and # cif2pdb.shar.Z in directory # .. # # # # Provide here a path to mkdecompln and rmdecompln # MKDECOMPLN = $(CSHELL) ./mkdecompln RMDECOMPLN = $(CSHELL) ./rmdecompln # # Directory for shars # SHARDIR = .. # # define the directory for temporary uncompressed files # #EXPAND = /var/tmp #EXPAND = /var/tmp #EXPAND = /var/tmp #EXPAND = . EXPAND = /var/tmp # # The definition of VPATH must be the httpd virtual path to # the directory holding this version of the directory, i.e. # containing the cif2pdb_n.n.n directory MANIFEST.html # and README.cif2pdb.html must be rebuilt if VPATH changes #VPATH = NDB/mmcif/software #VPATH = ~yaya/software #VPATH = pb/pdb2cif #VPATH = .. VPATH = .. # # The definition of DECOMP must be the httpd virtual path to # the cgi-bin script decomp.cgi. If this script is not available # define DECOMP as NODECOMP #DECOMP = /cgi-bin/yaya/decomp.cgi #DECOMP = /~yaya/cgi-bin/decomp.cgi #DECOMP = /pb/pdb2cif/cgi-bin/decomp.cgi #DECOMP = NODECOMP DECOMP = NODECOMP # # # ZPATH = $(DECOMP)/$(VPATH) # # The suffixes for any files to be used or built: .SUFFIXES: .m4 .pl .awk .oawk .ent .acif .pcif .oacif .tcif \ .cif .pdb .tpdb .diff .wid .twid .wdiff # # The locations of any programs used CIF2PDB = ./cif2pdb # # The flags to be used in cif builds # And the default header file to be used # CIFFLAGS = CIFS = 5hvp.cif 1ace.cif 2ace.cif 1crn.cif 1cro.cif 4ins.cif 1hyh.cif \ 1cwp.cif ADH041.cif BDL001.cif BDLB13.cif DDF040.cif 4hir.cif 1zrt.cif PDBS = 5hvp.pdb 1ace.pdb 2ace.pdb 1crn.pdb 1cro.pdb 4ins.pdb 1hyh.pdb \ 1cwp.pdb ADH041.pdb BDL001.pdb BDLB13.pdb DDF040.pdb 4hir.pdb 1zrt.pdb WIDS = 5hvp.wid 1ace.wid 2ace.wid 1crn.wid 1cro.wid 4ins.wid 1hyh.wid \ 1cwp.wid ADH041.wid BDL001.wid BDLB13.wid DDF040.wid 4hir.wid 1zrt.wid TPDBS = 5hvp.tpdb 1ace.tpdb 2ace.tpdb 1crn.tpdb 1cro.tpdb 4ins.tpdb \ 1hyh.tpdb 1cwp.tpdb ADH041.tpdb BDL001.tpdb BDLB13.tpdb \ DDF040.tpdb 4hir.tpdb 1zrt.tpdb TWIDS = 5hvp.twid 1ace.twid 2ace.twid 1crn.twid 1cro.twid 4ins.twid \ 1hyh.twid 1cwp.twid ADH041.twid BDL001.twid BDLB13.twid \ DDF040.twid 4hir.twid 1zrt.twid CIFZS = 5hvp.cif.Z 1ace.cif.Z 2ace.cif.Z 1crn.cif.Z 1cro.cif.Z \ 4ins.cif.Z 1hyh.cif.Z 1cwp.cif.Z ADH041.cif.Z BDL001.cif.Z \ BDLB13.cif.Z DDF040.cif.Z 4hir.cif.Z 1zrt.cif.Z PDBZS = 5hvp.pdb.Z 1ace.pdb.Z 2ace.pdb.Z 1crn.pdb.Z 1cro.pdb.Z \ 4ins.pdb.Z 1hyh.pdb.Z 1cwp.pdb.Z ADH041.pdb.Z BDL001.pdb.Z \ BDLB13.pdb.Z DDF040.pdb.Z 4hir.pdb.Z 1zrt.pdb.Z WIDZS = 5hvp.wid.Z 1ace.wid.Z 2ace.wid.Z 1crn.wid.Z 1cro.wid.Z \ 4ins.wid.Z 1hyh.wid.Z 1cwp.wid.Z ADH041.wid.Z BDL001.wid.Z \ BDLB13.wid.Z DDF040.wid.Z 4hir.wid.Z 1zrt.wid.Z TPDBZS = 5hvp.tpdb.Z 1ace.tpdb.Z 2ace.tpdb.Z 1crn.tpdb.Z 1cro.tpdb.Z \ 4ins.tpdb.Z 1hyh.tpdb.Z 1cwp.tpdb.Z ADH041.tpdb.Z \ BDL001.tpdb.Z BDLB13.tpdb.Z DDF040.tpdb.Z 4hir.tpdb.Z 1zrt.tpdb.Z TWIDZS = 5hvp.twid.Z 1ace.twid.Z 2ace.twid.Z 1crn.twid.Z 1cro.twid.Z \ 4ins.twid.Z 1hyh.twid.Z 1cwp.twid.Z ADH041.twid.Z \ BDL001.twid.Z BDLB13.twid.Z DDF040.twid.Z 4hir.twid.Z 1zrt.twid.Z DIFFS = 5hvp.diff 1ace.diff 2ace.diff 1crn.diff 1cro.diff \ 4ins.diff 1hyh.diff 1cwp.diff ADH041.diff \ BDL001.diff BDLB13.diff DDF040.diff 4hir.diff 1zrt.diff \ 5hvp.wdiff 1ace.wdiff 2ace.wdiff 1crn.wdiff 1cro.wdiff \ 4ins.wdiff 1hyh.wdiff 1cwp.wdiff ADH041.wdiff \ BDL001.wdiff BDLB13.wdiff DDF040.wdiff 4hir.wdiff 1zrt.wdiff # FFLAGS = -g # # # The path to utilities such as sed # BINPATH = /usr/bin/ .cif.pdb: $(TIMER) $(CIF2PDB) -d cif_mm.dic -p $* < $< 2> $*.pdb.lst | \ compress > $*.pdb.Z $(MKDECOMPLN) $*.pdb $(EXPAND) .cif.wid: $(TIMER) $(CIF2PDB) -w yes -d cif_mm.dic -p $* < $< 2> $*.wid.lst | \ compress > $*.wid.Z $(MKDECOMPLN) $*.wid $(EXPAND) .cif.tpdb: $(TIMER) $(CIF2PDB) -d cif_mm.dic -p $* < $< 2> $*.tpdb.lst | \ compress > $*.tpdb.Z $(MKDECOMPLN) $*.tpdb $(EXPAND) .cif.twid: $(TIMER) $(CIF2PDB) -w yes -d cif_mm.dic -p $* < $< 2> $*.twid.lst | \ compress > $*.twid.Z $(MKDECOMPLN) $*.twid $(EXPAND) .pdb.diff: -@/bin/rm -f $*.diff -@/bin/rm -f $*.spdb -$(BINPATH)sed -e "1,\$$s/ 0\./ \./g" < $*.pdb | \ $(BINPATH)sed -e "1,\$$s/ -0\./ -\./g" >$*.spdb -uncompress < $*.tpdb.Z | \ $(BINPATH)sed -e "1,\$$s/ 0\./ \./g" | \ $(BINPATH)sed -e "1,\$$s/ -0\./ -\./g" | \ diff - $*.spdb > $*.diff -/bin/rm -f $*.spdb .wid.wdiff: -@/bin/rm -f $*.wdiff -@/bin/rm -f $*.swid -$(BINPATH)sed -e "1,\$$s/ 0\./ \./g" < $*.wid | \ $(BINPATH)sed -e "1,\$$s/ -0\./ -\./g" >$*.swid -uncompress < $*.twid.Z | \ $(BINPATH)sed -e "1,\$$s/ 0\./ \./g" | \ $(BINPATH)sed -e "1,\$$s/ -0\./ -\./g" | \ diff - $*.swid > $*.wdiff -/bin/rm -f $*.swid all: postshar cif2pdb allpdbs: postshar $(PDBS) allwids: postshar $(WIDS) Makefiles: Makefile_sdsc Makefile_ndb Makefile_pdb Makefile_expanded Makefile_local: Makefile.m4 m4 Makefile.m4 > Makefile_local cp Makefile_local Makefile Makefile_sdsc: Makefile.m4 m4 -DSITE=SDSC Makefile.m4 > Makefile_sdsc Makefile_ndb: Makefile.m4 m4 -DSITE=NDB Makefile.m4 > Makefile_ndb Makefile_pdb: Makefile.m4 m4 -DSITE=PDB Makefile.m4 > Makefile_pdb Makefile_expanded: Makefile.m4 m4 -DSITE=NODECOMP Makefile.m4 > Makefile_expanded # # If any of the following fail, it means the basic ciftbx # installation needs to be redone $(TBXPATH)/ciftbx.o: $(TBXPATH)/ciftbx.f \ $(TBXPATH)/ciftbx.sys \ $(TBXPATH)/ciftbx.cmv ( cd $(TBXPATH) ; make ciftbx.o ) $(TBXPATH)/hash_funcs.o: $(TBXPATH)/hash_funcs.f ( cd $(TBXPATH); make hash_funcs.o ) ciftbx.sys: $(TBXPATH)/ciftbx.sys ln -f -s $(TBXPATH)/ciftbx.sys ciftbx.sys ciftbx.cmn: $(TBXPATH)/ciftbx.cmn ln -f -s $(TBXPATH)/ciftbx.cmn ciftbx.cmn ciftbx.cmf: $(TBXPATH)/ciftbx.cmf ln -f -s $(TBXPATH)/ciftbx.cmf ciftbx.cmf ciftbx.cmv: $(TBXPATH)/ciftbx.cmv ln -f -s $(TBXPATH)/ciftbx.cmv ciftbx.cmv cif2pdb.o: cif2pdb.f cif2pdb.cmn ciftbx.sys ciftbx.cmn ciftbx.cmf \ ciftbx.cmv $(FC) $(FFLAGS) -c cif2pdb.f cif2pdb: cif2pdb.o $(TBXPATH)/hash_funcs.o $(TBXPATH)/ciftbx.o cif2pdb.o $(FC) $(FFLAGS) cif2pdb.o $(TBXPATH)/ciftbx.o \ $(TBXPATH)/hash_funcs.o -o cif2pdb postshar: compress $(TPDBS) compress $(TWIDS) compress $(CIFS) ./.symlinks touch postshar -@rm unpostshar clean: -@rm *.o -@rm *.diff -@rm *.wdiff -@rm *.BAK -@rm *.bak -@rm cif2pdb -@rm *.pdb.Z -@rm *.wid.Z -@$(RMDECOMPLN) *.uZ -@$(RMDECOMPLN) .DECOMP/*.uZ distclean: clean unpostshar ./.undosymlinks -@rm cif_mm.dic.Z -@rm postshar -@rm ciftbx.* unpostshar: postshar -@uncompress $(TPDBZS) -@uncompress $(CIFZS) -@uncompress $(TWIDZS) touch unpostshar tests: postshar testcif2pdb -@cat *diff testcif2pdb: cif2pdb cif_mm.dic $(CIFS) $(PDBS) $(WIDS) \ $(DIFFS) $(TPDBZS) $(TWIDZS) $(CIFS): $(CIFZS) $(MKDECOMPLN) $@ $(EXPAND) $(TPDBS): $(TPDBZS) $(MKDECOMPLN) $@ $(EXPAND) $(TWIDS): $(TWIDZS) $(MKDECOMPLN) $@ $(EXPAND) $(TPDBZS): $(CIFZS) make `echo $@ | $(BINPATH)sed -e "s/\.tpdb\.Z//"`.cif $(CIF2PDB) -d cif_mm.dic -p \ `echo $@ | $(BINPATH)sed -e "s/\.tpdb\.Z//"` < \ `echo $@ | $(BINPATH)sed -e "s/\.tpdb\.Z//"`.cif | \ compress > `echo $@ | $(BINPATH)sed -e "s/\.tpdb\.Z//"`.tpdb.Z $(TWIDZS): $(CIFZS) make `echo $@ | $(BINPATH)sed -e "s/\.twid\.Z//"`.cif $(CIF2PDB) -w yes -d cif_mm.dic -p \ `echo $@ | $(BINPATH)sed -e "s/\.twid\.Z//"` < \ `echo $@ | $(BINPATH)sed -e "s/\.twid\.Z//"`.cif | \ compress > `echo $@ | $(BINPATH)sed -e "s/\.twid\.Z//"`.twid.Z cif_mm.dic: cif_mm.dic.Z $(MKDECOMPLN) cif_mm.dic $(EXPAND) MANIFEST.html: MANIFEST.html.m4 Makefile -@rm MANIFEST.html.BAK -@mv MANIFEST.html MANIFEST.html.BAK m4 -DZPATH=$(ZPATH) -DDECOMP=$(DECOMP) < MANIFEST.html.m4 \ > MANIFEST.html README.cif2pdb.html: README.cif2pdb.html.m4 Makefile -@rm README.cif2pdb.html.BAK -@mv README.cif2pdb.html README.cif2pdb.html.BAK m4 -DGRAPHICS=1 \ -DZPATH=$(ZPATH) -DDECOMP=$(DECOMP) < \ README.cif2pdb.html.m4 \ > README.cif2pdb.html expanded: cif2pdb.cshar.Z cif2pdb.shar.Z \ cif_mm.dic.Z $(CIFS) $(TPDBS) .DECOMP $(MKDECOMPLN) cif2pdb.cshar $(EXPAND) $(MKDECOMPLN) cif2pdb.shar $(EXPAND) $(MKDECOMPLN) cif_mm.dic $(EXPAND) $(DIFFS): $(PDBS) $(TPDBZS) $(WIDS) $(TWIDZS) $(PDBS): cif2pdb $(CIFZS) shars: postshar $(CIFS) $(TPDBS) $(TWIDS) DISCUSS.cif2pdb.html \ IUCR_POLICY IUCR_POLICY.html Makefile Makefile.m4 \ NOTICE NOTICE.html \ README README.cif2pdb.html README.cif2pdb.html.m4 \ cif2pdb.cmn cif2pdb.f mkdecompln rmdecompln \ MANIFEST MANIFEST.html MANIFEST.html.m4 $(SHARDIR) -@/bin/rm -f $(SHARDIR)/cif2pdb.cshar.Z -@/bin/rm -f $(SHARDIR)/cif2pdb.shar.Z (cd .. ; makekit -c -icif2pdb.src/MANIFEST -ocif2pdb.src/MANIFEST -h2 -p -s30000k) mv ../Part01 $(SHARDIR)/cif2pdb.cshar compress $(SHARDIR)/cif2pdb.cshar -@/bin/rm -f cif2pdb.cshar.Z ln -s $(SHARDIR)/cif2pdb.cshar.Z cif2pdb.cshar.Z (cd .. ; makekit -icif2pdb.src/MANIFEST -ocif2pdb.src/MANIFEST -h2 -p -s30000k) mv ../Part01 $(SHARDIR)/cif2pdb.shar compress $(SHARDIR)/cif2pdb.shar -@/bin/rm -f cif2pdb.shar.Z ln -s $(SHARDIR)/cif2pdb.shar.Z cif2pdb.shar.Z .DECOMP: -@mkdir .DECOMP $(SHARDIR): -@mkdir $(SHARDIR)