Remove sci-chemistry/validation

7 files changed, 0 insertions, 440 deletions

diff --git a/sci-chemistry/validation/ChangeLog b/sci-chemistry/validation/ChangeLog
deleted file mode 100644
index f73de1d40cc2..000000000000
--- a/sci-chemistry/validation/ChangeLog
+++ /dev/null
@@ -1,48 +0,0 @@
-# ChangeLog for sci-chemistry/validation
-# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/validation/ChangeLog,v 1.10 2007/03/15 22:01:27 kugelfang Exp $
-
-  15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> validation-6.2.ebuild:
-  QA: Removed illegal use of ${ROOT}. Bug #168043
-
-  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  (#148281) Change herd to sci-chemistry from sci.
-
-  07 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>;
-  validation-6.2.ebuild:
-  Keyword ~ppc.
-
-  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Remove myself as maintainer, anyone feel free to work on this, although I'll
-  continue to do so as well.
-
-  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Update to my new email address.
-
-  15 Jun 2006; Donnie Berkholz <dberkholz@gentoo.org>;
-  validation-6.2.ebuild:
-  Drop acronym in description.
-
-  23 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>;
-  validation-6.2.ebuild:
-  Remove redundant src_compile(), reported by ciaranm.
-
-*validation-6.2 (20 Dec 2005)
-
-  20 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>; +files/README,
-  +files/README-source, +files/respect-cflags-and-fix-install.patch,
-  -files/respect-flags-and-add-gcc4.patch, +validation-6.2.ebuild,
-  -validation-8.061.ebuild:
-  Add a fixed version; works with other RCSB apps and libraries.
-
-  19 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>;
-  validation-8.061.ebuild:
-  Remove commented-out sections.
-
-*validation-8.061 (19 Dec 2005)
-
-  19 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>;
-  +files/respect-flags-and-add-gcc4.patch, +metadata.xml,
-  +validation-8.061.ebuild:
-  Add a set of tools used by the PDB for processing and checking structure data.
-
diff --git a/sci-chemistry/validation/Manifest b/sci-chemistry/validation/Manifest
deleted file mode 100644
index b7a7b409c13a..000000000000
--- a/sci-chemistry/validation/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX README 688 RMD160 eb7edefdf163c829024bd4fded22fb64a6a8f589 SHA1 6605d8cccc1b7c6cc9eb1f85d150fca718a0a9a9 SHA256 8edeb6d336f4fcb27d3d04b0e7460cc99008309ce3d9755810ddf1117355ca2b
-AUX README-source 5259 RMD160 725754b51f08f8d13fd6eab0b8e84eaefb5ef67a SHA1 95edb6a587c430d0b8ba9ea582a98e1c6023f41c SHA256 cd224e701094858b84b56e471bbd67c29c6071be2efddc36c4ecb55996f872d5
-AUX respect-cflags-and-fix-install.patch 6330 RMD160 5e37c7ec65a0e6032760d121c463a7c5b7c5b28f SHA1 61dee3878be27012eb9669fe224413335ccb4923 SHA256 40df5558ac2bccc6f63e1a1dc8a5af8089c2f6bb1185df377a89ae106a05b751
-DIST pdb-extract-v1.700-prod-src.tar.gz 9081548 RMD160 c565de9af1cea09ccf0bd59527191fc76a4b7aa1 SHA1 27eedd1d46e95e7006c90694e379bdcb4f20fd92 SHA256 b35d2bf5d7f96580782a3645ab288aec1be21926bf52969f4de74d4f514a471c
-EBUILD validation-6.2.ebuild 1501 RMD160 8e2c698c9a046ed61f38bb3a5733f816b2965dd7 SHA1 1c473ffdee81e676293d9803798627c5b0c307f2 SHA256 a4ffed7cf551a0a0db3a2f9150cccf9a4534f6cb86685277ed8fd0e28ad5b9ef
-MISC ChangeLog 1802 RMD160 813031d2161ae328e2ad655809beb8d3f9d3d870 SHA1 14c384d15d8b63481f3a839c797a4a4b5dbfa995 SHA256 dd03a780bfa7b83f102212bb7cf6e1bf3a989c6c44da52651db177806cc69cd9
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/validation/files/README b/sci-chemistry/validation/files/README
deleted file mode 100644
index a0d2fbc07b11..000000000000
--- a/sci-chemistry/validation/files/README
+++ /dev/null
@@ -1,14 +0,0 @@
-The PDB Validation Suite is a set of applications programs that create
-validation reports about 3D structure data.  It is designed to work
-with files in mmCIF or PDB format.
-
-This is the same software used in the Validation step of ADIT (AutoDep
-Input Tool) at http://pdb.rutgers.edu/adit/.
-
-Note: Binary distribution of this tool contains an additional submodule
-"procheck", which does additional structure checking. This submodule is
-not part of the source distribution. Therefore the users are advised to
-use the binary distribution, if possible.
-
-Refer to README-source or README-binary, depending on the distribution, for
-details on installation, build, demos and application usage.
diff --git a/sci-chemistry/validation/files/README-source b/sci-chemistry/validation/files/README-source
deleted file mode 100644
index 28ed96b06139..000000000000
--- a/sci-chemistry/validation/files/README-source
+++ /dev/null
@@ -1,150 +0,0 @@
-             Installation and Usage Notes for the Validation Application
-                            (Source Distribution)
-
-Note: It is highly recommended to utilize binary distribution,
-since it contains an additional submodule, called PROCHECK, which does more
-structure checking. This source distribution does not contain PROCHECK.
-
-1.  Installation
-
-a.  Uncompress and unbundle the distribution using the following command:
-
-        zcat validation-vX.XXX-XXX.tar.gz | tar -xf - 
-
-    The result of this command is a subdirectory validation-vX.XXX-XXX in the
-    current directory. It contains subdirectories of various source modules
-    and the following items important for the user:
-
-        bin - subdirectory in which the application executable "validation-v8"
-          will be placed after the build process.
-        data - subdirectory that contains some data files needed by the
-          application. 
-
-
-b.  Set up the environment variables.
-
-    - Define the RCSBROOT environment variable to point to the installation
-    directory.  Note that the RCSBROOT environment is also used for other RCSB
-    applications like ADIT and PDB_EXTRACT. If all these applications are
-    running on a computer, the last instance of setenv command will define the
-    environment. Thus, set the environment at the command line as follows,
-    just prior to running the application. Assuming that the installation
-    directory is
-
-    /home/username/validation-vX.XXX-XXX, execute in the shell:
-
-        For C shell users:
-          setenv RCSBROOT /home/username/validation-vX.XXX-XXX
-
-        For Bourne shell users:
-          RCSBROOT=/home/username/validation-vX.XXX-XXX; export RCSBROOT
-
-    - Add "bin" subdirectory to the PATH environment variable.
-    Execute in the shell:
-
-        For C shell users:
-          setenv PATH "$RCSBROOT/bin:"$PATH
-
-        For Bourne shell users:
-          PATH="$RCSBROOT/bin:"$PATH; export PATH
-
-
-2.  Building the Application
-
-a.  Position in the validation-vX.XXX-XXX directory and run "make" command:
-
-        cd validation-vX.XXX-XXX 
-        make
-
-    The application executable "validation-v8" will be placed in the "bin"
-    subdirectory.
-
-
-    NOTE: The users who are working on Sun platform are strongly advised to
-    check the compiler flags in etc/make.platform.sunos5 file. Depending on
-    the compiler version, users may be required to make modifications to those
-    compiler flags.
-
-b.  Make binary data from ASCII data
-
-    - Position in the validation-vX.XXX-XXX directory and run "make" command as
-    follows:
-
-        make binary
-
-    This command will create certain binary data files, using the ASCII data
-    files in data/ascii directory. The resulting files are stored in
-    data/binary directory. Note that it may take several minutes for this
-    step to complete. This step must be executed before the tool can be
-    utilized.
-
-
-3.  Application Usage Notes
-
-Usage:
-
-For mmCIF files (Please note, only mmCIF format files downloaded from the PDB
-or generated by PDB_EXTRACT should be used):
-
-    validation-v8 -f file_name -o 2 -adit -exchange -public
-
-For PDB files:
-
-    validation-v8 -f file_name -o 0 -adit
-
-
-For example, to create reports for a file in mmCIF format named 1xyz.cif
-type:
-
-    validation-v8 -f 1xyz.cif -o 2 -adit -exchange -public
-
-Output:
-
-The names of the output files begin with the root identifier <ID>,
-which is followed by an extension that indicates the file type.
-
-For a PDB format file, the program converts the file name without 
-extension into uppercase for the <ID>. For an mmCIF format file, the program 
-uses data block identifier as the <ID>. 
-
-The application creates the following files:
-
-A. <ID>.letter: a text file that contains a summary validation letter.
-
-B. <ID>.ps: a PostScript file that contains molecular graphics of the structure.  
-For crystal structures, this includes a view of the asymmetric unit 
-and crystal packing.  If the mmCIF file was validated and the biological unit
-of the entry is either larger or smaller than the asymmetric unit, and the
-struct_biol_gen category was appropriately completed in the mmCIF 
-file, then a view of the biological unit(s) will be included. 
-
-For NMR ensemble structures, a view of the first model and the ensemble
-of all models is included.  If the NMR entry contains one model, a view
-of the model will be included.
-
-NUCHECK output: If the structure contains nucleic acids, the <ID>.ps file 
-also includes plots describing the geometry, torsion, and base morphology of 
-the nucleic acids generated by the program NUCHECK.
-
-C.  <ID>.html:  This html file is an Atlas summary containing the following:
-
-For all structures:
-The sequence of the residues in each chain (from entity_poly for a mmCIF file,
-from SEQRES for a PDB file, or from the coordinates if entity_poly or SEQRES 
-are not provided).
-Citation information (if provided).
-Refinement information (if provided).
-
-For crystal structures, additional information is listed:
-Space group and cell constants.
-Crystallization conditions (if provided).
-Refinement information (if provided).
-
-3. REFERENCES
-
-NUCHECK:
-Zukang Feng, John Westbrook, Helen M. Berman. NUCheck: Rutgers University,
-New Brunswick, NJ; 1998.  Report No.: NDB-407.
-
-
-
diff --git a/sci-chemistry/validation/files/respect-cflags-and-fix-install.patch b/sci-chemistry/validation/files/respect-cflags-and-fix-install.patch
deleted file mode 100644
index 623efd194fb9..000000000000
--- a/sci-chemistry/validation/files/respect-cflags-and-fix-install.patch
+++ /dev/null
@@ -1,167 +0,0 @@
-diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3 pdb-extract-v1.700-prod-src/etc/make.platform.gnu3
---- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu3	2005-12-19 00:32:21.000000000 -0800
-+++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu3	2005-12-19 00:33:04.000000000 -0800
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR= /usr/lib
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -89,7 +91,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES= -I/usr/include/rcsb
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -107,8 +109,8 @@
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-                $(INCLUDES) 
- 
- ## C++ compiler
-@@ -128,9 +130,9 @@
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-         $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-                  $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -144,7 +146,7 @@
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4 pdb-extract-v1.700-prod-src/etc/make.platform.gnu4
---- pdb-extract-v1.700-prod-src.orig/etc/make.platform.gnu4	2005-12-19 00:32:21.000000000 -0800
-+++ pdb-extract-v1.700-prod-src/etc/make.platform.gnu4	2005-12-19 00:33:04.000000000 -0800
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
- 
-+LIBDIR= /usr/lib
-+
- #-----Lexer and Parser section-------------------------------------------#
- 
- # Lexer executable
-@@ -34,7 +36,7 @@
- 
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
- # warnings as errors.
--WARNINGS_AS_ERRORS=-Werror
-+WARNINGS_AS_ERRORS=
- 
- # ALL_WARNINGS defines flags to instruct all compilers to report all
- # warnings.
-@@ -90,7 +92,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
- 
- ## Global include directories
--GINCLUDES= 
-+GINCLUDES= -I/usr/include/rcsb
- 
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -108,8 +110,8 @@
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-                $(INCLUDES) 
- 
- ## C++ compiler
-@@ -129,9 +131,9 @@
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-         $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-                  $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -145,7 +147,7 @@
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/Makefile pdb-extract-v1.700-prod-src/Makefile
---- pdb-extract-v1.700-prod-src.orig/Makefile	2005-12-19 00:32:21.000000000 -0800
-+++ pdb-extract-v1.700-prod-src/Makefile	2005-12-19 00:33:04.000000000 -0800
-@@ -22,10 +22,7 @@
- 
- DATADIRS = data pdb-extract-data
- 
--LIBDIRS =  misclib-v2.1 regex-v2.1 ciflib-common-v3.02 cifobj-common-v4.04 \
--           btree-obj-v3.1 cif-table-obj-v6.1 cifparse-obj-v6.3 \
--           htmllib-v3.1 connect-v2.2 filterlib-v8.2 $(EXTRACT) \
--           validation-v6.2 maxit-v8.2
-+LIBDIRS =  validation-v6.2
- 
- all:	compile
- 
-@@ -60,7 +57,7 @@
- 		echo "------------------------------------------------------------"; \
- 		echo "**** Making $$libdir ****"; \
- 		echo "------------------------------------------------------------"; \
--		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
-+		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" install) || exit 1; \
- 	done
- 
- binary:
-diff -ur -x Makefile.platform pdb-extract-v1.700-prod-src.orig/validation-v6.2/Makefile pdb-extract-v1.700-prod-src/validation-v6.2/Makefile
---- pdb-extract-v1.700-prod-src.orig/validation-v6.2/Makefile	2005-12-19 00:32:21.000000000 -0800
-+++ pdb-extract-v1.700-prod-src/validation-v6.2/Makefile	2005-12-19 00:33:43.000000000 -0800
-@@ -35,15 +35,15 @@
- #----------------------------------------------------------------------------
- #  Target definitions.
- #----------------------------------------------------------------------------
--LIBS    = $(LIBINSTDIR)/libndbfilter.a \
--          $(LIBINSTDIR)/libconnect.a \
--          $(LIBINSTDIR)/libciffileobj.a \
--          $(LIBINSTDIR)/libcifobj.a \
--          $(LIBINSTDIR)/libistable.a \
--          $(LIBINSTDIR)/libregex.a \
--          $(LIBINSTDIR)/libtblindex.a \
--          $(LIBINSTDIR)/libcifstr.a \
--          $(LIBINSTDIR)/libndbmisc.a
-+LIBS    = $(LIBDIR)/libndbfilter.a \
-+          $(LIBDIR)/libconnect.a \
-+          $(LIBDIR)/libciffileobj.a \
-+          $(LIBDIR)/libcifobj.a \
-+          $(LIBDIR)/libistable.a \
-+          $(LIBDIR)/libregex.a \
-+          $(LIBDIR)/libtblindex.a \
-+          $(LIBDIR)/libcifstr.a \
-+          $(LIBDIR)/libndbmisc.a
- 
- NDBLIB  = $(LIB)/libvalidation.a
- 
diff --git a/sci-chemistry/validation/metadata.xml b/sci-chemistry/validation/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a41..000000000000
--- a/sci-chemistry/validation/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/validation/validation-6.2.ebuild b/sci-chemistry/validation/validation-6.2.ebuild
deleted file mode 100644
index cc6410b436ce..000000000000
--- a/sci-chemistry/validation/validation-6.2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/validation/validation-6.2.ebuild,v 1.5 2007/03/15 22:01:27 kugelfang Exp $
-
-inherit eutils toolchain-funcs multilib
-
-# pdb-extract includes a newer 'validation' than 'validation' tarball does,
-# and the filterlib from pdb-extract is incompatible with the validation tarball
-MY_PN="pdb-extract"
-MY_PV="1.700"
-MY_P="${MY_PN}-v${MY_PV}-prod-src"
-DESCRIPTION="Set of tools used by the Protein Data Base (PDB) for processing and checking structure data"
-HOMEPAGE="http://sw-tools.pdb.org/apps/VAL/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE=""
-RDEPEND="sci-libs/rcsb-data"
-DEPEND="${RDEPEND}
-	sci-chemistry/pdb-extract"
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
-	unpack ${A}
-	epatch ${FILESDIR}/respect-cflags-and-fix-install.patch
-	cd ${S}
-
-	# Get rid of unneeded directories, to make sure we use system files
-	ebegin "Deleting redundant directories"
-	rm -rf btree-obj* ciflib-common* cifobj-common* cif-table-obj* maxit* \
-		misclib* regex* pdb-extract*
-	eend
-
-	sed -i \
-		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
-		-e "s:^\(GINCLUDE=\).*:\1-I/usr/include/rcsb:g" \
-		-e "s:^\(LIBDIR=\).*:\1/usr/$(get_libdir):g" \
-		${S}/etc/make.*
-}
-
-src_install() {
-	exeinto /usr/bin
-	doexe bin/*
-	dolib.a lib/*
-	insinto /usr/include/rcsb
-	doins include/*
-	dodoc ${FILESDIR}/README*
-}