Removed sci-chemistry/maxit

7 files changed, 0 insertions, 428 deletions

diff --git a/sci-chemistry/maxit/ChangeLog b/sci-chemistry/maxit/ChangeLog
deleted file mode 100644
index b912ec76276a..000000000000
--- a/sci-chemistry/maxit/ChangeLog
+++ /dev/null
@@ -1,29 +0,0 @@
-# ChangeLog for sci-chemistry/maxit
-# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maxit/ChangeLog,v 1.7 2007/03/15 17:38:54 kugelfang Exp $
-
-  15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> maxit-8.2.ebuild:
-  QA: Removed illegal use of ${ROOT}. Bug #168043
-
-  01 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Remove myself as maintainer so it goes to all of the sci-chemistry team.
-
-  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>; maxit-8.2.ebuild:
-  Keyword ~ppc.
-
-  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Update to my new email address.
-
-  23 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>; maxit-8.2.ebuild:
-  Remove redundant src_compile(), reported by ciaranm.
-
-*maxit-8.2 (20 Dec 2005)
-
-  20 Dec 2005; Donnie Berkholz <dberkholz@gentoo.org>; +files/README,
-  +files/README-source, +files/respect-cflags-and-fix-install.patch,
-  +metadata.xml, +maxit-8.2.ebuild:
-  An application for processing and curation of macromolecular structure data.
-
diff --git a/sci-chemistry/maxit/Manifest b/sci-chemistry/maxit/Manifest
deleted file mode 100644
index c8d05299940f..000000000000
--- a/sci-chemistry/maxit/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX README 1298 RMD160 4ab2a8ad7e0f564151c3aad364ede0dd122425f4 SHA1 c5ea1f61fde96180780f4b5f46b9279d4fa975c1 SHA256 a388f90bf1a14f124e2be10b00ba1a558ca3cebb1567468f74949080dfa08682
-AUX README-source 3409 RMD160 ae334a2d6961db63d2976792ed6d4b643bb65f00 SHA1 eda3034daf1482299faed86b758df736fe817e0d SHA256 92c4cbfe36e65e35decfbd7442a8e35c50beb334ef29b2f997528bbf71d49fdb
-AUX respect-cflags-and-fix-install.patch 7536 RMD160 2a312749ddd1ef76380b0f786eaf7238713cd6aa SHA1 a149473a3c42ef889373420e520bd058b01cbd3f SHA256 20f637004197d7829e6d92db968470389ff81848610965c2d6699148db66f450
-DIST pdb-extract-v1.700-prod-src.tar.gz 9081548 RMD160 c565de9af1cea09ccf0bd59527191fc76a4b7aa1 SHA1 27eedd1d46e95e7006c90694e379bdcb4f20fd92 SHA256 b35d2bf5d7f96580782a3645ab288aec1be21926bf52969f4de74d4f514a471c
-EBUILD maxit-8.2.ebuild 1464 RMD160 c40cbcb66922837567781130ee6a8e43040742cc SHA1 148c5af65214028a086f0c096bcae6b039fff3f3 SHA256 35a64f043eff513f5f78f3eb0bc7ef8b206b473a02d196b2ff9348b2a2c57eeb
-MISC ChangeLog 1205 RMD160 dee258ba28f58f53686f55cb309f0f9cf44b16e6 SHA1 0774a282c7de549bab9d3f3019d26f9bdc0835a3 SHA256 7b3dfbb6166b6228edfa64e27da29508cb17250a23866a87a52d8009a4c39387
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/maxit/files/README b/sci-chemistry/maxit/files/README
deleted file mode 100644
index 00cac52fc88a..000000000000
--- a/sci-chemistry/maxit/files/README
+++ /dev/null
@@ -1,31 +0,0 @@
-The MAXIT Program Suite was developed by the PDB (Protein Data Bank) and
-NDB (Nucleic Acid Database) to assist in the processing and curation of
-macromolecular structure data. The functions of the program suite are
-summarized as follows:
-
-(1) Reading and writing PDB and mmCIF format files, and translating between
-file formats.
-
-(2) Performing a variety of consistency checks on coordinates, sequence, and
-crystal data.
-
-(3) Constructing, transforming, and merging information between formats in
-order to minimize the human intervention during file translation and data
-processing operations.
-
-(4) Residue numbering in the coordinate section is aligned with the sequence
-
-(5) Atoms in standard and nonstandard residues and atoms in ligands are
-reordered and renamed in a standard manner. The residue and ligand description
-is held in mmCIF dictionary.
-
-(6) Detection of missing or additional atoms.
-
-
-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/maxit/files/README-source b/sci-chemistry/maxit/files/README-source
deleted file mode 100644
index 45ec67c76454..000000000000
--- a/sci-chemistry/maxit/files/README-source
+++ /dev/null
@@ -1,101 +0,0 @@
-
-             Installation and Usage Notes for the Maxit Application
-                            (Source Distribution)
-
-Note: It is highly recommended to utilize binary distribution, if possible,
-since it contains an additional submodule, called PROCHECK, which does more
-structure checking. This source distribution does not contain PROCHECK, since
-the PROCHECK module is only available in binary form. 
-
-1.  Installation
-
-a.  Uncompress and unbundle the distribution using the following command:
-
-        zcat maxit-vX.XXX-XXX.tar.gz | tar -xf - 
-
-    The result of this command is a subdirectory maxit-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 "maxit-v8.01-O"
-          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 RCSBROOT environment variable to point to the installation
-    directory. Assuming that the installation directory is
-    /home/username/maxit-vX.XXX-XXX, execute in the shell:
-
-        For C shell users:
-          setenv RCSBROOT /home/username/maxit-vX.XXX-XXX
-
-        For Bourne shell users:
-          RCSBROOT=/home/username/maxit-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 maxit-vX.XXX-XXX directory and run "make" command:
-
-        cd maxit-vX.XXX-XXX 
-        make
-
-    The application executable "maxit-v8.01-O" 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 maxit-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
-
-Maxit application supports many options for all kinds of data processing
-operations. To see all supported options, execute:
-
-    maxit-v8.01-O -
-
-For the purpose of data deposit, only three options are necessary for preparing
-the deposit file.
-
-1. This will translate a PDB format file into mmCIF format file. The output file
-name is file_name.pdb.cif (with extension .cif).
-
-    maxit-v8.01-O -i file_name.pdb -o 1 -exchange_out
-
-2. This will translate a mmCIF format file into PDB format file. The output file
-name is file_name.cif.pdb (with extension .pdb).
-
-    maxit-v8.01-O -i file_name.cif -o 2 -exchange_in
-
-3. This will update a mmCIF format file. The output file name is
-file_name.cif.cif (with extension .cif).
-
-    maxit-v8.01-O -i file_name.cif -o 8 -exchange_in -exchange_out
-
diff --git a/sci-chemistry/maxit/files/respect-cflags-and-fix-install.patch b/sci-chemistry/maxit/files/respect-cflags-and-fix-install.patch
deleted file mode 100644
index 7ab999b640eb..000000000000
--- a/sci-chemistry/maxit/files/respect-cflags-and-fix-install.patch
+++ /dev/null
@@ -1,207 +0,0 @@
-diff -ur 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 00:48:25.000000000 -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 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 00:48:25.000000000 -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 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 00:48:25.000000000 -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 =  maxit-v8.2
- 
- 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 pdb-extract-v1.700-prod-src.orig/maxit-v8.2/Makefile pdb-extract-v1.700-prod-src/maxit-v8.2/Makefile
---- pdb-extract-v1.700-prod-src.orig/maxit-v8.2/Makefile	2005-12-19 00:32:21.000000000 -0800
-+++ pdb-extract-v1.700-prod-src/maxit-v8.2/Makefile	2005-12-19 00:51:46.000000000 -0800
-@@ -33,35 +33,35 @@
- #----------------------------------------------------------------------------
- include ../etc/Makefile.platform
- 
--LIBS    = $(LIBINSTDIR)/libvalidation.a \
--          $(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
--
--LIBS1   = $(LIBINSTDIR)/liberfiolib.a \
--          $(LIBINSTDIR)/liberfutil.a \
--          $(LIBINSTDIR)/libciffileobj.a \
--          $(LIBINSTDIR)/libcifobj.a \
--          $(LIBINSTDIR)/libistable.a \
--          $(LIBINSTDIR)/libtblindex.a \
--          $(LIBINSTDIR)/libcifstr.a \
--          $(LIBINSTDIR)/libndbmisc.a
--
--LIBS2   = $(LIBINSTDIR)/liberfiolib.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)/libvalidation.a \
-+          $(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
-+
-+LIBS1   = $(LIBDIR)/liberfiolib.a \
-+          $(LIBDIR)/liberfutil.a \
-+          $(LIBDIR)/libciffileobj.a \
-+          $(LIBDIR)/libcifobj.a \
-+          $(LIBDIR)/libistable.a \
-+          $(LIBDIR)/libtblindex.a \
-+          $(LIBDIR)/libcifstr.a \
-+          $(LIBDIR)/libndbmisc.a
-+
-+LIBS2   = $(LIBDIR)/liberfiolib.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)/libmaxit.a
- #
diff --git a/sci-chemistry/maxit/maxit-8.2.ebuild b/sci-chemistry/maxit/maxit-8.2.ebuild
deleted file mode 100644
index bdc03b39a1de..000000000000
--- a/sci-chemistry/maxit/maxit-8.2.ebuild
+++ /dev/null
@@ -1,48 +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/maxit/maxit-8.2.ebuild,v 1.4 2007/03/15 17:38:54 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="An application for processing and curation of macromolecular structure data"
-HOMEPAGE="http://sw-tools.pdb.org/apps/MAXIT/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
-	sci-chemistry/validation"
-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* misclib* \
-		regex* pdb-extract* validation*
-	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/*
-	dodoc ${FILESDIR}/README*
-}
diff --git a/sci-chemistry/maxit/metadata.xml b/sci-chemistry/maxit/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a41..000000000000
--- a/sci-chemistry/maxit/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>