nnmake/dipolar_nn.f | 2 +- nnmake/make.system | 33 ++++++++++++++++----------------- nnmake/make_fragments.pl | 36 ++++++++++++++++++------------------ nnmake/makefile | 2 +- 4 files changed, 36 insertions(+), 37 deletions(-) diff --git a/nnmake/dipolar_nn.f b/nnmake/dipolar_nn.f index c159888..4412a20 100644 --- a/nnmake/dipolar_nn.f +++ b/nnmake/dipolar_nn.f @@ -1396,7 +1396,7 @@ car pairDipolar(1,i) .le. pairDipolar(1,i+1) write(0,*)'rejected' write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset) do i=1,maplength(iset) - write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), + write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), # b(i) enddo goto 300 diff --git a/nnmake/make.system b/nnmake/make.system index 34bea8f..2fbfabf 100644 --- a/nnmake/make.system +++ b/nnmake/make.system @@ -55,18 +55,17 @@ endif ########## once COMPILER is set, here are the options # defaults -F77=f77 -FFLAGS= -FOPTIMFLAGS=-O -FDEBUGFLAGS=-g -FPROFILEFLAGS=-P +F77?=f77 +FOPTIMFLAGS= +FDEBUGFLAGS= +FPROFILEFLAGS= ifeq ($(COMPILER),gnu) - F77 = g77 - FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit - FOPTIMFLAGS = -O -ffast-math -malign-double - FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W - FPROFILEFLAGS = -pg + F77 ?= g77 + FFLAGS += -W -ffixed-line-length-132 -Wimplicit + FOPTIMFLAGS += -malign-double + FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W + FPROFILEFLAGS = endif ifeq ($(COMPILER),pgi) # on mary, good bounds checking @@ -82,9 +81,9 @@ ifeq ($(COMPILER),pgi) # on mary, good bounds checking endif ifeq ($(COMPILER),absoft) # on mary, fast - F77 = f77 - FFLAGS = -N109 -s -W - LINKFLAGS = -lU77 + F77 ?= f77 + FFLAGS ?= -N109 -s -W + LINKFLAGS += -lU77 FDEBUGFLAGS = -C -g FOPTIMFLAGS = -O -N18 FPROFILEFLAGS = -P -O @@ -103,10 +102,10 @@ endif # Suse ppc gnu ifeq ($(COMPILER),ppc) - F77 = g77 - FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132 - FDEBUGFLAGS = -g -C -Mbounds - FOPTIMFLAGS = + F77 ?= g77 + FFLAGS += -Wall -W -ffixed-line-length-132 + FDEBUGFLAGS += -C -Mbounds + FOPTIMFLAGS += endif # alpha flags diff --git a/nnmake/make_fragments.pl b/nnmake/make_fragments.pl index 5273685..29619a2 100755 --- a/nnmake/make_fragments.pl +++ b/nnmake/make_fragments.pl @@ -19,38 +19,38 @@ my $TAIL = "_v1_3"; -$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments'; -$shareware_dir = '/work/chu/src/shareware'; -$scratch = "/scratch/shared"; +$src_dir = '@GENTOO_PORTAGE_EPREFIX@/'; +$shareware_dir = '$src_dir/usr/share'; +$scratch = "$src_dir/scratch/shared"; # psi-blast #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin"; -my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp"; # PSI-BLAST (duh.) -my $NR = "/$scratch/genomes/nr"; # nr blast database filename -my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') -my $BLOSUM = "$scratch/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') +my $PSIBLAST = "$src_dir/usr/bin/blastpgp"; # PSI-BLAST (duh.) +my $NR = "$shareware_dir/nr"; # nr blast database filename +my $VALL_BLAST_DB = "$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') +my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') # psipred -my $FILTNR = "$scratch/genomes/filtnr"; # filtnr blast database filename -my $MAKEMAT = "$shareware_dir/blast/bin/makemat"; # makemat utility (part of NCBI tools) -my $PSIPRED = "$shareware_dir/psipred/bin/psipred"; # psipred -my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2"; # psipass2 (part of psipred pkg) +my $FILTNR = "$src_dir/tmp/filtnr"; # filtnr blast database filename +my $MAKEMAT = "$src_dir/usr/bin/makemat"; # makemat utility (part of NCBI tools) +my $PSIPRED = "$src_dir/usr/bin/psipred"; # psipred +my $PSIPASS2 = "$src_dir/usr/bin/psipass2"; # psipass2 (part of psipred pkg) my $PSIPRED_DATA = "$shareware_dir/psipred/data"; # dir containing psipred data files. # prof #my $PROF = "$shareware_dir/prof/run_prof.py"; -my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof executable location in run_prof.py +my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof executable location in run_prof.py # nnmake -my $VALL = "$scratch/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') -my $VALL2 = "$scratch/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') +my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') +my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall (vall.dat. and vall_cst_coord.dat. must exist) -my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu"; # nnmake binary (cvs respository 'nnmake') -my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') +my $NNMAKE = "$src_dir/usr/bin/pNNMAKE"; # nnmake binary (cvs respository 'nnmake') +my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') # chemshift -my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary (cvs repository 'chemshift') -my $TALOS_DB = "$scratch/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') +my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT"; # chemshift binary (cvs repository 'chemshift') +my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') # jufo (secondary structure prediction software) my $JUFO = "$shareware_dir/jufo/molecule.exe"; # jufo executable diff --git a/nnmake/makefile b/nnmake/makefile index c09ac1c..ebfde68 100644 --- a/nnmake/makefile +++ b/nnmake/makefile @@ -102,7 +102,7 @@ VallCoord: coord_compile # rule to compile executable compile: print $(BASE_NAME).$(COMPILER) $(BASE_NAME).$(COMPILER) : ${OBJS} - $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS) + $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS) coord_compile: print $(COORD_BASE_NAME).$(COMPILER) $(COORD_BASE_NAME).$(COMPILER) : ${COORD_OBJS}