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-rw-r--r--sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch153
1 files changed, 0 insertions, 153 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
deleted file mode 100644
index 91da48017eff..000000000000
--- a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch
+++ /dev/null
@@ -1,153 +0,0 @@
- 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}
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-05 15:20:14 +0000