reinit the tree, so we can have metadata

5 files changed, 286 insertions, 0 deletions

diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest
new file mode 100644
index 000000000000..a4b4008cb433
--- /dev/null
+++ b/sci-libs/rosetta-fragments/Manifest
@@ -0,0 +1,7 @@
+AUX rosetta-fragments-3.1-chemshift.patch 1721 SHA256 02ab89d1d762c65653c6582481f5ece77c57d79c79bc6b16609c522ceafcbb49 SHA512 3475a4fd7a433d4d380ccd5ab11cf32f326fafc828d1bead0dbb0e03f5e53c613bf57c7950e090d8a2eb34c4ba93ecf25b25afcc9f251ff5f943e6b7e3112bb1 WHIRLPOOL d86a5147f7be585bcae825f0ab03eac84ab173aa781351ac4414cfd9ddc0329815097609beb2fc54a88636e3cb277894fe1ad73d5bda77d6d6cb528365fd594a
+AUX rosetta-fragments-3.1-nnmake.patch 7030 SHA256 cfb08b00ee66e4342afda54129c735358b3fbd6a70ef88647b9ca18d96ce33b1 SHA512 de6d41f68911a5beddc8a15c9ce33013b03462642229aaf3b09ae4123c281260fa725bbd55593eea305b05d2ed21e1d17394686ee4e42bda20825d71d9367501 WHIRLPOOL 8ae1e9b64c3842e2091bc0cac434673f40ca8e0512ee417a78eeb4ea11c2c48368aa1bf1547843cb26e41c2c5f1e49e6ce3e4487d1b53e248f496db2a07ef5ed
+DIST rosetta3.1_fragments.tgz 221931894 SHA256 2211cab76e4848d80d6fd311e97535de220a865d8afc72d8ca12f90b7d4641bf SHA512 a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1 WHIRLPOOL 32d0758e6782da8088178e11af5bfe23b457e98a3ab9a8cbb583d4e4aa48e5d1ef9005825ff62944c5c755a0ac99b3ff88fb7c1d1b249940110287969ff0118a
+EBUILD rosetta-fragments-3.1-r1.ebuild 1133 SHA256 2447cade451d79957ac718d4abff4c7e266949c2866d3a1506f538e21df30750 SHA512 7d424dcfeed1d073c27c2ba5a86d75877c597bfea95f40ab7acff767d41786b66576dbedb0a626e84d00ca63cd0f9131227d3ff200c35ad6b4d33ff485be5ab7 WHIRLPOOL 1c9b9e8eae47c7bab86c8264b438b3050f0542658eb4dcaeeed2fc09fe303f00f26bc52cf7581836332cf347a8d321676593fe4970494730c1a08f4375f21d19
+MISC ChangeLog 2747 SHA256 f27e11f976b2e5f1e144b14a1cdcd603c97d21ea27919a1a99ab7125dfe499b1 SHA512 62a4ec9d7aa0a05a074083ebf74295be4d608317cd86c66b0b46b7932da02388b1fa095b03472e04432d2993670c8e6e602bea31ecd90ed20037621d328e9172 WHIRLPOOL a57ed1ba5934098532e525b2071bdbf1b9e4c66c0d0099acbfe3dcee4909e0331d75838909e2b4c1f95f9dd5ff4b7f932ba2c43cad708c5931f1acf3612fad7b
+MISC ChangeLog-2015 1336 SHA256 83a5ea22bb3a9e8e19728f9c48c63adca8912fd367264f98f1c8ad258b674c92 SHA512 74f65c0d5dd99e7fa1d5b0c569917f7d4b66f169f1dbacbaaf91d3151f46b3befc1d75bbe79f26a1f58f370daedc25f337482c6405f6a4ed77e1708478467a3a WHIRLPOOL 9ab4b9cc9d0246d7433d73b864cfd11536d76543f46fa53cf5c2393e386e1c731c670631cd6491d4ef8d686357bb66c812736f811341c5b37892c9aa32165569
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
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) :  ${COORD_OBJS}
diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-libs/rosetta-fragments/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
new file mode 100644
index 000000000000..055c225edf1d
--- /dev/null
+++ b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic prefix toolchain-funcs
+
+DESCRIPTION="Fragment library for rosetta"
+HOMEPAGE="http://www.rosettacommons.org"
+SRC_URI="rosetta3.1_fragments.tgz"
+
+LICENSE="rosetta"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )
+	sci-biology/psipred"
+
+RESTRICT="fetch"
+
+S="${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
+}