proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

7 files changed, 421 insertions, 0 deletions

diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest
new file mode 100644
index 000000000000..efbeb3f09970
--- /dev/null
+++ b/sci-libs/rosetta-fragments/Manifest
@@ -0,0 +1 @@
+DIST rosetta3.1_fragments.tgz 221931894 SHA256 2211cab76e4848d80d6fd311e97535de220a865d8afc72d8ca12f90b7d4641bf SHA512 a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1 WHIRLPOOL 32d0758e6782da8088178e11af5bfe23b457e98a3ab9a8cbb583d4e4aa48e5d1ef9005825ff62944c5c755a0ac99b3ff88fb7c1d1b249940110287969ff0118a
diff --git a/sci-libs/rosetta-fragments/files/3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/3.1-chemshift.patch
new file mode 100644
index 000000000000..6ea69b210e82
--- /dev/null
+++ b/sci-libs/rosetta-fragments/files/3.1-chemshift.patch
@@ -0,0 +1,33 @@
+--- chemshift/makefile	2009-01-09 16:08:00.000000000 +0100
++++ chemshift/makefile.new	2009-04-09 11:30:34.179824057 +0200
+@@ -64,7 +64,7 @@
+ # rule to compile executable
+ compile: $(BASE_NAME).$(COMPILER)
+ $(BASE_NAME).$(COMPILER) : print ${OBJS}
+-	$(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
++	$(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
+ 
+ # rule to compile object files:
+ .$(COMPILER).%.o: %.f
+--- chemshift/make.system	2009-01-09 16:08:00.000000000 +0100
++++ chemshift/make.system.new	2009-04-09 11:35:16.126466293 +0200
+@@ -61,16 +61,14 @@
+ 
+ # defaults
+ F77=f77
+-FFLAGS=
+ FOPTIMFLAGS=-O
+ FDEBUGFLAGS=-g
+ FPROFILEFLAGS=-P
+ 
+ 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
++	F77 = $(FORTRANC)
++	FOPTIMFLAGS = 
++	FDEBUGFLAGS = 
+ 	FPROFILEFLAGS = -pg
+ endif
+ 
diff --git a/sci-libs/rosetta-fragments/files/3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/3.1-nnmake.patch
new file mode 100644
index 000000000000..35568bb9f805
--- /dev/null
+++ b/sci-libs/rosetta-fragments/files/3.1-nnmake.patch
@@ -0,0 +1,107 @@
+--- nnmake/make.system	2009-01-09 16:07:59.000000000 +0100
++++ nnmake/make.system.new	2009-04-09 10:54:50.000000000 +0200
+@@ -62,10 +62,9 @@
+ FPROFILEFLAGS=-P
+ 
+ ifeq ($(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
++	F77 = $(FORTRANC)
++	FOPTIMFLAGS = 
++	FDEBUGFLAGS = 
+ 	FPROFILEFLAGS = -pg
+ endif
+ 
+--- nnmake/dipolar_nn.f	2009-01-09 16:08:00.000000000 +0100
++++ nnmake/dipolar_nn.f.new	2009-04-09 11:06:24.923302302 +0200
+@@ -1396,7 +1396,7 @@
+             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
+--- nnmake/make.system	2009-04-09 11:10:34.399945087 +0200
++++ nnmake/make.system.new	2009-04-09 11:19:41.287390259 +0200
+@@ -55,7 +55,6 @@
+ 
+ # defaults
+ F77=f77
+-FFLAGS=
+ FOPTIMFLAGS=-O
+ FDEBUGFLAGS=-g
+ FPROFILEFLAGS=-P
+--- nnmake/makefile	2009-01-09 16:08:00.000000000 +0100
++++ nnmake/makefile.new	2009-04-09 11:22:43.454037887 +0200
+@@ -102,7 +102,7 @@
+ # 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}
+--- nnmake/make_fragments.pl	2009-01-09 15:53:33.000000000 +0100
++++ nnmake/make_fragments.pl.new	2009-04-09 13:01:52.987174602 +0200
+@@ -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";
++$src_dir = '/';
++$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/blast-db/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/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
new file mode 100644
index 000000000000..cb8fd9197d1b
--- /dev/null
+++ b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
@@ -0,0 +1,62 @@
+ chemshift/make.system | 24 ++++++++++++------------
+ chemshift/makefile    |  2 +-
+ 2 files changed, 13 insertions(+), 13 deletions(-)
+
+diff --git a/chemshift/make.system b/chemshift/make.system
+index 53bbd38..d105802 100644
+--- a/chemshift/make.system
++++ b/chemshift/make.system
+@@ -60,18 +60,18 @@ endif
+ ########## once COMPILER is set, here are the options
+ 
+ # defaults
+-F77=f77
+-FFLAGS=
+-FOPTIMFLAGS=-O
+-FDEBUGFLAGS=-g
++F77?=f77
++FFLAGS?=
++FOPTIMFLAGS?=
++FDEBUGFLAGS?=
+ FPROFILEFLAGS=-P
+ 
+ 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
+@@ -108,9 +108,9 @@ endif
+ 
+ # Suse ppc gnu
+ ifeq ($(COMPILER),ppc)
+-	F77 = g77
+-	FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132
+-	FDEBUGFLAGS = -g -C -Mbounds
++	F77 ?= g77
++	FFLAGS += -Wall -W -ffixed-line-length-132
++	FDEBUGFLAGS += -C -Mbounds
+ 	FOPTIMFLAGS =
+ endif
+ 
+diff --git a/chemshift/makefile b/chemshift/makefile
+index 712e98f..05d3b64 100644
+--- a/chemshift/makefile
++++ b/chemshift/makefile
+@@ -64,7 +64,7 @@ regular: compile
+ # rule to compile executable
+ compile: $(BASE_NAME).$(COMPILER)
+ $(BASE_NAME).$(COMPILER) : print ${OBJS}
+-	$(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
++	$(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
+ 
+ # rule to compile object files:
+ .$(COMPILER).%.o: %.f
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}
diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml
new file mode 100644
index 000000000000..ae9ec7c5f6a4
--- /dev/null
+++ b/sci-libs/rosetta-fragments/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
new file mode 100644
index 000000000000..c659931015d9
--- /dev/null
+++ b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic prefix toolchain-funcs
+
+DESCRIPTION="Fragment library for rosetta"
+HOMEPAGE="http://www.rosettacommons.org"
+SRC_URI="rosetta3.1_fragments.tgz"
+
+LICENSE="rosetta"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )
+	sci-biology/psipred"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}"/${PN/-/_}
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${PN}.tgz and rename it to ${A}"
+	einfo "which must be placed in ${DISTDIR}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-nnmake.patch \
+		"${FILESDIR}"/${P}-chemshift.patch
+	tc-export F77
+	eprefixify nnmake/*.pl
+}
+
+src_compile() {
+	emake -C nnmake
+	emake -C chemshift
+}
+
+src_install() {
+	esvn_clean .
+
+	newbin nnmake/pNNMAKE.gnu pNNMAKE
+	newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT
+
+	dobin nnmake/*.pl
+
+	insinto /usr/share/${PN}
+	doins -r *_database
+	dodoc fragments.README nnmake/{nnmake.README,vall/*.pl} chemshift/chemshift.README
+}