diff options
Diffstat (limited to 'sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch')
-rw-r--r-- | sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch | 153 |
1 files changed, 153 insertions, 0 deletions
diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch new file mode 100644 index 000000000000..91da48017eff --- /dev/null +++ b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch @@ -0,0 +1,153 @@ + 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} |