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