| 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} |
