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|
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.<id> and vall_cst_coord.dat.<id> 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}
|
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