sci-libs/rosetta-fragments: Remove last-rited package

Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>

5 files changed, 0 insertions, 286 deletions

diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest
deleted file mode 100644
index 838f4129d740..000000000000
--- a/sci-libs/rosetta-fragments/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rosetta3.1_fragments.tgz 221931894 BLAKE2B 0fb5764f24f3386cdbce9afce7da3f81cce91a6a0a57a265e5dbe0bf06146e4ab057c02961ed0dd8074f86309257bcf5b42ca0d1c6adf92c9f8ebf36b3f25f5d SHA512 a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1
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
deleted file mode 100644
index cb8fd9197d1b..000000000000
--- a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
+++ /dev/null
@@ -1,62 +0,0 @@
- 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
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) :  ${COORD_OBJS}
diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-libs/rosetta-fragments/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
deleted file mode 100644
index bc262a212a42..000000000000
--- a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic prefix toolchain-funcs vcs-clean
-
-DESCRIPTION="Fragment library for rosetta"
-HOMEPAGE="http://www.rosettacommons.org"
-SRC_URI="rosetta3.1_fragments.tgz"
-
-LICENSE="rosetta"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	sci-biology/ncbi-tools
-	sci-biology/update-blastdb
-	sci-biology/psipred"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}"/${PN/-/_}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-nnmake.patch
-	"${FILESDIR}"/${P}-chemshift.patch
-)
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and get ${PN}.tgz and rename it to ${A}"
-	einfo "which must be placed into your DISTDIR directory."
-}
-
-src_prepare() {
-	default
-	tc-export F77
-	eprefixify nnmake/*.pl
-}
-
-src_compile() {
-	emake -C nnmake
-	emake -C chemshift
-}
-
-src_install() {
-	esvn_clean .
-
-	newbin nnmake/pNNMAKE.gnu pNNMAKE
-	newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT
-
-	dobin nnmake/*.pl
-
-	insinto /usr/share/${PN}
-	doins -r *_database
-	dodoc \
-		fragments.README \
-		nnmake/{nnmake.README,vall/*.pl} \
-		chemshift/chemshift.README
-}