QA: Removed unused versions.

Package-Manager: portage-2.1.2_pre2-r1

31 files changed, 98 insertions, 1197 deletions

diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest
index 7b727ad135ca..5ca591fd97c8 100644
--- a/sci-chemistry/gamess/Manifest
+++ b/sci-chemistry/gamess/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX comp-lked-20060222.2.patch 3547 RMD160 a8b1a0a2e671ded8ea6dc72880c6858822cb88f2 SHA1 27f5451cde2f332bc29b669afbc084de0402b748 SHA256 1cca96ac59a1756f25c90efae67bfa00606dbfb97722054ba322b0e66d0c0206
 MD5 f35051be79ba967ce07ad02fcbcbccb1 files/comp-lked-20060222.2.patch 3547
 RMD160 a8b1a0a2e671ded8ea6dc72880c6858822cb88f2 files/comp-lked-20060222.2.patch 3547
@@ -22,35 +25,26 @@ AUX rungms-runall-20060222.2.patch 2293 RMD160 22b884e347d08a2041006a7789a7e9daf
 MD5 8088ad360fe8b034b5b36deeac7a9a3b files/rungms-runall-20060222.2.patch 2293
 RMD160 22b884e347d08a2041006a7789a7e9daf3d83483 files/rungms-runall-20060222.2.patch 2293
 SHA256 6b995a78ca1b74e2936f553e8cc286303211d040c9f35a8c540f4b8ce88ae331 files/rungms-runall-20060222.2.patch 2293
-DIST gamess-20060222.2.tar.gz 6438153 RMD160 e833f0562591ac1bc56b88653012733e63025b6f SHA1 f31cd02beb8e3f38772be416a7d1d6c7bee9a579 SHA256 480c21c3c684fe384cb6612438b9e2112588ce7518a3fe1c82643e8a69edc304
-DIST gamess-20060222.5.tar.gz 7546444 RMD160 3c0c0f758578106c5ae74a12a8c18d663cc81291 SHA1 adb7e923f4308d211ba87208aeec7ee2d9a263fe SHA256 a383ce26a770c7ad0d5107f470f0baae80e45778e0f8b2c7a10a57e4aa3f662c
 DIST gamess-20060907.4.tar.gz 7864905 RMD160 6e01ab4aabc41980fff74b512ef3b952a5e3f0c8 SHA1 f48ad18115b24861fffdc16cebe97e6b1ed80091 SHA256 8361f50e18ce5301e42375f820d8c41297ca1639fe02441c0a376b19d5e61ea9
-EBUILD gamess-20060222.2.ebuild 7646 RMD160 a420b964d1f966cc0671e85b9ca93476edbde1bc SHA1 44b5d3461fc3488c32fa224d7d890e9d9a18ca95 SHA256 b62a9d4c6995f792e14b6a66d55360a7ced3dc43682d6b154cf7bc0636ff9539
-MD5 7ec74a1330233f8db990fee265d8badd gamess-20060222.2.ebuild 7646
-RMD160 a420b964d1f966cc0671e85b9ca93476edbde1bc gamess-20060222.2.ebuild 7646
-SHA256 b62a9d4c6995f792e14b6a66d55360a7ced3dc43682d6b154cf7bc0636ff9539 gamess-20060222.2.ebuild 7646
-EBUILD gamess-20060222.5.ebuild 6160 RMD160 e015c592facca2de9ae4a3dbaa6f00bf0118be42 SHA1 761eca7fb5d402c952ac84609101717457882568 SHA256 43e567cceb37f5318a752e6f66cb8eb6e08474430e56ae2118bf4eed01f3d5fe
-MD5 8c91c53032104a1a9789e2c00aeea8b9 gamess-20060222.5.ebuild 6160
-RMD160 e015c592facca2de9ae4a3dbaa6f00bf0118be42 gamess-20060222.5.ebuild 6160
-SHA256 43e567cceb37f5318a752e6f66cb8eb6e08474430e56ae2118bf4eed01f3d5fe gamess-20060222.5.ebuild 6160
 EBUILD gamess-20060907.4.ebuild 6389 RMD160 4a54c20a380ed94502bd6e2d43f1169139db81db SHA1 21bfaa151b199fc0d2e1aad31072338f6f372182 SHA256 e9464dd66c6e2ef6c04c89eb5b7efe82cc53055c7df848b60c47b106401c747c
 MD5 735849b937e40986b685994c6968064c gamess-20060907.4.ebuild 6389
 RMD160 4a54c20a380ed94502bd6e2d43f1169139db81db gamess-20060907.4.ebuild 6389
 SHA256 e9464dd66c6e2ef6c04c89eb5b7efe82cc53055c7df848b60c47b106401c747c gamess-20060907.4.ebuild 6389
-MISC ChangeLog 4704 RMD160 eb7a17b3c93dc1fcba08449095c682e9e760cd28 SHA1 ca9a0d11cb5cd131a5442a7acb555c0cdf0f4718 SHA256 63fdc3e572e28755365157095448922ad924a1b72c9f066bb32c167ada956237
-MD5 1060f419102707f5a2f92d5e4b042460 ChangeLog 4704
-RMD160 eb7a17b3c93dc1fcba08449095c682e9e760cd28 ChangeLog 4704
-SHA256 63fdc3e572e28755365157095448922ad924a1b72c9f066bb32c167ada956237 ChangeLog 4704
+MISC ChangeLog 4845 RMD160 86098f8474ec0c04b2177da1c5448afe0eb4e9af SHA1 5634ed67ed4892d5fd8c6566418f6eee956f69fb SHA256 b08ce552954af0d7481c9d5c04b3c43e3b0cf4eea12dd4cd97e08557817736cc
+MD5 78c0378f3625270cb95e841257317b8c ChangeLog 4845
+RMD160 86098f8474ec0c04b2177da1c5448afe0eb4e9af ChangeLog 4845
+SHA256 b08ce552954af0d7481c9d5c04b3c43e3b0cf4eea12dd4cd97e08557817736cc ChangeLog 4845
 MISC metadata.xml 264 RMD160 f2d7d7c401f209aec88c85770c5d1fc73ee66c89 SHA1 90b72142265c0cf5b2e2c37f6d14209fc12de279 SHA256 a6dba0fee2e8489ae831c04e7240ee646ac65c2333485a3ae46da9ed000c4d9f
 MD5 77147e914a4b31a9394148a47cccbf2d metadata.xml 264
 RMD160 f2d7d7c401f209aec88c85770c5d1fc73ee66c89 metadata.xml 264
 SHA256 a6dba0fee2e8489ae831c04e7240ee646ac65c2333485a3ae46da9ed000c4d9f metadata.xml 264
-MD5 48cee4f6d91822b3ecd488c91faa8edc files/digest-gamess-20060222.2 256
-RMD160 fe5736ffd391b5bbb8c2b0fd0ca1cc8f16d6289f files/digest-gamess-20060222.2 256
-SHA256 d4dfab6eb88cc38fcf5528e937579905ab4d21ed7d8e6947871d53a12e0c8b21 files/digest-gamess-20060222.2 256
-MD5 8d7a30849b18431a71e82c57c33114cf files/digest-gamess-20060222.5 256
-RMD160 e522464f96aded4ee678c21d15f6b8aa236b89fa files/digest-gamess-20060222.5 256
-SHA256 374123c0ff566869b45c0513e8aefddea579f42be9c7d9794d69956f1fa04465 files/digest-gamess-20060222.5 256
 MD5 b68f0d67985e27d9dd87e253b24562b0 files/digest-gamess-20060907.4 256
 RMD160 dee7f73ba970a9f2752d051bfe5b9fb63a64ccf2 files/digest-gamess-20060907.4 256
 SHA256 9d599766437686873907e88b32e456763da018fb1c3a10291e5c34a8802dac9e files/digest-gamess-20060907.4 256
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFiU5mJXAu5GbtIRAqPQAJ9OJnsWBe2TpFIBdKvNVPVYrwiCFQCfUmkI
+ruFpkBmBBeVTCSTEI2Z1IBI=
+=Taax
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gamess/files/digest-gamess-20060222.2 b/sci-chemistry/gamess/files/digest-gamess-20060222.2
deleted file mode 100644
index 6880ae0f9c7e..000000000000
--- a/sci-chemistry/gamess/files/digest-gamess-20060222.2
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 d488b090c8b5001c5c22a06f4fe06997 gamess-20060222.2.tar.gz 6438153
-RMD160 e833f0562591ac1bc56b88653012733e63025b6f gamess-20060222.2.tar.gz 6438153
-SHA256 480c21c3c684fe384cb6612438b9e2112588ce7518a3fe1c82643e8a69edc304 gamess-20060222.2.tar.gz 6438153
diff --git a/sci-chemistry/gamess/files/digest-gamess-20060222.5 b/sci-chemistry/gamess/files/digest-gamess-20060222.5
deleted file mode 100644
index 93b4855cee72..000000000000
--- a/sci-chemistry/gamess/files/digest-gamess-20060222.5
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 c39a64ddba87dffb8ac54db859565a70 gamess-20060222.5.tar.gz 7546444
-RMD160 3c0c0f758578106c5ae74a12a8c18d663cc81291 gamess-20060222.5.tar.gz 7546444
-SHA256 a383ce26a770c7ad0d5107f470f0baae80e45778e0f8b2c7a10a57e4aa3f662c gamess-20060222.5.tar.gz 7546444
diff --git a/sci-chemistry/gamess/gamess-20060222.2.ebuild b/sci-chemistry/gamess/gamess-20060222.2.ebuild
deleted file mode 100644
index ba0a973fe03d..000000000000
--- a/sci-chemistry/gamess/gamess-20060222.2.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20060222.2.ebuild,v 1.7 2006/06/30 14:33:50 markusle Exp $
-
-inherit eutils toolchain-funcs fortran flag-o-matic
-
-DESCRIPTION="A powerful quantum chemistry package"
-LICENSE="gamess"
-HOMEPAGE="http://www.msg.ameslab.gov/GAMESS/GAMESS.html"
-SRC_URI="${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE="hardened blas"
-
-RESTRICT="fetch"
-
-DEPEND="app-shells/tcsh
-	hardened? ( sys-apps/paxctl )
-	blas? ( virtual/blas )"
-
-RDEPEND="app-shells/tcsh
-	net-misc/openssh"
-
-S="${WORKDIR}/${PN}"
-
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
-GAMESS_VERSION="22 FEB 2006 (R2)"
-FORTRAN="ifc g77 gfortran"
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${PN}-current.tar.gz from"
-	einfo "${GAMESS_DOWNLOAD}."
-	einfo "Be sure to select the version ${GAMESS_VERSION} tarball!!"
-	einfo "Then move the tarball to"
-	einfo "${DISTDIR}/${P}.tar.gz"
-	echo
-}
-
-pkg_setup() {
-	fortran_pkg_setup
-
-	# blas and ifc don't go together
-	if use blas && [[ "${FORTRANC}" = "ifc" ]]; then
-		echo
-		ewarn "${PN} can not be compiled with USE=blas and ifc."
-		ewarn "Linking against GAMESS' internal blas instead."
-		echo
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-
-	# apply LINUX-arch patches to gamess makesfiles
-	epatch "${FILESDIR}"/comp-lked-20060222.2.patch
-	epatch "${FILESDIR}"/ddi-use-ssh-gentoo.patch
-	epatch "${FILESDIR}"/rungms-runall-20060222.2.patch
-	epatch "${FILESDIR}"/gamess-glibc-2.4-gentoo.patch
-
-	# for hardened-gcc let't turn off ssp, since it breakes
-	# a few routines
-	cd "${S}"
-	if use hardened && [[ "${FORTRANC}" = "g77" ]]; then
-		FFLAGS="${FFLAGS} -fno-stack-protector-all"
-	fi
-
-	# some fixes for gfortan; 
-	# also append -w otherwise we get flooded with Hollerith 
-	# constant warnings
-	if [[ "${FORTRANC}" == "gfortran" ]]; then
-		FFLAGS="${FFLAGS} -w"
-
-		sed -e "s|-fno-move-all-movables|-w|g" \
-			-e "s|*F2C|*F77|g" \
-			-e "s|-Wno-globals -fno-globals||g" \
-			-i comp || die "Failed removing compile flags"
-
-		# need to use _gfortran_ namespace
-		sed -e "s|iargc_|_gfortran_iargc|g" \
-			-e "s|getarg_|_gfortran_getarg_i4|g" \
-			-i ddi/src/ddi_fortran.c || \
-			die "Failed to fix gfortran namespace in ddi_fortran.c"
-	fi
-
-	# greate proper activate sourcefile 
-	cp "./tools/actvte.code" "./tools/actvte.f" || \
-		die || "Failed to create actvte.f"
-	sed -e "s/^\*UNX/    /" -i "./tools/actvte.f" || \
-		die || "Failed to perform UNX substitutions in actvte.f"
-
-	# fix GAMESS' compall script to use proper CC
-	sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
-		-i compall || die "Failed setting up compall script"
-
-	# insert proper FFLAGS into GAMESS' comp makefile
-	# in case we're using ifc let's strip all the gcc
-	# specific stuff
-	if [[ "${FORTRANC}" == "ifc" ]]; then
-		sed -e "s/-malign-double -fautomatic /-cm -w \$MODULE.f/" \
-			-e "s/-Wno-globals -fno-globals \$MODULE.f//" \
-			-e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
-			-e "s/gentoo-g77/${FORTRANC}/" \
-			-i comp || die "Failed setting up comp script"
-	elif ! use x86; then
-		sed -e "s/-malign-double //" \
-			-e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
-			-e "s/gentoo-g77/${FORTRANC}/" \
-			-i comp || die "Failed setting up comp script"
-	else
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
-			-e "s/gentoo-g77/${FORTRANC}/" \
-			-i comp || die "Failed setting up comp script"
-	fi
-
-	# use proper blas 
-	if ! use blas || [[ "${FORTRANC}" = "ifc" ]]; then
-		sed -e "s|/usr/lib/libblas.a|/usr/lib/dontuselibblas.a|" \
-			-i lked || die "Failed to adjust blas in lked"
-	fi
-
-	# fix up GAMESS' linker script;
-	if [[ "${FORTRANC}" == "ifc" ]]; then
-		sed -e "s/gentoo-LDR='g77'/LDR='${FORTRANC}'/" \
-			-e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
-			-i lked || die "Failed setting up lked script"
-	else
-		sed -e "s/gentoo-LDR='g77'/LDR='${FORTRANC}'/" \
-			-e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
-			-i lked || die "Failed patching lked script"
-	fi
-
-	# fix up GAMESS' ddi TCP/IP socket build
-	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
-		-i ddi/compddi || die "Failed setting up compddi script"
-
-	# for ifc/gcc-4.x we have to fix the number of underscores of 
-	# fortran symbols, otherwise the linker will barf
-	if [[ "${FORTRANC}" == "ifc" ]] || \
-		[[ $(gcc-major-version) -ge 4 ]]; then
-		sed -e "s/gentoo-F77_OPTS = '-DINT_SIZE=int -D_UNDERSCORES=2/F77_OPTS = '-DINT_SIZE=int -D_UNDERSCORES=1/" \
-			-i ddi/compddi || die "Failed fixing underscores in compddi"
-	else
-		sed -e "s/gentoo-F77_OPTS/F77_OPTS/" \
-			-i ddi/compddi || die "Failed fixing underscores in compddi"
-	fi
-
-	# fix up the checker scripts for gamess tests
-	sed -e "s:set GMSPATH:#set GMSPATH:g" \
-		-e "s:\$GMSPATH/tools/checktst:.:g" \
-		-i tools/checktst/checktst
-}
-
-src_compile() {
-	# build actvte
-	cd "${S}"/tools
-	"${FORTRANC}" -o actvte.x actvte.f || \
-		die "Failed to compile actvte.x"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then
-		/sbin/paxctl -PemRxS actvte.x 2> /dev/null || \
-			die "paxctl failed on actvte.x"
-	fi
-
-	# build gamess
-	cd "${S}"
-	./compall || die "compall failed"
-
-	# build the ddi TCP/IP socket stuff
-	cd ${S}/"ddi"
-	./compddi || die "compddi failed"
-
-	# finally, link it all together
-	cd "${S}"
-	./lked || die "lked failed"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then
-		/sbin/paxctl -PemRxS ${PN}.00.x 2> /dev/null || \
-			die "paxctl failed on actvte.x"
-	fi
-}
-
-src_install() {
-	cd "${S}"
-
-	# the executables
-	dobin ${PN}.00.x ddi/ddikick.x rungms \
-		|| die "Failed installing binaries"
-
-	# the docs
-	dodoc *.DOC || die "Failed installing docs"
-
-	# install ericftm
-	insinto /usr/share/${PN}/ericfmt
-	doins ericfmt.dat || die "Failed installing ericfmt.dat"
-
-	# install mcpdata
-	insinto /usr/share/${PN}/mcpdata
-	doins mcpdata/* || die "Failed installing mcpdata"
-
-	# install the tests the user should run, and
-	# fix up the runscript; also grab a copy of rungms
-	# so the user is ready to run the tests
-	insinto /usr/share/${PN}/tests
-	insopts -m0644
-	doins tests/* || die "Failed installing tests"
-	insopts -m0744
-	doins runall || die "Failed installing tests"
-	doins tools/checktst/checktst tools/checktst/chkabs || \
-		die "Failed to install main test checker"
-	doins tools/checktst/exam* || \
-		die "Failed to install individual test files"
-}
-
-pkg_postinst() {
-	echo
-	einfo "Before you use GAMESS for any serious work you HAVE"
-	einfo "to run the supplied test files located in"
-	einfo "/usr/share/gamess/tests and check them thoroughly."
-	einfo "Otherwise all scientific publications resulting from"
-	einfo "your GAMESS runs should be immediately rejected :)"
-	einfo "To do so copy the content of /usr/share/gamess/tests"
-	einfo "to some temporary location and execute './runall'. "
-	einfo "Then run the checktst script in the same directory to"
-	einfo "validate the tests."
-	einfo "Please consult TEST.DOC and the other docs!"
-
-	if [[ "${FORTRANC}" == "ifc" ]]; then
-		echo
-		ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
-		ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
-		ewarn "compilers UNLESS you can run through ALL of the "
-		ewarn "test cases (see above) successfully."
-	fi
-
-	echo
-	einfo "If you want to run on more than a single CPU"
-	einfo "you will have to acquaint yourself with the way GAMESS"
-	einfo "does multiprocessor runs and adjust rungms according to"
-	einfo "your target network architecture."
-	echo
-}
diff --git a/sci-chemistry/gamess/gamess-20060222.5.ebuild b/sci-chemistry/gamess/gamess-20060222.5.ebuild
deleted file mode 100644
index 0e3af474ff13..000000000000
--- a/sci-chemistry/gamess/gamess-20060222.5.ebuild
+++ /dev/null
@@ -1,209 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20060222.5.ebuild,v 1.1 2006/09/26 14:43:09 markusle Exp $
-
-inherit eutils toolchain-funcs fortran flag-o-matic
-
-DESCRIPTION="A powerful quantum chemistry package"
-LICENSE="gamess"
-HOMEPAGE="http://www.msg.ameslab.gov/GAMESS/GAMESS.html"
-SRC_URI="${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE="hardened blas"
-
-RESTRICT="fetch"
-
-DEPEND="app-shells/tcsh
-	hardened? ( sys-apps/paxctl )
-	blas? ( virtual/blas )"
-
-RDEPEND="app-shells/tcsh
-	net-misc/openssh"
-
-S="${WORKDIR}/${PN}"
-
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
-GAMESS_VERSION="22 FEB 2006 (R5)"
-FORTRAN="ifc g77 gfortran"
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${PN}-current.tar.gz from"
-	einfo "${GAMESS_DOWNLOAD}."
-	einfo "Be sure to select the version ${GAMESS_VERSION} tarball!!"
-	einfo "Then move the tarball to"
-	einfo "${DISTDIR}/${P}.tar.gz"
-	echo
-}
-
-pkg_setup() {
-	fortran_pkg_setup
-
-	# blas and ifc don't go together
-	if use blas && [[ "${FORTRANC}" = "ifc" ]]; then
-		echo
-		ewarn "${PN} can not be compiled with USE=blas and ifc."
-		ewarn "Linking against GAMESS' internal blas instead."
-		echo
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-
-	# apply LINUX-arch patches to gamess makesfiles
-	epatch "${FILESDIR}"/${P}.gentoo.patch
-
-	# for hardened-gcc let't turn off ssp, since it breakes
-	# a few routines
-	cd "${S}"
-	if use hardened && [[ "${FORTRANC}" = "g77" ]]; then
-		FFLAGS="${FFLAGS} -fno-stack-protector-all"
-	fi
-
-	# greate proper activate sourcefile 
-	cp "./tools/actvte.code" "./tools/actvte.f" || \
-		die || "Failed to create actvte.f"
-	sed -e "s/^\*UNX/    /" -i "./tools/actvte.f" || \
-		die || "Failed to perform UNX substitutions in actvte.f"
-
-	# fix GAMESS' compall script to use proper CC
-	sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
-		-i compall || die "Failed setting up compall script"
-
-	# insert proper FFLAGS into GAMESS' comp makefile
-	# in case we're using ifc let's strip all the gcc
-	# specific stuff
-	if [[ "${FORTRANC}" == "ifc" ]]; then
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
-			-e "s/gentoo-g77/${FORTRANC}/" \
-			-i comp || die "Failed setting up comp script"
-	elif ! use x86; then
-		sed -e "s/-malign-double //" \
-			-e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
-			-e "s/gentoo-g77/${FORTRANC}/" \
-			-i comp || die "Failed setting up comp script"
-	else
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
-			-e "s/gentoo-g77/${FORTRANC}/" \
-			-i comp || die "Failed setting up comp script"
-	fi
-
-	# use proper blas 
-	if ! use blas || [[ "${FORTRANC}" = "ifc" ]]; then
-		sed -e "s|/usr/lib/libblas.a|/usr/lib/dontuselibblas.a|" \
-			-i lked || die "Failed to adjust blas in lked"
-	fi
-
-	# fix up GAMESS' linker script;
-	sed -e "s/gentoo-g77/${FORTRANC}/" \
-		-e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
-		-i lked || die "Failed setting up lked script"
-
-	# fix up GAMESS' ddi TCP/IP socket build
-	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
-		-e "s/gentoo-g77/${FORTRANC}/" \
-		-i ddi/compddi || die "Failed setting up compddi script"
-
-
-	# fix up the checker scripts for gamess tests
-	sed -e "s:set GMSPATH:#set GMSPATH:g" \
-		-e "s:\$GMSPATH/tools/checktst:.:g" \
-		-i tools/checktst/checktst
-}
-
-src_compile() {
-	# build actvte
-	cd "${S}"/tools
-	"${FORTRANC}" -o actvte.x actvte.f || \
-		die "Failed to compile actvte.x"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then
-		/sbin/paxctl -PemRxS actvte.x 2> /dev/null || \
-			die "paxctl failed on actvte.x"
-	fi
-
-	# build gamess
-	cd "${S}"
-	./compall || die "compall failed"
-
-	# build the ddi TCP/IP socket stuff
-	cd ${S}/"ddi"
-	./compddi || die "compddi failed"
-
-	# finally, link it all together
-	cd "${S}"
-	./lked || die "lked failed"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then
-		/sbin/paxctl -PemRxS ${PN}.00.x 2> /dev/null || \
-			die "paxctl failed on actvte.x"
-	fi
-}
-
-src_install() {
-	cd "${S}"
-
-	# the executables
-	dobin ${PN}.00.x ddi/ddikick.x rungms \
-		|| die "Failed installing binaries"
-
-	# the docs
-	dodoc *.DOC || die "Failed installing docs"
-
-	# install ericftm
-	insinto /usr/share/${PN}/ericfmt
-	doins ericfmt.dat || die "Failed installing ericfmt.dat"
-
-	# install mcpdata
-	insinto /usr/share/${PN}/mcpdata
-	doins mcpdata/* || die "Failed installing mcpdata"
-
-	# install the tests the user should run, and
-	# fix up the runscript; also grab a copy of rungms
-	# so the user is ready to run the tests
-	insinto /usr/share/${PN}/tests
-	insopts -m0644
-	doins tests/* || die "Failed installing tests"
-	insopts -m0744
-	doins runall || die "Failed installing tests"
-	doins tools/checktst/checktst tools/checktst/chkabs || \
-		die "Failed to install main test checker"
-	doins tools/checktst/exam* || \
-		die "Failed to install individual test files"
-}
-
-pkg_postinst() {
-	echo
-	einfo "Before you use GAMESS for any serious work you HAVE"
-	einfo "to run the supplied test files located in"
-	einfo "/usr/share/gamess/tests and check them thoroughly."
-	einfo "Otherwise all scientific publications resulting from"
-	einfo "your GAMESS runs should be immediately rejected :)"
-	einfo "To do so copy the content of /usr/share/gamess/tests"
-	einfo "to some temporary location and execute './runall'. "
-	einfo "Then run the checktst script in the same directory to"
-	einfo "validate the tests."
-	einfo "Please consult TEST.DOC and the other docs!"
-
-	if [[ "${FORTRANC}" == "ifc" ]]; then
-		echo
-		ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
-		ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
-		ewarn "compilers UNLESS you can run through ALL of the "
-		ewarn "test cases (see above) successfully."
-	fi
-
-	echo
-	einfo "If you want to run on more than a single CPU"
-	einfo "you will have to acquaint yourself with the way GAMESS"
-	einfo "does multiprocessor runs and adjust rungms according to"
-	einfo "your target network architecture."
-	echo
-}
diff --git a/sci-chemistry/gopenmol/Manifest b/sci-chemistry/gopenmol/Manifest
index e1b58429d5a9..7b843515868a 100644
--- a/sci-chemistry/gopenmol/Manifest
+++ b/sci-chemistry/gopenmol/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 3.00-include-config-for-plugins.patch 383 RMD160 d086101593c41bc9a046e41bf35fbf7dcbd2cc5f SHA1 0277405809f2e5b76ecaa520de11ec2e43f4df90 SHA256 1683ce6661bc32eebe7263752ac176a96eaf4f6cc70260dd1d41ff8952e33d3d
 MD5 804493c5ad07a3849352770e90549266 files/3.00-include-config-for-plugins.patch 383
 RMD160 d086101593c41bc9a046e41bf35fbf7dcbd2cc5f files/3.00-include-config-for-plugins.patch 383
@@ -7,21 +10,21 @@ EBUILD gopenmol-3.00-r1.ebuild 1449 RMD160 d1d0f7b0aa0e38ba18c3a6daf9c899857b7b6
 MD5 11acebed44a75bbaf172fe525845661e gopenmol-3.00-r1.ebuild 1449
 RMD160 d1d0f7b0aa0e38ba18c3a6daf9c899857b7b6595 gopenmol-3.00-r1.ebuild 1449
 SHA256 d16e569c1082510b456b2e6702f9550680b8a873c60912e345ecd91504491b80 gopenmol-3.00-r1.ebuild 1449
-EBUILD gopenmol-3.00.ebuild 1240 RMD160 5b4600061757982839ba37d7de9c424315672844 SHA1 ac68c71ac921354015945891446b035b23469420 SHA256 b4aaebb41072176b6e5ef13a6e377e2488e6f5fe100ecb2deadec977d4c9a48a
-MD5 4493524a588dbb204c34e36dbadf00de gopenmol-3.00.ebuild 1240
-RMD160 5b4600061757982839ba37d7de9c424315672844 gopenmol-3.00.ebuild 1240
-SHA256 b4aaebb41072176b6e5ef13a6e377e2488e6f5fe100ecb2deadec977d4c9a48a gopenmol-3.00.ebuild 1240
-MISC ChangeLog 1164 RMD160 29ab896e67b39d45d02e6b2fa13221b34528f395 SHA1 732f2885ff0d5d4dd29db48183366c1cf22b9ab1 SHA256 f7c02880def8b5e411e45cf6349e537eb7a304a8608d4f71479e793aa5ce91be
-MD5 0471a8453f2ffe0b99f5603e7566ca60 ChangeLog 1164
-RMD160 29ab896e67b39d45d02e6b2fa13221b34528f395 ChangeLog 1164
-SHA256 f7c02880def8b5e411e45cf6349e537eb7a304a8608d4f71479e793aa5ce91be ChangeLog 1164
+MISC ChangeLog 1271 RMD160 95ebdb91ad84cb969f3d3a1944a1121b9320beaf SHA1 d4f6b9905db2532e0d135042bdcf7aee4d25e187 SHA256 363ef2b969c2c1b54bcb8622c843b338731c824f9e028525d2318bad1416771e
+MD5 13f3db9389bf989c7ea0a697aceab757 ChangeLog 1271
+RMD160 95ebdb91ad84cb969f3d3a1944a1121b9320beaf ChangeLog 1271
+SHA256 363ef2b969c2c1b54bcb8622c843b338731c824f9e028525d2318bad1416771e ChangeLog 1271
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 b04cc90ffc28f35e00391b5885cd77c7 files/digest-gopenmol-3.00 265
-RMD160 3d9ae42436abec9561f081555da60baa1d9f5a4c files/digest-gopenmol-3.00 265
-SHA256 24183c50b9e1f884875dfe71168c598a309e36957ead20e79582c8c04f88afd8 files/digest-gopenmol-3.00 265
 MD5 b04cc90ffc28f35e00391b5885cd77c7 files/digest-gopenmol-3.00-r1 265
 RMD160 3d9ae42436abec9561f081555da60baa1d9f5a4c files/digest-gopenmol-3.00-r1 265
 SHA256 24183c50b9e1f884875dfe71168c598a309e36957ead20e79582c8c04f88afd8 files/digest-gopenmol-3.00-r1 265
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFiS5mJXAu5GbtIRAo92AJ9sPZGOAwfxcAMVV0vUaTkgj5F/WgCfQRMq
+w4ucRreKfrdze4w7FADV5ag=
+=fERF
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gopenmol/files/digest-gopenmol-3.00 b/sci-chemistry/gopenmol/files/digest-gopenmol-3.00
deleted file mode 100644
index 516dc395dd1e..000000000000
--- a/sci-chemistry/gopenmol/files/digest-gopenmol-3.00
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 4e12ee6680c093a3bf056dde1d28fea2 gopenmol-3.00-linux.tar.gz 29615195
-RMD160 8ed743925bf2c8583228fa19d8afbdc37c0af8de gopenmol-3.00-linux.tar.gz 29615195
-SHA256 314494a751f65c28d015fee854d2ee347fecbca6ccf31bb7e04db7eda6a16a23 gopenmol-3.00-linux.tar.gz 29615195
diff --git a/sci-chemistry/gopenmol/gopenmol-3.00.ebuild b/sci-chemistry/gopenmol/gopenmol-3.00.ebuild
deleted file mode 100644
index ca6664fc640e..000000000000
--- a/sci-chemistry/gopenmol/gopenmol-3.00.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gopenmol/gopenmol-3.00.ebuild,v 1.1 2005/12/03 04:25:44 spyderous Exp $
-
-inherit eutils
-
-DESCRIPTION="gOpenMol is a tool for the visualization and analysis of molecular structures"
-HOMEPAGE="http://www.csc.fi/gopenmol"
-SRC_URI="${HOMEPAGE}/distribute/${P}-linux.tar.gz"
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-
-RDEPEND="=dev-lang/tcl-8.4*
-	=dev-lang/tk-8.4*
-	dev-tcltk/bwidget
-	virtual/opengl
-	virtual/glut
-	media-libs/jpeg
-	dev-lang/python
-	|| ( (
-			x11-libs/libXmu
-			x11-libs/libICE
-			x11-libs/libXau
-			x11-libs/libXdmcp
-			x11-libs/libXi
-			x11-libs/libXxf86vm
-		)
-		virtual/x11
-	)"
-
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/gOpenMol-${PV}/src"
-
-src_unpack() {
-	unpack ${A}
-	epatch ${FILESDIR}/${PV}-include-config-for-plugins.patch
-}
-
-src_compile() {
-	econf || die "./configure failed"
-
-	emake || die "emake failed"
-
-	# Plugins are not build by default
-	cd ${S}/plugins
-	emake || die "emake failed"
-}
-
-src_install() {
-	einstall || die
-
-	cd ${S}/plugins
-	einstall || die
-
-	dosed /usr/bin/rungOpenMol
-}
-
-pkg_postinst() {
-	einfo "Run gOpenMol using the rungOpenMol script."
-}
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 1eaa40f97333..b861380e8154 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX gromacs-alpha-axp_asm.patch 613 RMD160 56a617d34b9aa96f71cb84124271107d56557773 SHA1 96518a8fa20c0d597b5cb26b843f28f26d998942 SHA256 d6ae7d258e975a0c12a8b09bef11874eb0e25d4708f299b3e265c97ada69afee
 MD5 aa14e5e53e2eb5409072fd53896b4578 files/gromacs-alpha-axp_asm.patch 613
 RMD160 56a617d34b9aa96f71cb84124271107d56557773 files/gromacs-alpha-axp_asm.patch 613
@@ -8,47 +11,32 @@ RMD160 e6bdccd29a29fb9ee85f0ca4a15f2ea229b6f52a files/gromacs-ppc64-altivec.patc
 SHA256 1e60a3a12cfd706af1860ca2ff36074291540f8ffa3616636eb612037f0611c3 files/gromacs-ppc64-altivec.patch 571
 DIST gromacs-3.2.1.tar.gz 3302723 RMD160 778fb44b4b113eb5ba6e758884276165a8f003e9 SHA1 ddc86120c578e1147daf6e2f849da2096d75469b SHA256 de85710553202e17a3ac67049d2cf51117939d3d8944a34aa0909aa3771bef53
 DIST gromacs-3.3.1.tar.gz 7992897 RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff SHA1 8c67ee772cadf93067b3c8bcec65d7b3520df1dc SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f
-DIST gromacs-3.3.tar.gz 5906342
 EBUILD gromacs-3.2.1-r1.ebuild 1975 RMD160 ff5dfc572d27eda698c76845a88f58422bfabccc SHA1 c0b27b9543c669cb59d65a0c6cf4d4994c51acef SHA256 b5b43f7f1d032e64f95b1247530404556db7a57e623c9ceaf4384f2c7f65b0ef
 MD5 9b6492c32d8c96d94266e78f314fdcf4 gromacs-3.2.1-r1.ebuild 1975
 RMD160 ff5dfc572d27eda698c76845a88f58422bfabccc gromacs-3.2.1-r1.ebuild 1975
 SHA256 b5b43f7f1d032e64f95b1247530404556db7a57e623c9ceaf4384f2c7f65b0ef gromacs-3.2.1-r1.ebuild 1975
-EBUILD gromacs-3.2.1.ebuild 1897 RMD160 1abe85e471969fcde5ee6a714b76d820418178f0 SHA1 6e34da780f6b86863f4aa0d5ba4b70c831b3cb6e SHA256 7785a56bace8bbef4bdec432128c9d88d2427b667645790ea78df90929074c20
-MD5 5af09df5d0c864672c46c64a841c0177 gromacs-3.2.1.ebuild 1897
-RMD160 1abe85e471969fcde5ee6a714b76d820418178f0 gromacs-3.2.1.ebuild 1897
-SHA256 7785a56bace8bbef4bdec432128c9d88d2427b667645790ea78df90929074c20 gromacs-3.2.1.ebuild 1897
 EBUILD gromacs-3.3.1-r1.ebuild 5665 RMD160 6f92c2636308e10f01b34e8eb8cf1a5a2bf0fcad SHA1 3209942b89892b685cdc89e93a73b3662ea7a175 SHA256 b32c622ffc455ff3b2c49afe6788cdcb56672fe563e43b227d4465421e46bdf3
 MD5 3d6760743e1e92e0381a03b67614aab8 gromacs-3.3.1-r1.ebuild 5665
 RMD160 6f92c2636308e10f01b34e8eb8cf1a5a2bf0fcad gromacs-3.3.1-r1.ebuild 5665
 SHA256 b32c622ffc455ff3b2c49afe6788cdcb56672fe563e43b227d4465421e46bdf3 gromacs-3.3.1-r1.ebuild 5665
-EBUILD gromacs-3.3.1.ebuild 2163 RMD160 b7748b8989987d6acb0562e744702e38f79acd47 SHA1 fa5febc72867f35d1cc9714f558a9a2c9ed36353 SHA256 cabc59520dd654c54b45aa9175785e57d8826d15f93868efeadd9a895a940306
-MD5 a4e8a17060ded547ec8d8288bbbc3594 gromacs-3.3.1.ebuild 2163
-RMD160 b7748b8989987d6acb0562e744702e38f79acd47 gromacs-3.3.1.ebuild 2163
-SHA256 cabc59520dd654c54b45aa9175785e57d8826d15f93868efeadd9a895a940306 gromacs-3.3.1.ebuild 2163
-EBUILD gromacs-3.3.ebuild 1956 RMD160 3ff47faef23a3860b42d2fec7c2fa0f845ccab2a SHA1 862e3823e1439a00d6c217e7c8ae40a25570a2cf SHA256 4c51f3241c5d14d8aec8037c2f07f6a17ccbbb4189684c9f67a3a55d7fe02eeb
-MD5 d963556dde12c545dc60726f29fd3128 gromacs-3.3.ebuild 1956
-RMD160 3ff47faef23a3860b42d2fec7c2fa0f845ccab2a gromacs-3.3.ebuild 1956
-SHA256 4c51f3241c5d14d8aec8037c2f07f6a17ccbbb4189684c9f67a3a55d7fe02eeb gromacs-3.3.ebuild 1956
-MISC ChangeLog 5149 RMD160 e2cfe4842de01ce46a9b32a0bdf77794621aa355 SHA1 7366c86988ed92951702fcf5bc6784a3f93e1a4d SHA256 b19bcb7a48d00e199c21cd5b24971e9cd6d3a7b4b05ff07dcff146fb6c7f0e4b
-MD5 a1f9392bd3b1fa00ba4132e1762a3ddc ChangeLog 5149
-RMD160 e2cfe4842de01ce46a9b32a0bdf77794621aa355 ChangeLog 5149
-SHA256 b19bcb7a48d00e199c21cd5b24971e9cd6d3a7b4b05ff07dcff146fb6c7f0e4b ChangeLog 5149
+MISC ChangeLog 5305 RMD160 5eed659b6a282ed174f205e549255915029d4023 SHA1 e10cd8298bdc290f4c5e53b4f206c98b0a540cb3 SHA256 184bfb76da554a0e9e8ee7a864464d18a75a54dc22327756a1f4ac90db113f21
+MD5 9427163790e5d159cee32ff1764a2080 ChangeLog 5305
+RMD160 5eed659b6a282ed174f205e549255915029d4023 ChangeLog 5305
+SHA256 184bfb76da554a0e9e8ee7a864464d18a75a54dc22327756a1f4ac90db113f21 ChangeLog 5305
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 5610b09ddd25c07046dc98731e997221 files/digest-gromacs-3.2.1 244
-RMD160 5967b1bae7c1d24be5d9f0dce62b256f6f084cc7 files/digest-gromacs-3.2.1 244
-SHA256 c24822d0c5dd0545585fa9ebe51c7a1126da729c375ca035c3baaddd5d2d454b files/digest-gromacs-3.2.1 244
 MD5 5610b09ddd25c07046dc98731e997221 files/digest-gromacs-3.2.1-r1 244
 RMD160 5967b1bae7c1d24be5d9f0dce62b256f6f084cc7 files/digest-gromacs-3.2.1-r1 244
 SHA256 c24822d0c5dd0545585fa9ebe51c7a1126da729c375ca035c3baaddd5d2d454b files/digest-gromacs-3.2.1-r1 244
-MD5 b35c347e16c4563524f8cacd04a61f33 files/digest-gromacs-3.3 64
-RMD160 47474a9eacd1d4e08149437b2f7ce587044c68f3 files/digest-gromacs-3.3 64
-SHA256 590f94df114cae1a0a53387dfead13fadd4cad00003a6b3f454f2ae1a7f3e6e9 files/digest-gromacs-3.3 64
-MD5 0ad487900dfecda21c7258f45d995525 files/digest-gromacs-3.3.1 244
-RMD160 427f90b98362a786e7d5fca69d9069742b943ebf files/digest-gromacs-3.3.1 244
-SHA256 2eaa348fdc15b37c1fb15fb5394f6a26578c22bfd21ea4e719ba6308bbab40fc files/digest-gromacs-3.3.1 244
 MD5 0ad487900dfecda21c7258f45d995525 files/digest-gromacs-3.3.1-r1 244
 RMD160 427f90b98362a786e7d5fca69d9069742b943ebf files/digest-gromacs-3.3.1-r1 244
 SHA256 2eaa348fdc15b37c1fb15fb5394f6a26578c22bfd21ea4e719ba6308bbab40fc files/digest-gromacs-3.3.1-r1 244
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFkx5mJXAu5GbtIRAqHTAJ9gR/FsG3cklvyOmSp5JkS47jPmCACfbLx7
+KJ+gajpTqKVJ7F9pAmvpmbM=
+=VP9R
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/files/digest-gromacs-3.2.1 b/sci-chemistry/gromacs/files/digest-gromacs-3.2.1
deleted file mode 100644
index 8b61dbb9179c..000000000000
--- a/sci-chemistry/gromacs/files/digest-gromacs-3.2.1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 d298386495f6ee39b3155ce951984485 gromacs-3.2.1.tar.gz 3302723
-RMD160 778fb44b4b113eb5ba6e758884276165a8f003e9 gromacs-3.2.1.tar.gz 3302723
-SHA256 de85710553202e17a3ac67049d2cf51117939d3d8944a34aa0909aa3771bef53 gromacs-3.2.1.tar.gz 3302723
diff --git a/sci-chemistry/gromacs/files/digest-gromacs-3.3 b/sci-chemistry/gromacs/files/digest-gromacs-3.3
deleted file mode 100644
index 757b2815589c..000000000000
--- a/sci-chemistry/gromacs/files/digest-gromacs-3.3
+++ /dev/null
@@ -1 +0,0 @@
-MD5 99ea6f25a89f1511f51c350a66a2fdc4 gromacs-3.3.tar.gz 5906342
diff --git a/sci-chemistry/gromacs/files/digest-gromacs-3.3.1 b/sci-chemistry/gromacs/files/digest-gromacs-3.3.1
deleted file mode 100644
index dc4a56cb42ec..000000000000
--- a/sci-chemistry/gromacs/files/digest-gromacs-3.3.1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 1af34a99950813ca7cf893253c447cd1 gromacs-3.3.1.tar.gz 7992897
-RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff gromacs-3.3.1.tar.gz 7992897
-SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f gromacs-3.3.1.tar.gz 7992897
diff --git a/sci-chemistry/gromacs/gromacs-3.2.1.ebuild b/sci-chemistry/gromacs/gromacs-3.2.1.ebuild
deleted file mode 100644
index 6631cbe813d4..000000000000
--- a/sci-chemistry/gromacs/gromacs-3.2.1.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.2.1.ebuild,v 1.3 2006/06/25 00:28:25 spyderous Exp $
-
-inherit eutils
-
-IUSE="mpi xml"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="x86 amd64"
-
-#mpi is a local USE flag now
-#May become official when situation with mpich is cleared (now the only mpi implementation awailable is lam-mpi)
-DEPEND="=sci-libs/fftw-2.1*
-	mpi? ( >=sys-cluster/lam-mpi-6.5.6 )
-	>=sys-devel/binutils-2.10.91.0.2
-	app-shells/tcsh
-	xml? ( dev-libs/libxml2 )"
-
-src_compile() {
-#!!!Please note!!!
-#for troublesome work gromacs should be compiled with the same mpi setting as fftw.
-#Unfortunately portage cannot trace optional dependencies of dependencies at present.
-#Until this (planned) feature is completed, please try to do corresponding check yourself.
-	local myconf
-
-	# Enable asm on Alphas
-	if [ "${ARCH}" = "alpha" ]
-	then
-		myconf="${myconf} --enable-axp-asm"
-	fi
-
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-	econf \
-		--enable-fortran \
-		--datadir=/usr/share/${P} \
-		--bindir=/usr/bin \
-		--libdir=/usr/lib \
-		`use_with xml` \
-		`use_enable mpi` \
-		${myconf} || die "configure failed"
-
-	#	`use_enable static all-static` \
-
-	emake || die
-}
-
-src_install () {
-	make DESTDIR=${D} install || die
-
-	# Install documentation.
-	dodoc AUTHORS COPYING INSTALL README
-
-	#move html docs under /usr/share/doc
-	#and leave examples and templates under /usr/gromacs...
-	mv ${D}/usr/share/${P}/html ${D}/usr/share/doc/${PF}
-}
diff --git a/sci-chemistry/gromacs/gromacs-3.3.1.ebuild b/sci-chemistry/gromacs/gromacs-3.3.1.ebuild
deleted file mode 100644
index 28aa7591c039..000000000000
--- a/sci-chemistry/gromacs/gromacs-3.3.1.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1.ebuild,v 1.1 2006/08/08 02:54:41 markusle Exp $
-
-inherit eutils fortran
-
-IUSE="altivec mpi xml"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64 ~ppc64"
-
-# gromacs uses fortran intrinsics such as RSHIFT that
-# are currently missing from gfortran; hence we need
-# to require g77 for the time being (see bug #141672).
-FORTRAN="g77"
-
-
-#mpi is a local USE flag now
-#May become official when situation with mpich is cleared (now the only mpi implementation awailable is lam-mpi)
-DEPEND="=sci-libs/fftw-2.1*
-	mpi? ( >=sys-cluster/lam-mpi-6.5.6 )
-	>=sys-devel/binutils-2.10.91.0.2
-	app-shells/tcsh
-	xml? ( dev-libs/libxml2 )"
-
-pkg_setup() {
-	# !!!Please note!!!
-	# for troublesome work gromacs should be compiled with the same mpi setting
-	# as fftw.
-	if use mpi; then
-		if ! built_with_use =sci-libs/fftw-2.1* mpi; then
-			die "=sci-libs/fftw-2.1* must be built with USE=mpi."
-		fi
-	fi
-
-	fortran_pkg_setup
-}
-
-src_unpack() {
-	unpack ${A}
-	if use ppc64 && use altivec ; then
-		epatch ${FILESDIR}/${PN}-ppc64-altivec.patch
-	fi
-}
-
-src_compile() {
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-	econf \
-		--enable-fortran \
-		--datadir=/usr/share/${P} \
-		--bindir=/usr/bin \
-		--libdir=/usr/lib \
-		$(use_with xml) \
-		$(use_enable mpi) \
-		$(use_enable altivec ppc-altivec) \
-		$(use_enable alpha axp-asm) || die "configure failed"
-
-#		$(use_enable static all-static) \
-
-	emake || die
-}
-
-src_install () {
-	make DESTDIR=${D} install || die
-
-	# Install documentation.
-	dodoc AUTHORS COPYING INSTALL README
-
-	#move html docs under /usr/share/doc
-	#and leave examples and templates under /usr/gromacs...
-	mv ${D}/usr/share/${P}/html ${D}/usr/share/doc/${PF}
-}
diff --git a/sci-chemistry/gromacs/gromacs-3.3.ebuild b/sci-chemistry/gromacs/gromacs-3.3.ebuild
deleted file mode 100644
index a89111212188..000000000000
--- a/sci-chemistry/gromacs/gromacs-3.3.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.ebuild,v 1.2 2006/06/25 00:28:25 spyderous Exp $
-
-inherit eutils
-
-IUSE="altivec mpi xml"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64 ~ppc64"
-
-#mpi is a local USE flag now
-#May become official when situation with mpich is cleared (now the only mpi implementation awailable is lam-mpi)
-DEPEND="=sci-libs/fftw-2.1*
-	mpi? ( >=sys-cluster/lam-mpi-6.5.6 )
-	>=sys-devel/binutils-2.10.91.0.2
-	app-shells/tcsh
-	xml? ( dev-libs/libxml2 )"
-
-pkg_setup() {
-	# !!!Please note!!!
-	# for troublesome work gromacs should be compiled with the same mpi setting
-	# as fftw.
-	if use mpi; then
-		if ! built_with_use =sci-libs/fftw-2.1* mpi; then
-			die "=sci-libs/fftw-2.1* must be built with USE=mpi."
-		fi
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-	if use ppc64 && use altivec ; then
-		epatch ${FILESDIR}/${PN}-ppc64-altivec.patch
-	fi
-}
-
-src_compile() {
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-	econf \
-		--enable-fortran \
-		--datadir=/usr/share/${P} \
-		--bindir=/usr/bin \
-		--libdir=/usr/lib \
-		$(use_with xml) \
-		$(use_enable mpi) \
-		$(use_enable altivec ppc-altivec) \
-		$(use_enable alpha axp-asm) || die "configure failed"
-
-#		$(use_enable static all-static) \
-
-	emake || die
-}
-
-src_install () {
-	make DESTDIR=${D} install || die
-
-	# Install documentation.
-	dodoc AUTHORS COPYING INSTALL README
-
-	#move html docs under /usr/share/doc
-	#and leave examples and templates under /usr/gromacs...
-	mv ${D}/usr/share/${P}/html ${D}/usr/share/doc/${PF}
-}
diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest
index 62918566a296..41434a840d21 100644
--- a/sci-chemistry/mopac7/Manifest
+++ b/sci-chemistry/mopac7/Manifest
@@ -1,31 +1,26 @@
-DIST mopac7-1.00.tgz 1184447
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST mopac7-1.10.tgz 1596446 RMD160 19c6c97c91d3762269e8add5b2c43c9473efcf90 SHA1 42889de7ac0385a65f87ca4e423a2d2858ce615a SHA256 993ace860c77345d1c8629f416bfc765610b9f264e9885b3777f44b745817ab5
-EBUILD mopac7-1.00-r1.ebuild 1343 RMD160 290408b19c5c39b421898755a1f7993819a1484e SHA1 529deecaa0faaae03d2252994210d7667d0dd087 SHA256 d67cb3dddc0d560924e479691bd449963cb5c10b0ef668ca6112de09635bd6c1
-MD5 1d7b0ca5032abbacaafbeafc6371d033 mopac7-1.00-r1.ebuild 1343
-RMD160 290408b19c5c39b421898755a1f7993819a1484e mopac7-1.00-r1.ebuild 1343
-SHA256 d67cb3dddc0d560924e479691bd449963cb5c10b0ef668ca6112de09635bd6c1 mopac7-1.00-r1.ebuild 1343
 EBUILD mopac7-1.10-r1.ebuild 1558 RMD160 fe4628df7db86945db65637ae0829fb658e949b2 SHA1 40a92c5e209ed45c80cf6498e664e6dfb39898e6 SHA256 2b1caa1297c9e2b401fef0bcf41b6293c90c8861e2c57cb5ab5ca1a566e658d5
 MD5 b0ca0948e20bea276802a15cb7da2b8c mopac7-1.10-r1.ebuild 1558
 RMD160 fe4628df7db86945db65637ae0829fb658e949b2 mopac7-1.10-r1.ebuild 1558
 SHA256 2b1caa1297c9e2b401fef0bcf41b6293c90c8861e2c57cb5ab5ca1a566e658d5 mopac7-1.10-r1.ebuild 1558
-EBUILD mopac7-1.10.ebuild 1340 RMD160 44166645b9a5d99fb714ee3551eea4981b93f7cc SHA1 b75d369dc8b776023fc9454b84847814db5b87d4 SHA256 1310de75ed4e4ddaa1e6f9b359dcf5cc24ee6b9a942e04745260566a6e83671b
-MD5 722dfc3dcfe0a3f1617d21d35ef99579 mopac7-1.10.ebuild 1340
-RMD160 44166645b9a5d99fb714ee3551eea4981b93f7cc mopac7-1.10.ebuild 1340
-SHA256 1310de75ed4e4ddaa1e6f9b359dcf5cc24ee6b9a942e04745260566a6e83671b mopac7-1.10.ebuild 1340
-MISC ChangeLog 2134 RMD160 409ce9a2b68ea1e40de39494b2e63c356c2582a2 SHA1 ae012b0ce37236532622d1bb5e3569e56a7f8ab5 SHA256 41e88ea411d761d7e4044f32c4e4683cdca003f83f7563f22581339950c56bb1
-MD5 753143a0d131806ccb6f38aa68343c1e ChangeLog 2134
-RMD160 409ce9a2b68ea1e40de39494b2e63c356c2582a2 ChangeLog 2134
-SHA256 41e88ea411d761d7e4044f32c4e4683cdca003f83f7563f22581339950c56bb1 ChangeLog 2134
+MISC ChangeLog 2268 RMD160 ad6a5b94e8ab1b83d04b61c10ae29e68c23a80dc SHA1 f2923dcd66436d2e80f7aa5ce4d508c8cac8e3d4 SHA256 4d0306e021f0903789eced67c1fbce5e3a2d8a8dc2a32d117e482e43fe0004be
+MD5 c1ed4da5df4dbb8356f14146ecd6979d ChangeLog 2268
+RMD160 ad6a5b94e8ab1b83d04b61c10ae29e68c23a80dc ChangeLog 2268
+SHA256 4d0306e021f0903789eced67c1fbce5e3a2d8a8dc2a32d117e482e43fe0004be ChangeLog 2268
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 87fd0c849cee4758e25fa67f07f7240e files/digest-mopac7-1.00-r1 61
-RMD160 3fbf0dd28dc51b3f5367dc93d9227d210462e3d2 files/digest-mopac7-1.00-r1 61
-SHA256 13074a7e46c9190aede8f009a0b178cedf99699275ff263f7bdb2feba5ff0c47 files/digest-mopac7-1.00-r1 61
-MD5 803ea66052591a35eeebb0d5c690f36f files/digest-mopac7-1.10 229
-RMD160 3b5b99649b35aa0f36ea934fc30290e23e40b5a3 files/digest-mopac7-1.10 229
-SHA256 de06f6845712fea9e017e3d5b90121a60c742afa699323b7a8d8801499609193 files/digest-mopac7-1.10 229
 MD5 803ea66052591a35eeebb0d5c690f36f files/digest-mopac7-1.10-r1 229
 RMD160 3b5b99649b35aa0f36ea934fc30290e23e40b5a3 files/digest-mopac7-1.10-r1 229
 SHA256 de06f6845712fea9e017e3d5b90121a60c742afa699323b7a8d8801499609193 files/digest-mopac7-1.10-r1 229
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFlC5mJXAu5GbtIRAnQyAJ42Tdi1jeUmOk/7ozKBEHpBE65oiwCdEP9V
+5X02+z4Q7KiRS5aPYVJRlJw=
+=9zfK
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/mopac7/files/digest-mopac7-1.00-r1 b/sci-chemistry/mopac7/files/digest-mopac7-1.00-r1
deleted file mode 100644
index dacf853ca0d4..000000000000
--- a/sci-chemistry/mopac7/files/digest-mopac7-1.00-r1
+++ /dev/null
@@ -1 +0,0 @@
-MD5 d556f7166bcc809dd84ee93c8d874fa2 mopac7-1.00.tgz 1184447
diff --git a/sci-chemistry/mopac7/files/digest-mopac7-1.10 b/sci-chemistry/mopac7/files/digest-mopac7-1.10
deleted file mode 100644
index da9189352166..000000000000
--- a/sci-chemistry/mopac7/files/digest-mopac7-1.10
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 d5352a3cf349b9ac4df943bb7992cfa9 mopac7-1.10.tgz 1596446
-RMD160 19c6c97c91d3762269e8add5b2c43c9473efcf90 mopac7-1.10.tgz 1596446
-SHA256 993ace860c77345d1c8629f416bfc765610b9f264e9885b3777f44b745817ab5 mopac7-1.10.tgz 1596446
diff --git a/sci-chemistry/mopac7/mopac7-1.00-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.00-r1.ebuild
deleted file mode 100644
index dd0f29911435..000000000000
--- a/sci-chemistry/mopac7/mopac7-1.00-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mopac7/mopac7-1.00-r1.ebuild,v 1.3 2006/11/24 21:41:10 beandog Exp $
-
-inherit flag-o-matic
-
-DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package"
-HOMEPAGE="http://sourceforge.net/projects/mopac7/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-LICENSE="mopac7"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-DEPEND="dev-libs/libf2c
-	sys-devel/autoconf
-	sys-devel/automake
-	sys-devel/libtool"
-RDEPEND="dev-libs/libf2c"
-
-src_compile() {
-	libtoolize --copy --force
-
-	# This is absolutely required to avoid odd errors on MAIN__() not existing
-	# and to build the mopac7 binary, not just the library.
-	einfo "Adding required LDFLAGS for configure"
-	econf LDFLAGS="-Xlinker -defsym -Xlinker MAIN__=main" || die "econf failed"
-
-	# We need the appended LDFLAGS to activate building of the mopac7 binary,
-	# but they break the actual linking of it. Something's obviously broken.
-	einfo "Removing LDFLAGS, as they break the build"
-	sed -i "/^LDFLAGS/d" src/Makefile.in
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	make DESTDIR=${D} install || die
-	sed -i "s:./src/mopac7:mopac7:g" run_mopac7
-	dobin run_mopac7 src/.libs/mopac7
-	dodoc AUTHORS README ChangeLog
-}
diff --git a/sci-chemistry/mopac7/mopac7-1.10.ebuild b/sci-chemistry/mopac7/mopac7-1.10.ebuild
deleted file mode 100644
index de07bbb0dc51..000000000000
--- a/sci-chemistry/mopac7/mopac7-1.10.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mopac7/mopac7-1.10.ebuild,v 1.2 2006/11/24 21:41:10 beandog Exp $
-
-inherit flag-o-matic
-
-DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package"
-HOMEPAGE="http://sourceforge.net/projects/mopac7/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-LICENSE="mopac7"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-DEPEND="dev-libs/libf2c
-	sys-devel/autoconf
-	sys-devel/automake
-	sys-devel/libtool"
-RDEPEND="dev-libs/libf2c"
-
-src_compile() {
-	libtoolize --copy --force
-
-	# This is absolutely required to avoid odd errors on MAIN__() not existing
-	# and to build the mopac7 binary, not just the library.
-	einfo "Adding required LDFLAGS for configure"
-	econf LDFLAGS="-Xlinker -defsym -Xlinker MAIN__=main" || die "econf failed"
-
-	# We need the appended LDFLAGS to activate building of the mopac7 binary,
-	# but they break the actual linking of it. Something's obviously broken.
-	einfo "Removing LDFLAGS, as they break the build"
-	sed -i "/^LDFLAGS/d" src/Makefile.in
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	make DESTDIR=${D} install || die
-	sed -i "s:./src/mopac7:mopac7:g" run_mopac7
-	dobin run_mopac7 src/.libs/mopac7
-	dodoc AUTHORS README ChangeLog
-}
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
index 6f1fad2463b6..f00512b1b662 100644
--- a/sci-chemistry/namd/Manifest
+++ b/sci-chemistry/namd/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX namd-2.6-gentoo.patch 3650 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa SHA1 f5525811cc092c5125be93cdce0e8c4e22fbee38 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9
 MD5 5d1edba2a5c3fbaa8df6a84cbffe2d8a files/namd-2.6-gentoo.patch 3650
 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa files/namd-2.6-gentoo.patch 3650
@@ -19,19 +22,14 @@ MD5 11475a5133058462e1e7a1fd33052974 files/namd-tcl-lib-gentoo.patch 576
 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 files/namd-tcl-lib-gentoo.patch 576
 SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01 files/namd-tcl-lib-gentoo.patch 576
 DIST NAMD_2.6_Source.tar.gz 8963319 RMD160 186f79322226a20398031618011104a666237298 SHA1 3b3d83fdc54a520cb6c59b34cde03c9f74d2f443 SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b
-DIST NAMD_2.6b1_Source.tar.gz 8805263
 EBUILD namd-2.6.ebuild 2284 RMD160 2360a865aa1a029b2aae83b7c906bc625b959464 SHA1 757795138abd2eb5c13abb68c29d46f535768b78 SHA256 1e3b1c80b98e342e234588e1bea9245aba8e3b0db12786e00ef753827fc91e19
 MD5 34d117d6a8a0c4fd79648772cebb6e3b namd-2.6.ebuild 2284
 RMD160 2360a865aa1a029b2aae83b7c906bc625b959464 namd-2.6.ebuild 2284
 SHA256 1e3b1c80b98e342e234588e1bea9245aba8e3b0db12786e00ef753827fc91e19 namd-2.6.ebuild 2284
-EBUILD namd-2.6_beta1.ebuild 2727 RMD160 4124cf25699df813f4da9553072350e919fddba9 SHA1 ea1859e30eb8c776d6c4053bad81880b0d4e38db SHA256 6c34a3a6e135086cbfa62c175cc31ce6a033025af31235071f93301cb19dc376
-MD5 8b3e7b8076242855669122ddd67d053f namd-2.6_beta1.ebuild 2727
-RMD160 4124cf25699df813f4da9553072350e919fddba9 namd-2.6_beta1.ebuild 2727
-SHA256 6c34a3a6e135086cbfa62c175cc31ce6a033025af31235071f93301cb19dc376 namd-2.6_beta1.ebuild 2727
-MISC ChangeLog 1264 RMD160 06ab9f81abeb0680ba2821d083e5827a3f7df325 SHA1 4b02a8d1e6871532c331c3513486fe199fcdebe0 SHA256 1f105f618e16e9002ee3dc7cf15b7a24cdc0c46df8bb8ebb24a51f1d097aea5f
-MD5 3d87f83bcfb8fd59f483ea12fed7b8c7 ChangeLog 1264
-RMD160 06ab9f81abeb0680ba2821d083e5827a3f7df325 ChangeLog 1264
-SHA256 1f105f618e16e9002ee3dc7cf15b7a24cdc0c46df8bb8ebb24a51f1d097aea5f ChangeLog 1264
+MISC ChangeLog 1372 RMD160 38c0b7f76d85e911f5dd996367f62cbd1338c103 SHA1 5765455a17da54b68b94ae92db83a48b937347e8 SHA256 dee2cafc26e255db981b8268259eda8900595217b1e0c0c511a99a473369da77
+MD5 4badd9efcfbfa1c2a151730bab8645d7 ChangeLog 1372
+RMD160 38c0b7f76d85e911f5dd996367f62cbd1338c103 ChangeLog 1372
+SHA256 dee2cafc26e255db981b8268259eda8900595217b1e0c0c511a99a473369da77 ChangeLog 1372
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
 MD5 cf7436fe44a27481d1001082eb06326e metadata.xml 282
 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 metadata.xml 282
@@ -39,6 +37,10 @@ SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349 metadata
 MD5 f125c37a6c730dd4213cc69fb280de0f files/digest-namd-2.6 250
 RMD160 b71b7ad56f3f23d002ecca0ec623636690c7c895 files/digest-namd-2.6 250
 SHA256 2a4f6569fcce7447d6c81a24a115b4b410ccc4247fb4c4e5a11c63c6708aa4a1 files/digest-namd-2.6 250
-MD5 657770d1760ff431fb8f8972c1c11ccc files/digest-namd-2.6_beta1 70
-RMD160 5b059f5b89f50a8a96afee174f7d66fcd5377e1d files/digest-namd-2.6_beta1 70
-SHA256 e7cfa75427a67aeeac7e8e221fbd86aab09846d5216194769e1bee46f35d3497 files/digest-namd-2.6_beta1 70
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFl95mJXAu5GbtIRArpIAJwOvFT0Wl4iKTyut6ZiO6Sw0szzowCdEGyT
+kKnRWnQSsgIdwskSe5mlglI=
+=Cn+U
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/namd/files/digest-namd-2.6_beta1 b/sci-chemistry/namd/files/digest-namd-2.6_beta1
deleted file mode 100644
index 53ebf08ed8e8..000000000000
--- a/sci-chemistry/namd/files/digest-namd-2.6_beta1
+++ /dev/null
@@ -1 +0,0 @@
-MD5 71fd3eb8717b27ab5af80edc5a01b5a5 NAMD_2.6b1_Source.tar.gz 8805263
diff --git a/sci-chemistry/namd/namd-2.6_beta1.ebuild b/sci-chemistry/namd/namd-2.6_beta1.ebuild
deleted file mode 100644
index 7688c045b102..000000000000
--- a/sci-chemistry/namd/namd-2.6_beta1.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.6_beta1.ebuild,v 1.3 2005/12/22 16:32:19 markusle Exp $
-
-inherit eutils toolchain-funcs flag-o-matic
-
-DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
-LICENSE="namd"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
-
-MY_PN="NAMD"
-MY_PV="2.6b1"
-
-SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
-
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="hardened"
-
-RESTRICT="fetch"
-
-DEPEND="|| ( app-shells/csh
-			app-shells/tcsh )
-	virtual/libc
-	=sys-cluster/charm-5.9
-	=sci-libs/fftw-2*
-	=dev-lang/tcl-8.4*
-	hardened? ( sys-apps/paxctl )"
-
-CHARM="charm-5.9"
-NAMD_ARCH="Linux-i686-g++"
-
-NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
-
-S="${WORKDIR}/${MY_PN}_${MY_PV}_Source"
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${MY_PN}_${MY_PV}_Source.tar.gz from"
-	einfo "${NAMD_DOWNLOAD}"
-	einfo "after agreeing to the license and then move it to"
-	einfo "${DISTDIR}"
-	einfo "Be sure to select the ${MY_PV} version!"
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-
-	# apply a few small fixes to make NAMD compile and
-	# link to the proper libraries
-	epatch "${FILESDIR}"/namd-barrier-fix-gentoo.patch
-	epatch "${FILESDIR}"/namd-tcl-lib-gentoo.patch
-	epatch "${FILESDIR}"/namd-fftw-lib-gentoo.patch
-	epatch "${FILESDIR}"/namd-makefile-gentoo.patch
-
-	cd "${S}"
-
-	# for hardened turn ssp off
-	if use hardened; then
-		append-flags -fno-stack-protector-all
-	fi
-
-	# proper compiler and cflags
-	sed -e "s/g++/$(tc-getCXX)/" \
-		-e "s/CXXOPTS = -O3 -march=pentiumpro -ffast-math -static/CXXOPTS = ${CXXFLAGS}/" \
-		-e "s/gcc/$(tc-getCC)/" \
-		-e "s/COPTS = -O3 -march=pentiumpro -ffast-math -static/COPTS = ${CFLAGS}/" \
-		-i arch/${NAMD_ARCH}.arch || \
-		die "Failed to setup ${NAMD_ARCH}.arch"
-
-	# configure
-	./config tcl fftw ${NAMD_ARCH}
-}
-
-src_compile() {
-	# build namd
-	cd "${S}/${NAMD_ARCH}"
-	emake || die "Failed to build namd"
-
-	# for hardened disable MPROTECT on namd2 binary
-	if use hardened; then
-		/sbin/paxctl -PemRxS ./namd2 || \
-			die "paxctl failed on namd2"
-	fi
-}
-
-src_install() {
-	cd "${S}/${NAMD_ARCH}"
-
-	# the binaries
-	dobin ${PN}2 psfgen flipbinpdb flipdcd || \
-		die "Failed to install binaries"
-
-	cd "${S}"
-
-	# some docs
-	dodoc announce.txt license.txt notes.txt || \
-		die "Failed to install docs"
-}
-
-pkg_postinst() {
-	echo
-	einfo "For detailed instructions on how to run and configure"
-	einfo "NAMD please consults the extensive documentation at"
-	einfo "http://www.ks.uiuc.edu/Research/namd/"
-	einfo "and the NAMD tutorials available at"
-	einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
-	einfo "Have fun :)"
-	echo
-}
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 628ea8a08bd5..38d210725f35 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,32 +1,26 @@
-DIST openbabel-1.100.2.tar.gz 1010494 RMD160 e56c399455cab3068b7eded7d47f4c9b8dfa20bc SHA1 01738acc3a37a23b67697f7f877d46cd6347f921 SHA256 15c2f968c475bf8b9e0759ae455b0d7b06e6810c78a2cc2ae1de4cc11bb5f8fb
-DIST openbabel-2.0.1.tar.gz 2454398 RMD160 7b39b78bedf13ff975086a18422f713ff1a1e8f9 SHA256 c2f0f1c0dffd357593a57e1bce43895de988c48dae55771b7227fc96bf9546b0
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST openbabel-2.0.2.tar.gz 2712813 RMD160 3fee81f9d7c1605b36fa22d0676bfb9c18500443 SHA1 48ae2579c55d57d1a357825f498fc4091b6b30b4 SHA256 f85e600fad398df63290690e0e8d62e02d37ead941bc0d5bc8de5e44a01c7de3
-EBUILD openbabel-1.100.2.ebuild 860 RMD160 b39cfb1a044aacc98676d67d221f878585eb1edd SHA1 b0eba2558aa79add45f5ff1d2b09d16a731eaa38 SHA256 66e256b50c2e311119dd0d504a50f09adfdae625817ad3fb3758f441e8ff620b
-MD5 b7e8a54dab6b03ecba9ed705c173300a openbabel-1.100.2.ebuild 860
-RMD160 b39cfb1a044aacc98676d67d221f878585eb1edd openbabel-1.100.2.ebuild 860
-SHA256 66e256b50c2e311119dd0d504a50f09adfdae625817ad3fb3758f441e8ff620b openbabel-1.100.2.ebuild 860
-EBUILD openbabel-2.0.1.ebuild 666 RMD160 e6cedebffd886a0e479db69c80d2bcc7f8aa859a SHA1 2b8c3a086fa3ddfa0c94b21492c6c7da988b93af SHA256 8c626345a14ad79457d02875e13289bfef933430c04058659cdecb9c8ed0b3a8
-MD5 ac5a9cbfeceefe8823b0b15dc0f942c9 openbabel-2.0.1.ebuild 666
-RMD160 e6cedebffd886a0e479db69c80d2bcc7f8aa859a openbabel-2.0.1.ebuild 666
-SHA256 8c626345a14ad79457d02875e13289bfef933430c04058659cdecb9c8ed0b3a8 openbabel-2.0.1.ebuild 666
 EBUILD openbabel-2.0.2.ebuild 665 RMD160 fbd69ae436f693862b1066ff6903e2e1dea8c54d SHA1 0ff0c203786fcfcd8f23d304b1888398dc0e9516 SHA256 e3014ff0b7e4ee0b3871e0124c21118a7ce3ff2f7174adb467b179416c7556db
 MD5 9ffd1ea4db5314935e5a07665efe2a9c openbabel-2.0.2.ebuild 665
 RMD160 fbd69ae436f693862b1066ff6903e2e1dea8c54d openbabel-2.0.2.ebuild 665
 SHA256 e3014ff0b7e4ee0b3871e0124c21118a7ce3ff2f7174adb467b179416c7556db openbabel-2.0.2.ebuild 665
-MISC ChangeLog 2405 RMD160 f7a9076478df29d03b672fd62a103a96eb7b3628 SHA1 51ccec7e066214f3ea015e7a7ae9a657793cda36 SHA256 b844b06a34d157bb01967a64df21d2b3adddef0693348caf48938748676ffce6
-MD5 a7805c1b6c65a2fba7877ce063e7ebc1 ChangeLog 2405
-RMD160 f7a9076478df29d03b672fd62a103a96eb7b3628 ChangeLog 2405
-SHA256 b844b06a34d157bb01967a64df21d2b3adddef0693348caf48938748676ffce6 ChangeLog 2405
+MISC ChangeLog 2543 RMD160 4c08907c3f43ead27f45886025c912f033095c5e SHA1 39eca536c24dd0658f5cd554e0fd62a0a063d514 SHA256 ef1746438ebe8e44809c7233a0a70b405dda7dc7934d442236a854fe56813cea
+MD5 b5b9fcdbbf2296b0af75070c437ab023 ChangeLog 2543
+RMD160 4c08907c3f43ead27f45886025c912f033095c5e ChangeLog 2543
+SHA256 ef1746438ebe8e44809c7233a0a70b405dda7dc7934d442236a854fe56813cea ChangeLog 2543
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 d9689adfaa082d24189d8a093ac18093 files/digest-openbabel-1.100.2 256
-RMD160 140e84b18e54e83fc5a2edac592aa1d0458763e4 files/digest-openbabel-1.100.2 256
-SHA256 c8b61496992ce6fcbe0ad0182edb18520c62747e2d882101ef7210bca2a5df52 files/digest-openbabel-1.100.2 256
-MD5 d773de0c9645094a87b202373a4ae09b files/digest-openbabel-2.0.1 250
-RMD160 1724d624a1730d6197901449c57bd3a302dd1927 files/digest-openbabel-2.0.1 250
-SHA256 60ebb267ac56987aa89f41c9cba34abc56eef48ff7f32b1225b0e381af406f5f files/digest-openbabel-2.0.1 250
 MD5 cf37985a19405ada669b052795b87bcb files/digest-openbabel-2.0.2 250
 RMD160 a592104d92dece45fa61cd3824259fd61d60f924 files/digest-openbabel-2.0.2 250
 SHA256 b0b9a5dc9d678d2627bc9fe170876f1337b637711dc1450a9ab44ddcaac3757a files/digest-openbabel-2.0.2 250
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFnN5mJXAu5GbtIRAh/DAJ0WezKPWUHZycYbh9/8F5DxgxYA4gCfd9JZ
+0zDeWWO4OlQW/9k9bc1e84c=
+=t5V+
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/openbabel/files/digest-openbabel-1.100.2 b/sci-chemistry/openbabel/files/digest-openbabel-1.100.2
deleted file mode 100644
index 43f0b1fcb4be..000000000000
--- a/sci-chemistry/openbabel/files/digest-openbabel-1.100.2
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 03de74acaadc4beb651f96485169ec65 openbabel-1.100.2.tar.gz 1010494
-RMD160 e56c399455cab3068b7eded7d47f4c9b8dfa20bc openbabel-1.100.2.tar.gz 1010494
-SHA256 15c2f968c475bf8b9e0759ae455b0d7b06e6810c78a2cc2ae1de4cc11bb5f8fb openbabel-1.100.2.tar.gz 1010494
diff --git a/sci-chemistry/openbabel/files/digest-openbabel-2.0.1 b/sci-chemistry/openbabel/files/digest-openbabel-2.0.1
deleted file mode 100644
index 2d2da68dd9dc..000000000000
--- a/sci-chemistry/openbabel/files/digest-openbabel-2.0.1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 843a8d46c56a204cf20500b29b5a79cc openbabel-2.0.1.tar.gz 2454398
-RMD160 7b39b78bedf13ff975086a18422f713ff1a1e8f9 openbabel-2.0.1.tar.gz 2454398
-SHA256 c2f0f1c0dffd357593a57e1bce43895de988c48dae55771b7227fc96bf9546b0 openbabel-2.0.1.tar.gz 2454398
diff --git a/sci-chemistry/openbabel/openbabel-1.100.2.ebuild b/sci-chemistry/openbabel/openbabel-1.100.2.ebuild
deleted file mode 100644
index f90160459c47..000000000000
--- a/sci-chemistry/openbabel/openbabel-1.100.2.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel/openbabel-1.100.2.ebuild,v 1.1 2004/12/24 16:54:33 ribosome Exp $
-
-DESCRIPTION="Open Babel interconverts file formats used in molecular modeling."
-
-SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-KEYWORDS="x86 sparc ppc amd64"
-
-SLOT="0"
-LICENSE="GPL-2"
-IUSE=""
-
-DEPEND="!sci-chemistry/babel"
-
-src_compile() {
-	econf || die "configure failed"
-	emake || die "make failed"
-}
-
-src_install () {
-
-	make DESTDIR=${D} install || die
-	dohtml doc/FAQ.html doc/Migration.html doc/dioxin.png
-	dodoc 	README \
-		doc/README.dioxin.pov \
-		doc/README.povray \
-		doc/babel31.inc \
-		doc/dioxin.inc \
-		doc/dioxin.mol2 \
-		doc/dioxin.pov
-	doman doc/babel.1
-
-}
-
diff --git a/sci-chemistry/openbabel/openbabel-2.0.1.ebuild b/sci-chemistry/openbabel/openbabel-2.0.1.ebuild
deleted file mode 100644
index 6653674513bb..000000000000
--- a/sci-chemistry/openbabel/openbabel-2.0.1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel/openbabel-2.0.1.ebuild,v 1.3 2006/08/03 22:52:28 gustavoz Exp $
-
-DESCRIPTION="Open Babel interconverts file formats used in molecular modeling."
-SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-KEYWORDS="~amd64 ppc sparc x86"
-SLOT="0"
-LICENSE="GPL-2"
-IUSE=""
-RDEPEND="!sci-chemistry/babel"
-
-src_install () {
-	make DESTDIR=${D} install || die
-	dodoc AUTHORS ChangeLog NEWS README THANKS
-	cd doc
-	dohtml *.html *.png
-	dodoc *.inc README* *.inc *.mol2
-}
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index f28294443c66..df6804bc560a 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX pdb2pqr-1.1.2-fpic-gentoo.patch 668 RMD160 e076ebcfe1e0fd39ca7b2219b6d9938b6f4870c8 SHA1 38018f5494b21296dfabe02c61824d0af6d6ce36 SHA256 6455be2583ded00bea43f49789cde72cdd240858f187db6d59ed67c87163af45
 MD5 d1c597eaafca05caa2cffb3b6c214f75 files/pdb2pqr-1.1.2-fpic-gentoo.patch 668
 RMD160 e076ebcfe1e0fd39ca7b2219b6d9938b6f4870c8 files/pdb2pqr-1.1.2-fpic-gentoo.patch 668
@@ -14,27 +17,26 @@ AUX pdb2pqr-propka-gentoo.patch 383 RMD160 aba20c68558d3131b9f04b4188c70e42611f0
 MD5 3700078df26942f1b406cb767bfd9f97 files/pdb2pqr-propka-gentoo.patch 383
 RMD160 aba20c68558d3131b9f04b4188c70e42611f013e files/pdb2pqr-propka-gentoo.patch 383
 SHA256 5f75dfd2a72861b46685568ea6c55be0ed055ab5d72d231e328f7f482252101a files/pdb2pqr-propka-gentoo.patch 383
-DIST pdb2pqr-1.0.2.tar.gz 582352 RMD160 ef3a743eff3533ccb3a72c90721362a217f6e038 SHA256 081eba71c84d2a0437503bf7aa909de9f2ff311acef5f214af2f906b90c1d23a
 DIST pdb2pqr-1.1.2.tar.gz 653600 RMD160 40510384a6b03213d6c857a270d508d4bbefa884 SHA1 89ae9b50e64fc3bbd2a868af01da708fb3f45395 SHA256 ea45ec40b420044e5c7a11744a5db867c544b93d25a8bccf27ebac43cd7d6f94
-EBUILD pdb2pqr-1.0.2.ebuild 1645 RMD160 ebecb11e695825c9d8e82d9d833dbe8ee51e2643 SHA1 858f0b02221798201bc2109444321c63398945b9 SHA256 5d9cafa88d8aa70d119223f5858c31bad7e5e1285869c1b632e5a81b9f7e6005
-MD5 08a7a0573e1ce75bfc1fb14570a8f6b5 pdb2pqr-1.0.2.ebuild 1645
-RMD160 ebecb11e695825c9d8e82d9d833dbe8ee51e2643 pdb2pqr-1.0.2.ebuild 1645
-SHA256 5d9cafa88d8aa70d119223f5858c31bad7e5e1285869c1b632e5a81b9f7e6005 pdb2pqr-1.0.2.ebuild 1645
 EBUILD pdb2pqr-1.1.2.ebuild 1878 RMD160 f06c5c4ec3a0eecbf2aae7898468436b17c13970 SHA1 06fcb9de61dc8d7a54ee23bba4d2d9abdadc4699 SHA256 8f74188fcbae9b1bdd2cdd7b98b3b68c17d18762e374be8e6a8dc9d409d2cd1d
 MD5 92eda2823510951cf21d4c677eeb7469 pdb2pqr-1.1.2.ebuild 1878
 RMD160 f06c5c4ec3a0eecbf2aae7898468436b17c13970 pdb2pqr-1.1.2.ebuild 1878
 SHA256 8f74188fcbae9b1bdd2cdd7b98b3b68c17d18762e374be8e6a8dc9d409d2cd1d pdb2pqr-1.1.2.ebuild 1878
-MISC ChangeLog 1173 RMD160 63fb132c6d1ccb8ef3f3b81880676aaa2cece9cf SHA1 960a8b8557756bf28134cbb4fbf21c955c665b13 SHA256 daa1e680f3c70050fdc5ba624228d1dd54e9f0e125531fdd86ce8b6ebd64a15b
-MD5 a1f7813db96f5f6518b22c1eb5d2b06e ChangeLog 1173
-RMD160 63fb132c6d1ccb8ef3f3b81880676aaa2cece9cf ChangeLog 1173
-SHA256 daa1e680f3c70050fdc5ba624228d1dd54e9f0e125531fdd86ce8b6ebd64a15b ChangeLog 1173
+MISC ChangeLog 1283 RMD160 d90d199565c426810cdc0bbb7b1e3cb2c5737d5a SHA1 d002438cb5b1d1f633e7f92cf26e6bb5f8b01bfe SHA256 006eadaeeb0d18944323c63027be91619f069292dca3b95233ab29283a52ccc8
+MD5 34065fd6177a386cb31098263888641a ChangeLog 1283
+RMD160 d90d199565c426810cdc0bbb7b1e3cb2c5737d5a ChangeLog 1283
+SHA256 006eadaeeb0d18944323c63027be91619f069292dca3b95233ab29283a52ccc8 ChangeLog 1283
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 ab0a8a7c1095b9e755a10ed3f3640f6e files/digest-pdb2pqr-1.0.2 241
-RMD160 15e27b785c4ff5163da1ec819523ad3f2e37e75e files/digest-pdb2pqr-1.0.2 241
-SHA256 e6ab0164f55ac7850ae70b7fbea47161adfdd519cd21aaf888aad26266653240 files/digest-pdb2pqr-1.0.2 241
 MD5 81f7d39024c32ceff1cda274993ace06 files/digest-pdb2pqr-1.1.2 241
 RMD160 043e9c03c065830075fec6a4b561282371f0eb9c files/digest-pdb2pqr-1.1.2 241
 SHA256 362b2c4e1ec25dd3971cef2e00039728697329cecef2432a7e19bd6b2bd6ba62 files/digest-pdb2pqr-1.1.2 241
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoFn15mJXAu5GbtIRAvHPAJ9PYah3Sd+mFog+dsGu/gFdNetGpwCfajcx
+piAkizB6LjmysWMc1WMK0pE=
+=NO5u
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.0.2 b/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.0.2
deleted file mode 100644
index a909e4fb8b23..000000000000
--- a/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.0.2
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 4294713d22ae34079fcd4f652f2c793a pdb2pqr-1.0.2.tar.gz 582352
-RMD160 ef3a743eff3533ccb3a72c90721362a217f6e038 pdb2pqr-1.0.2.tar.gz 582352
-SHA256 081eba71c84d2a0437503bf7aa909de9f2ff311acef5f214af2f906b90c1d23a pdb2pqr-1.0.2.tar.gz 582352
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild
deleted file mode 100644
index 4f6d3b4d0431..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild,v 1.1 2006/03/21 17:07:14 markusle Exp $
-
-inherit eutils fortran python multilib
-
-DESCRIPTION="pdb2pqr is an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations"
-LICENSE="GPL-2"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="http://umn.dl.sourceforge.net/sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="~x86"
-
-DEPEND="dev-lang/python"
-
-FORTRAN="g77 gfortran"
-
-src_unpack() {
-	unpack "${A}"
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PN}-gcc4-gentoo.patch
-	epatch "${FILESDIR}"/${PN}-propka-gentoo.patch
-}
-
-src_install() {
-	python_version
-	INPATH="/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}"
-
-	insinto "${INPATH}"
-	doins __init__.py constants.py || \
-		die "Setting up the pdb2pqr site-package failed."
-
-	exeinto "${INPATH}"
-	doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-	exeinto "${INPATH}"/propka
-	doexe propka/_propkalib.so || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/propka
-	doins propka/propkalib.py propka/__init__.py || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/src
-	doins src/* || die "Installing of python scripts failed."
-
-	insinto "${INPATH}"/dat
-	doins dat/* || die "Installing data failed."
-
-	into /usr/bin
-	dosym "${INPATH}"/${PN}.py /usr/bin/${PN} \
-		|| die "Failed to install symlink into /usr/bin."
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-	dohtml doc/* || die "Failed to install html docs."
-}
-