Initial commit of portage overlay.

author: Donnie Berkholz <donnie@supernova.(none)> 2006-04-17 22:30:24 -0700
committer: Donnie Berkholz <donnie@supernova.(none)> 2006-04-17 22:30:24 -0700
commit: b084e8250f714a5d67587f1d43f40d5774d25643 (patch)
tree: bc819fff34c32bd0c8c4c68df3a846f0b47316ca /sci-chemistry
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99 files changed, 3291 insertions, 0 deletions
diff --git a/sci-chemistry/abinit/Manifest b/sci-chemistry/abinit/Manifest
new file mode 100644
index 0000000..e72b734
--- /dev/null
+++ b/sci-chemistry/abinit/Manifest
@@ -0,0 +1,15 @@
+MD5 cee88059956385392eed0c248cc14619 abinit-5.0.1.ebuild 3017
+RMD160 22e77df54bd7f4f9be06996cdfd2af9dc11dfb7b abinit-5.0.1.ebuild 3017
+SHA256 cdb0b1897b54d78d0c6d16d0aeeb0ce57a34d95950689c8f23e56cd30164d718 abinit-5.0.1.ebuild 3017
+MD5 ac5259d6354fc868b91677d6f5156aa6 files/change-default-directories.patch 1101
+RMD160 3f5ca414d2bae77cbe63ae153040429a4c645acc files/change-default-directories.patch 1101
+SHA256 0e0da3c28440c55c58f16f57051cc808146d20f7efe38ca928e746a729f5b14a files/change-default-directories.patch 1101
+MD5 956f4439794a55f7201ea7350623bf41 files/digest-abinit-5.0.1 244
+RMD160 6cc6e7749fe836a04a043a862e8e896bc36348ac files/digest-abinit-5.0.1 244
+SHA256 f507cdd0d35fbf41c1b97960774ad47957a417b16f927420592439cf18a06a3a files/digest-abinit-5.0.1 244
+MD5 99d257d7a03119e049db21cc1cc9f905 files/fix-blas-lapack-check.patch 1512
+RMD160 ab0a96f451c24150894942129acc9e01be8eade5 files/fix-blas-lapack-check.patch 1512
+SHA256 12e1e65fa85589dad61046cbb25aba25fd58bd13a80dd9b7bce68ecd702fee35 files/fix-blas-lapack-check.patch 1512
+MD5 90e52517d839635e4fdcdf052461e548 files/fix-test-tarball.patch 477
+RMD160 b09cffa5e2933f9cf29224e12ce53fa506535493 files/fix-test-tarball.patch 477
+SHA256 e140381f053193737c4c1e474f65c25024319b296678aa52b1df2ac1161540bd files/fix-test-tarball.patch 477
diff --git a/sci-chemistry/abinit/abinit-5.0.1.ebuild b/sci-chemistry/abinit/abinit-5.0.1.ebuild
new file mode 100644
index 0000000..0246017
--- /dev/null
+++ b/sci-chemistry/abinit/abinit-5.0.1.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+inherit fortran toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
+HOMEPAGE="http://www.abinit.org/"
+SRC_URI="ftp://ftp.abinit.org/pub/abinitio/ABINIT_v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+#IUSE="mpi netcdf test"
+IUSE="mpi test"
+
+RDEPEND="virtual/blas
+	virtual/lapack"
+# Doesn't build with 4.1-20060210
+#	netcdf? ( sci-libs/netcdf )"
+DEPEND="${RDEPEND}"
+
+# F90 code, g77 won't work
+FORTRAN="gfortran ifc"
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	# Doesn't compile with gcc-4.0, only >=4.1-20060210
+	local diemsg="Requires gcc-4.1.0-beta20060210 or newer"
+	if [[ "${FORTRANC}" = "gfortran" ]]; then
+		if [[ $(gcc-major-version) -eq 4 ]]; then
+			if [[ $(gcc-minor-version) -lt 1  ]]; then
+				die "${diemsg}"
+			elif [[ $(gcc-minor-version) -eq 1 ]] \
+				&& [[ $(gcc-minor-version) -eq 0 ]]; then
+				# If it's not a snap, we're good, and gcc-snapshot-version()
+				# will be empty
+				if [[ -n "$(gcc-snapshot-version)" ]] \
+					&& [[ $(gcc-snapshot-version) -lt 20060210 ]]; then
+					die "${diemsg}"
+				fi
+			fi
+		fi
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	epatch ${FILESDIR}/change-default-directories.patch
+	epatch ${FILESDIR}/fix-blas-lapack-check.patch
+	epatch ${FILESDIR}/fix-test-tarball.patch
+	AT_M4DIR="config/m4" eautoreconf
+}
+
+src_compile() {
+	econf \
+		--with-install-type=debian \
+		--disable-autodetect \
+		--disable-config-file \
+		--disable-mpi-search \
+		--disable-library-search \
+		--disable-netcdf \
+		$(use_enable mpi) \
+		--with-blas-prefix=/usr \
+		--with-lapack-prefix=/usr \
+		--with-c-optflags="${CFLAGS}" \
+		--with-fortran-optflags="${FFLAGS}" \
+		FC="${FORTRANC}" \
+		CC="$(tc-getCC)" \
+		|| die "configure failed"
+#		$(use_enable netcdf) \
+
+	emake || die "make failed"
+}
+
+src_test() {
+	einfo "The tests take quite a while, on the order of 2-3 hours"
+	einfo "on a dual Athlon 2000+."
+	cd ${S}/tests
+	emake tests_dev
+
+	local REPORT
+	for REPORT in $(find . -name *fl*); do
+		einfo "Results for ${REPORT%%/*} tests"
+		cat ${REPORT}
+	done
+}
+
+src_install() {
+	make DESTDIR="${D}" install || die "install failed"
+
+	if use test; then
+		dodoc ${S}/tests/summary_tests.tar.gz
+	fi
+
+	dodoc ${S}/KNOWN_PROBLEMS
+	prepalldocs
+}
+
+pkg_postinst() {
+	ewarn "Upstream considers this version unready for production use."
+	ewarn "Major changes occurred in the build system since 4.x."
+	ewarn "If you intend to use it in production, be sure to run all tests"
+	ewarn "and read through the test results by emerging abinit"
+	ewarn "with FEATURES=test and USE=test. Also see the KNOWN_PROBLEMS document."
+	ewarn "The test results will be installed as summary_tests.tar.gz."
+}
+
+gcc-snapshot-version() {
+	echo "$(gcc-fullversion | cut -f3 -d. | cut -f2 -d- | sed -e "s:[[:alpha:]]::g")"
+}
diff --git a/sci-chemistry/abinit/files/change-default-directories.patch b/sci-chemistry/abinit/files/change-default-directories.patch
new file mode 100644
index 0000000..47c9152
--- /dev/null
+++ b/sci-chemistry/abinit/files/change-default-directories.patch
@@ -0,0 +1,24 @@
+diff -urN abinit-5.0.1.orig/config/m4/init.m4 abinit-5.0.1/config/m4/init.m4
+--- abinit-5.0.1.orig/config/m4/init.m4	2005-12-11 06:56:09.000000000 -0800
++++ abinit-5.0.1/config/m4/init.m4	2006-02-10 23:31:47.000000000 -0800
+@@ -132,9 +132,9 @@
+ 
+   debian)
+    abinit_prefix="/usr"
+-   abinit_bindir="/usr/lib/abinit/${ABINIT_VERSION_BASE}/bin"
++   abinit_bindir="/usr/bin"
+    abinit_datdir="/usr/share/abinit"
+-   abinit_docdir="/usr/share/doc/abinit/${ABINIT_VERSION_BASE}"
++   abinit_docdir="/usr/share/doc/abinit-${ABINIT_VERSION_BASE}"
+    abinit_libdir="/usr/lib/abinit/${ABINIT_VERSION_BASE}/lib"
+    abinit_incdir="/usr/include/abinit/${ABINIT_VERSION_BASE}"
+    abinit_mandir="/usr/share/man"
+@@ -212,7 +212,7 @@
+  ABINIT_VERSION_MICRO=`echo "${ABINIT_VERSION}" | cut -d. -f3`
+  ABINIT_VERSION_BUILD=`date '+%Y%m%d'`
+ 
+- ABINIT_VERSION_BASE="${ABINIT_VERSION_MAJOR}.${ABINIT_VERSION_MINOR}"
++ ABINIT_VERSION_BASE="${ABINIT_VERSION_MAJOR}.${ABINIT_VERSION_MINOR}.${ABINIT_VERSION_MICRO}"
+ 
+  dnl Make numbers available to source files
+  AC_DEFINE_UNQUOTED(ABINIT_VERSION,"${ABINIT_VERSION}",
diff --git a/sci-chemistry/abinit/files/digest-abinit-5.0.1 b/sci-chemistry/abinit/files/digest-abinit-5.0.1
new file mode 100644
index 0000000..386d13b
--- /dev/null
+++ b/sci-chemistry/abinit/files/digest-abinit-5.0.1
@@ -0,0 +1,3 @@
+MD5 8dd67f91a089e1ab1646ddbb6160fc92 abinit-5.0.1.tar.gz 19509561
+RMD160 427412872d41490dfaa1777c94131a774d5f793c abinit-5.0.1.tar.gz 19509561
+SHA256 21ac8dc5b264cc3848bc26333920b4c11f80f3ca73517789dde84314f19ef9c2 abinit-5.0.1.tar.gz 19509561
diff --git a/sci-chemistry/abinit/files/fix-blas-lapack-check.patch b/sci-chemistry/abinit/files/fix-blas-lapack-check.patch
new file mode 100644
index 0000000..92c20b9
--- /dev/null
+++ b/sci-chemistry/abinit/files/fix-blas-lapack-check.patch
@@ -0,0 +1,39 @@
+diff -urN abinit-5.0.1.orig/config/m4/extlibs.m4 abinit-5.0.1/config/m4/extlibs.m4
+--- abinit-5.0.1.orig/config/m4/extlibs.m4	2005-12-11 06:58:20.000000000 -0800
++++ abinit-5.0.1/config/m4/extlibs.m4	2006-02-10 23:53:34.000000000 -0800
+@@ -52,7 +52,7 @@
+ 
+    dnl Look for library
+    blas_lib="${with_blas_prefix}/lib/libblas.a"
+-   blas_ldflags="-L${with_blas_prefix}/lib -lblas"
++   blas_ldflags="-L${with_blas_prefix}/lib -lblas -lpthread"
+    if test ! -s "${blas_lib}"; then
+     build_blas="yes"
+    fi
+@@ -61,7 +61,7 @@
+ 
+  if test "${build_blas}" = "yes"; then
+   AC_MSG_NOTICE([the BLAS library will be built])
+-  blas_ldflags="-L\$(top_builddir)/lib/blas -lblas"
++  blas_ldflags="-L\$(top_builddir)/lib/blas -lblas -lpthread"
+   blas_lib="\$(top_builddir)/lib/blas/libblas.a"
+  else
+   AC_MSG_NOTICE([the BLAS library will not be built])
+@@ -109,7 +109,7 @@
+ 
+    dnl Look for library
+    lapack_lib="${with_lapack_prefix}/lib/liblapack.a"
+-   lapack_ldflags="-L${with_lapack_prefix}/lib -llapack"
++   lapack_ldflags="-L${with_lapack_prefix}/lib -llapack -lpthread"
+    if test ! -s "${lapack_lib}"; then
+     build_lapack="yes"
+    fi
+@@ -118,7 +118,7 @@
+ 
+  if test "${build_lapack}" = "yes"; then
+   AC_MSG_NOTICE([the LAPACK library will be built])
+-  lapack_ldflags="-L\$(top_builddir)/lib/lapack -llapack"
++  lapack_ldflags="-L\$(top_builddir)/lib/lapack -llapack -lpthread"
+   lapack_lib="\$(top_builddir)/lib/lapack/liblapack.a"
+  else
+   AC_MSG_NOTICE([the LAPACK library will not be built])
diff --git a/sci-chemistry/abinit/files/fix-test-tarball.patch b/sci-chemistry/abinit/files/fix-test-tarball.patch
new file mode 100644
index 0000000..585a3c8
--- /dev/null
+++ b/sci-chemistry/abinit/files/fix-test-tarball.patch
@@ -0,0 +1,11 @@
+--- abinit-5.0.1.orig/tests/Makefile.am	2006-02-12 14:41:17.000000000 -0800
++++ abinit-5.0.1/tests/Makefile.am	2006-02-12 14:41:41.000000000 -0800
+@@ -1756,7 +1756,7 @@
+ 	tar cvf summary_tests.tar \
+ 	 fast/,,test*/fl* fast/,,test*/*out* \
+ 	 v*/,,test*/fl* v*/,,test*/*out* \
+-	 paral/,,test*/fl* paral/,,test*/*out* \
++	 paral/,,test*/fl* paral/,,test*/*out*
+ 	gzip --best summary_tests.tar
+ 
+ # ---------------------------------------------------------------------------- #
diff --git a/sci-chemistry/caver/ChangeLog b/sci-chemistry/caver/ChangeLog
new file mode 100644
index 0000000..1cd00b2
--- /dev/null
+++ b/sci-chemistry/caver/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/caver
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/ChangeLog,v 1.1 2005/12/20 03:56:38 spyderous Exp $
+
+*caver-0.99.1 (20 Dec 2005)
+
+  20 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml,
+  +caver-0.99.1.ebuild:
+  New package providing rapid, accurate and fully automated calculation of
+  pathways leading from buried cavities to outside solvent in static and
+  dynamic protein structures. Also has a neat PyMol plugin.
+
diff --git a/sci-chemistry/caver/Manifest b/sci-chemistry/caver/Manifest
new file mode 100644
index 0000000..56f61c7
--- /dev/null
+++ b/sci-chemistry/caver/Manifest
@@ -0,0 +1,18 @@
+MD5 8ce02fd5913949883e8686e441725d75 ChangeLog 546
+RMD160 f7ce1bbaa6f53a12834d4df1745701ef453d1644 ChangeLog 546
+SHA256 74496aeb2366a28bd2483be7884bdd4088a04997b7a1eb918661ca028142cb7d ChangeLog 546
+MD5 5ad3b6ca759c8086c47b7f7ff3ea6464 caver-0.99.1.ebuild 1387
+RMD160 ae780284703969589b6814da33d2612c17e31d2b caver-0.99.1.ebuild 1387
+SHA256 61244eb8aa3bc1930b5fbb1ce10fba022dd141518ae758f1e4389d5cb8b0815b caver-0.99.1.ebuild 1387
+MD5 264b9cd6a5c908903498103e8f88ad40 caver-0.99.2.ebuild 1424
+RMD160 eb04af646b375ffe9c37767c98c3ce716dd12753 caver-0.99.2.ebuild 1424
+SHA256 0b694b6880632a20c325db43700aedba21a65fa734a87bf74f387e2e791a43b6 caver-0.99.2.ebuild 1424
+MD5 946c4f9350e2386e497befe7afbe9cc2 files/digest-caver-0.99.1 130
+RMD160 9ca2102fa7a9b2c5257ff4044202c040d82ce628 files/digest-caver-0.99.1 130
+SHA256 fb5d883d649a3227ef05372d785aa49851202133670d2199ac6aecdf11ecae08 files/digest-caver-0.99.1 130
+MD5 8524c8b5718aaac466fa34658468955a files/digest-caver-0.99.2 524
+RMD160 1e54afa8530246f319c0b0a235d9cce35dc050c4 files/digest-caver-0.99.2 524
+SHA256 e7815fe179e318f1f736e8f6cf473f92fb8df0aae52222de71f0ce2fc82c88cf files/digest-caver-0.99.2 524
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
diff --git a/sci-chemistry/caver/caver-0.99.1.ebuild b/sci-chemistry/caver/caver-0.99.1.ebuild
new file mode 100644
index 0000000..5872bf7
--- /dev/null
+++ b/sci-chemistry/caver/caver-0.99.1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-0.99.1.ebuild,v 1.1 2005/12/20 03:56:38 spyderous Exp $
+
+inherit multilib python
+
+MY_PN="${PN}_unix"
+MY_P="${MY_PN}_v${PV}"
+DESCRIPTION="Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures"
+HOMEPAGE="http://viper.chemi.muni.cz/caver/"
+SRC_URI="${MY_P}.tar.gz
+	pymol? ( pymolplug.tar.gz )"
+LICENSE="CAVER"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="pymol"
+RDEPEND="media-libs/qhull
+	pymol? ( sci-chemistry/pymol )"
+DEPEND="${RDEPEND}"
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+pkg_nofetch() {
+	einfo "Download ${MY_P}.tar.gz"
+	if use pymol; then
+		einfo "and pymolplug.tar.gz"
+	fi
+	einfo "from ${HOMEPAGE}. This requires registration."
+	einfo "Place them in ${DISTDIR}."
+}
+
+src_install() {
+	make DESTDIR="${D}" install
+	if use pymol; then
+		python_version
+		sed -i \
+			-e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \
+			${WORKDIR}/pymolplug/caver.py
+		insinto /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup
+		doins ${WORKDIR}/pymolplug/caver.py
+	fi
+}
+
+pkg_postinst() {
+	if use pymol; then
+		python_mod_compile \
+		/usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup/caver.py
+	fi
+}
diff --git a/sci-chemistry/caver/caver-0.99.2.ebuild b/sci-chemistry/caver/caver-0.99.2.ebuild
new file mode 100644
index 0000000..c0639d9
--- /dev/null
+++ b/sci-chemistry/caver/caver-0.99.2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-0.99.1.ebuild,v 1.1 2005/12/20 03:56:38 spyderous Exp $
+
+inherit multilib python
+
+MY_PN="${PN}_unix"
+MY_P="${MY_PN}_v${PV}"
+PLUG_P="${MY_P/caver/caverPLUG}"
+DESCRIPTION="Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures"
+HOMEPAGE="http://viper.chemi.muni.cz/caver/"
+SRC_URI="${MY_P}.tar.gz
+	pymol? ( ${PLUG_P}.tar.gz )"
+LICENSE="CAVER"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="pymol"
+RDEPEND="media-libs/qhull
+	pymol? ( sci-chemistry/pymol )"
+DEPEND="${RDEPEND}"
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+pkg_nofetch() {
+	einfo "Download ${MY_P}.tar.gz"
+	if use pymol; then
+		einfo "and ${PLUG_P}.tar.gz"
+	fi
+	einfo "from ${HOMEPAGE}. This requires registration."
+	einfo "Place tarballs in ${DISTDIR}."
+}
+
+src_install() {
+	make DESTDIR="${D}" install
+	if use pymol; then
+		python_version
+		sed -i \
+			-e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \
+			${WORKDIR}/${PLUG_P}/caver.py
+		insinto /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup
+		doins ${WORKDIR}/${PLUG_P}/caver.py
+	fi
+}
+
+pkg_postinst() {
+	if use pymol; then
+		python_mod_compile \
+		/usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup/caver.py
+	fi
+}
diff --git a/sci-chemistry/caver/files/digest-caver-0.99.1 b/sci-chemistry/caver/files/digest-caver-0.99.1
new file mode 100644
index 0000000..80f3e37
--- /dev/null
+++ b/sci-chemistry/caver/files/digest-caver-0.99.1
@@ -0,0 +1,2 @@
+MD5 7dfc10f67d345d81fa74f0c2c8bbca8d caver_unix_v0.99.1.tar.gz 898765
+MD5 522581ce929adb5d3bef0fa540382362 pymolplug.tar.gz 81137
diff --git a/sci-chemistry/caver/files/digest-caver-0.99.2 b/sci-chemistry/caver/files/digest-caver-0.99.2
new file mode 100644
index 0000000..d8d6005
--- /dev/null
+++ b/sci-chemistry/caver/files/digest-caver-0.99.2
@@ -0,0 +1,6 @@
+MD5 e498466fa232d17fb483cc4568576d2b caverPLUG_unix_v0.99.2.tar.gz 81270
+RMD160 58a5b2b7a1efe41a86d507831f754419ae912b12 caverPLUG_unix_v0.99.2.tar.gz 81270
+SHA256 5b7ca30f26023e2ed9eda6a5430ca5db0ebef7b34f7f8d2391a49182ec0663b1 caverPLUG_unix_v0.99.2.tar.gz 81270
+MD5 b258994fab2957ab20eac77d7a74c276 caver_unix_v0.99.2.tar.gz 1152263
+RMD160 01b877bef15d0f0e1ccce8a3dbcda83826ba76c5 caver_unix_v0.99.2.tar.gz 1152263
+SHA256 9934b5e80f375159132c5327df1fa8bd19ce90682c04c4cd9b91e62476e0f98b caver_unix_v0.99.2.tar.gz 1152263
diff --git a/sci-chemistry/caver/metadata.xml b/sci-chemistry/caver/metadata.xml
new file mode 100644
index 0000000..211b8bd
--- /dev/null
+++ b/sci-chemistry/caver/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
new file mode 100644
index 0000000..67521db
--- /dev/null
+++ b/sci-chemistry/ccp4/Manifest
@@ -0,0 +1,19 @@
+MD5 6297a21e1e45183fe8df70e18c8f2c2d ccp4-5.99.5.ebuild 12167
+MD5 b25f261958764a4ef684582b517d63c5 files/add-xdl-libdir.patch 1545
+MD5 5d4c15532a50ac2e00b68f9a57ce79f2 files/ccp4-5.99.5-install-libs-at-install-time.patch 890
+MD5 b7c4c90e38ef49651876128a209b4546 files/ccp4i-default-to-firefox.patch 717
+MD5 a9fd6533dc70e2c88e4623509e20c30b files/check-blas-lapack-pthread.patch 5335
+MD5 cee8a62b63386a13f4276cab7bf09260 files/clipper-find-mccp4-includes.patch 491
+MD5 fcf801c9c9f1cc7f35294ff95776ff5e files/create-mosflm-bindir.patch 438
+MD5 934ef33e2fc72b4c4ba6ec4fbc3d7122 files/digest-ccp4-5.99.5 129
+MD5 de25d6e610b32fbe607f62914e83a229 files/dont-build-pdb-extract.patch 914
+MD5 8638a4880d926711233e53382f35205a files/dont-build-rasmol.patch 725
+MD5 12cd3967d76e228401cfcd8d156e924d files/dont-chmod-python-binary.patch 606
+MD5 898701d32b28c3916d4374a6c58ef7b9 files/dont-make-dirs-in-configure.patch 2780
+MD5 5c89d8a6c5570d442a71a8c598a80f72 files/make-ipmosflm-dir.patch 375
+MD5 962cb5c0c55797f865254e4dc374183b files/make-mosflm-cbf-libdir.patch 415
+MD5 e38e0ef05c30c16148e8319e0bb0977d files/make-mosflm-index-libdir.patch 358
+MD5 703cb01ad626d4dbf4176a18ea5269a1 files/make-mosflm-libdir.patch 371
+MD5 88b9b19d31b2128746bb99fc27882357 files/make-phaser-bindir.patch 380
+MD5 e74f4860f9f1c929c3b4d4e06fba68e9 files/no-phaser-ld-assume-kernel.patch 581
+MD5 bcdb856dae7ea7b22d130474f6c17b7d files/pass-clipper-enablevals.patch 501
diff --git a/sci-chemistry/ccp4/ccp4-5.99.5.ebuild b/sci-chemistry/ccp4/ccp4-5.99.5.ebuild
new file mode 100644
index 0000000..65fc05e
--- /dev/null
+++ b/sci-chemistry/ccp4/ccp4-5.99.5.ebuild
@@ -0,0 +1,377 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit fortran eutils gnuconfig
+
+FORTRAN="g77 ifc"
+
+DESCRIPTION="Protein X-ray crystallography toolkit"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${PV}/packed/${PN}-core.tar.gz"
+#	ftp://ftp.ccp4.ac.uk/ccp4/${PV}/packed/phaser-cctbx.tar.gz"
+#	ftp://ftp.ccp4.ac.uk/ccp4/${PV}/prerelease/${P}_gfortran.tar.gz"
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="X"
+# app-office/sc overlaps sc binary and man page
+# We can't rename ours since the automated ccp4i interface expects it there,
+# as do many scripts. app-office/sc can't rename its because that's the name
+# of the package.
+RDEPEND="X? (
+			|| (
+				(
+					x11-libs/libX11
+					x11-libs/libXt
+					x11-libs/libXaw
+				)
+				virtual/x11
+			)
+		)
+		>=dev-lang/tcl-8.3
+		>=dev-lang/tk-8.3
+		>=dev-tcltk/blt-2.4
+		virtual/lapack
+		virtual/blas
+		=sci-libs/fftw-2*
+		sci-chemistry/pdb-extract
+		sci-chemistry/rasmol
+		sci-libs/mccp4
+		app-shells/tcsh
+		!app-office/sc"
+DEPEND="${RDEPEND}
+		X? (
+			|| (
+				(
+					x11-misc/imake
+					x11-proto/inputproto
+					x11-proto/xextproto
+				)
+				virtual/x11
+			)
+		)"
+
+src_unpack() {
+	unpack ${A}
+
+# These two only needed when attempting to install outside build dir via
+# --bindir and --libdir instead of straight copying after build
+	# it attempts to install some libraries during the build
+#	epatch ${FILESDIR}/${P}-install-libs-at-install-time.patch
+	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
+	# without this patch when --libdir is set
+	# Rotgen still needs more patching to find it
+#	epatch ${FILESDIR}/add-xdl-libdir.patch
+
+	# it tries to create libdir, bindir etc on live system in configure
+	epatch ${FILESDIR}/dont-make-dirs-in-configure.patch
+
+	# We already have sci-chemistry/rasmol
+	epatch ${FILESDIR}/dont-build-rasmol.patch
+
+	# We already have sci-chemistry/pdb-extract
+# Use configure option instead
+#	epatch ${FILESDIR}/dont-build-pdb-extract.patch
+
+	epatch ${FILESDIR}/create-mosflm-bindir.patch
+	epatch ${FILESDIR}/make-mosflm-libdir.patch
+	epatch ${FILESDIR}/make-mosflm-index-libdir.patch
+	epatch ${FILESDIR}/make-mosflm-cbf-libdir.patch
+	epatch ${FILESDIR}/make-ipmosflm-dir.patch
+
+# Don't use these when we aren't building phaser
+#	epatch ${FILESDIR}/make-phaser-bindir.patch
+#	epatch ${FILESDIR}/no-phaser-ld-assume-kernel.patch
+#	# scons config.py tries to chmod python on live system
+#	epatch ${FILESDIR}/dont-chmod-python-binary.patch
+
+	# Don't use this when we aren't building clipper
+	# For some reason clipper check for $enableval even when --enable is passed
+	epatch ${FILESDIR}/pass-clipper-enablevals.patch
+	epatch ${FILESDIR}/clipper-find-mccp4-includes.patch
+
+	# Default to firefox browser, not 'netscape'
+	epatch ${FILESDIR}/ccp4i-default-to-firefox.patch
+
+	# Also use -lpthread when linking blas and lapack
+	# We may need more fixing to use libcblas for the C files
+	epatch ${FILESDIR}/check-blas-lapack-pthread.patch
+
+	gnuconfig_update
+}
+
+src_compile() {
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${FORTRANC}" = "ifc" ]]; then
+		if use ia64; then
+			GENTOO_OSNAME="ia64_linux_intel"
+		else
+			# Should be valid for x86, maybe amd64
+			GENTOO_OSNAME="linux_intel_compilers"
+		fi
+	else
+		# Should be valid for x86 and amd64, at least
+		GENTOO_OSNAME="linux"
+	fi
+
+	# Sets up env
+	ln -s \
+		ccp4.setup-bash \
+		${S}/include/ccp4.setup
+
+	# We agree to the license by emerging this, set in LICENSE
+	sed -i \
+		-e "s~^\(^agreed=\).*~\1yes~g" \
+		${S}/configure
+
+	# Fix up variables -- need to reset CCP4_MASTER at install-time
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)/xtal~\1${WORKDIR}~g" \
+		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
+		${S}/include/ccp4.setup*
+
+	# Set up variables for build
+	source ${S}/include/ccp4.setup
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=${FORTRANC}
+	export FOPTIM=${FFLAGS:- -O2}
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		$(use_enable X x) \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-pdb_extract \
+		--disable-cctbx \
+		--disable-phaser \
+		${GENTOO_OSNAME} || die "econf failed"
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+# Only needed when using --bindir and --libdir
+	# Needed to avoid errors. Originally tried to make lib and bin
+	# in configure script, now patched out by dont-make-dirs-in-configure.patch
+#	dodir /usr/include /usr/$(get_libdir) /usr/bin
+
+	make install || die "install failed"
+
+	# Fix env
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
+		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
+		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/$(get_libdir)/ccp4/include~g" \
+		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/$(get_libdir)/ccp4/data~g" \
+		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
+		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
+		${S}/include/ccp4.setup*
+
+	# Get rid of S instances
+	# Also the main clipper library is built as libclipper-core, not libclipper
+	sed -i \
+		-e "s:${S}:${ROOT}usr:g" \
+		-e "s:lclipper :lclipper-core:g" \
+		${S}/bin/clipper-config
+#	sed -i \
+#		-e "s:${S}:${ROOT}usr:g" \
+#		${S}/$(get_libdir)/cctbx/cctbx_build/setpaths*
+
+	# Bins
+	EXEDESTTREE="/usr/bin" doexe ${S}/bin/*
+
+	# Libs
+	for file in ${S}/lib/*; do
+		if [[ -d ${file} ]]; then
+			continue
+		elif [[ -x ${file} ]]; then
+			dolib.so ${file}
+		else
+			INSDESTTREE="/usr/$(get_libdir)" doins ${file}
+		fi
+	done			
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
+		${D}/usr/$(get_libdir)/*.la
+
+	# Library symlinks
+	local LIBNAMES="libclipper-ccp4.so.0.0.0
+		libclipper-cif.so.0.0.0
+		libclipper-contrib.so.0.0.0
+		libclipper-core.so.0.0.0
+		libclipper-minimol.so.0.0.0
+		libclipper-mmdbold.so.0.0.0
+		libclipper-mmdb.so.0.0.0
+		libclipper-mtz.so.1.0.0
+		libclipper-phs.so.0.0.0
+		libjwc_c.so.0.1.1
+		libjwc_f.so.0.1.1
+		libssm.so.0.0.0
+		libxdl_viewextra.so.0.0.0
+		libxdl_view.so.2.0.0"
+
+	for LIBNAME in ${LIBNAMES}; do
+		library_dosym ${LIBNAME}
+	done
+
+#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
+#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
+#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
+#
+#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
+#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
+#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
+#
+#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
+#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
+#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
+#
+#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
+#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
+#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
+#
+#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
+#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
+#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
+#
+#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
+#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
+#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
+#
+#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
+#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
+#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
+#
+#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
+#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
+#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
+#
+#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
+#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
+#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
+#
+#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
+#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
+#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
+#
+#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
+#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
+#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
+#
+#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
+#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
+#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
+#
+#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
+#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
+#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
+#
+#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
+#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
+#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
+
+	# Environment files, setup scripts, etc.
+	INSDESTTREE="/usr/$(get_libdir)/ccp4/include" doins ${S}/include/*
+
+	# CCP4Interface - GUI
+	INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i
+	EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/*
+
+	# Data
+	INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/lib/data
+
+	# Include files
+	for i in ccp4 clipper mmdb ssm; do
+		INSDESTTREE="/usr/include" doins -r ${S}/include/${i}
+	done
+
+	# Install docs and examples
+
+	doman ${S}/man/cat1/*
+
+	mv ${S}/manual/README ${S}/manual/README-manual
+	dodoc ${S}/manual/*
+
+	dodoc ${S}/README ${S}/CHANGES
+
+	dodoc ${S}/doc/*
+	rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz
+	rm ${D}/usr/share/doc/${PF}/COPYING.gz
+
+	dohtml -r ${S}/html/*
+	dodoc ${S}/examples/README
+
+	for i in data rnase toxd; do
+		DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/*
+	done
+
+	DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html
+	DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css
+	for i in data results; do
+		DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/*
+	done
+
+	for i in non-runnable runnable; do
+		DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i}
+	done
+
+	# Needed for ccp4i docs to work
+	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
+	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/examples
+
+	# Fix overlaps with other packages
+	rm ${D}/usr/share/man/man1/rasmol.1.gz
+}
+
+pkg_postinst() {
+	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+	einfo "in /usr/$(get_libdir)/ccp4/include/ccp4.setup* to modify this."
+
+	ewarn "Set your .bashrc or other shell login file to source"
+	ewarn "one of the ccp4.setup* files in ${ROOT}usr/$(get_libdir)/ccp4/include."
+	ewarn "CCP4 will not work without this."
+}
+
+# Links libname.so, libname.so.major and libname.so.major.minor
+# to libname.so.major.minor.micro
+library_dosym() {
+	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
+
+	LIBNAME=${1}
+	LIBDIR=${2:-/usr/$(get_libdir)}
+
+	# Tag / on the end of libdir if needed
+	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
+		LIBDIR="${LIBDIR}/"
+	fi
+
+	if [[ "${LIBNAME}" != *.so.* ]]; then
+		msg="library_dosym() requires a shared, versioned library as an argument"
+		eerror "$msg"
+		die "$msg"
+	fi
+
+	SUFFIX=${LIBNAME##*so.}
+	CORE_LIBNAME=${LIBNAME%.so.*}
+	CORE_LIBNAME="${CORE_LIBNAME}.so"
+	LIB_MAJOR=${SUFFIX%%.*}
+	LIB_MINOR=${SUFFIX#*.}
+	LIB_MINOR=${SUFFIX%%.*}
+	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
+	for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do
+		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
+		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
+	done
+}
diff --git a/sci-chemistry/ccp4/files/add-xdl-libdir.patch b/sci-chemistry/ccp4/files/add-xdl-libdir.patch
new file mode 100644
index 0000000..fbb5dad
--- /dev/null
+++ b/sci-chemistry/ccp4/files/add-xdl-libdir.patch
@@ -0,0 +1,29 @@
+--- ccp4-5.99.5.orig/configure	2005-12-05 02:26:38.000000000 -0800
++++ ccp4-5.99.5 /configure	2005-12-05 02:30:35.000000000 -0800
+@@ -1616,7 +1616,7 @@
+                    sftools_FLAGS='$XFFLAGS $FOPTIM' \
+                    lgglib_FLAGS='$XFFLAGS -O0' \
+                arp_waters_FLAGS='$XFFLAGS $FOPTIM' "}
+-  XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"}
++  XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"}
+   XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"}
+   XTYPE=${XTYPE:-"LINUX"}
+   TIDY=${TIDY:-"rm -f sta*"}
+@@ -1752,7 +1752,7 @@
+                       arp_waters_FLAGS='$XFFLAGS $FOPTIM -fforce-mem' \
+                       mlphare_FLAGS='$XFFLAGS $FOPTIM -fno-move-all-movables' \
+                       stereo_FLAGS='$XFFLAGS $FOPTIM -fno-move-all-movables' "}
+-  XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"}
++  XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"}
+   XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"}
+   XTYPE=${XTYPE:-"LINUX"}
+   CXX_LIBS=${CXX_LIBS:-"-lstdc++"}
+@@ -1871,7 +1871,7 @@
+                       refmac5_FLAGS='$XFFLAGS $FOPTIM' \
+                       arp_waters_FLAGS='$XFFLAGS $FOPTIM'\
+                       distang_FLAGS='$XFFLAGS -O1' "}
+-  XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"}
++  XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"}
+   XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"}
+   XTYPE=${XTYPE:-"LINUX"}
+   if test "$shared_lib" = yes; then
diff --git a/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch b/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch
new file mode 100644
index 0000000..9170124
--- /dev/null
+++ b/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch
@@ -0,0 +1,40 @@
+--- ccp4-5.99.5.orig/x-windows/Makefile.in	2005-12-05 01:30:59.000000000 -0800
++++ ccp4-5.99.5.orig/x-windows/Makefile.in	2005-12-05 01:31:50.000000000 -0800
+@@ -42,8 +42,7 @@
+ xdlview_dir = $(srcdir)/xdl_view/src
+ xdlview :
+ 	cd $(xdlview_dir) ; \
+-	$(MAKE) $(MFLAGS) ; \
+-	$(MAKE) install 
++	$(MAKE) $(MFLAGS)
+ 
+ #
+ # rotgen and libraries
+@@ -56,15 +55,13 @@
+ #
+ libjwc_c :
+ 	cd $(libjwc_c_dir) ; \
+-	$(MAKE) $(MFLAGS) ; \
+-	$(MAKE) install
++	$(MAKE) $(MFLAGS)
+ #
+ # libjwc_f
+ #
+ libjwc_f :
+ 	cd $(libjwc_f_dir) ; \
+-	$(MAKE) $(MFLAGS) ; \
+-	$(MAKE) install
++	$(MAKE) $(MFLAGS)
+ #
+ # rotgen
+ #
+@@ -167,6 +164,9 @@
+ 	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
+ 	cd $(rotgen_dir); $(MAKE) install
+ 	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
++	cd $(xdlview_dir); $(MAKE) install
++	cd $(libjwc_c_dir); $(MAKE) install
++	cd $(libjwc_f_dir); $(MAKE) install
+ #
+ # clean
+ #
diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
new file mode 100644
index 0000000..106db89
--- /dev/null
+++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
@@ -0,0 +1,13 @@
+--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist	2006-01-06 17:54:17.000000000 -0800
++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist	2006-01-06 17:54:47.000000000 -0800
+@@ -54,8 +54,8 @@
+ MESSAGE                   _text				""
+ BLT_LIBRARY               _text                     ""
+ MENU_LENGTH               _positiveint              25
+-HYPERTEXT_VIEWER          _text                     netscape
+-START_NETSCAPE	          _text			    netscape
++HYPERTEXT_VIEWER          _text                     firefox
++START_NETSCAPE	          _text			    firefox
+ O_MAPMAN                  _text                     mapman
+ MAPMAN_MAXSIZE		  _positiveint		    4194304
+ QUANTA_MBKALL             _text                     mbkall
diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
new file mode 100644
index 0000000..02a2aa6
--- /dev/null
+++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
@@ -0,0 +1,103 @@
+--- ccp4-5.99.5.orig/configure	2006-01-17 00:35:36.000000000 -0800
++++ ccp4-5.99.5/configure	2006-01-17 10:44:39.000000000 -0800
+@@ -2410,12 +2410,12 @@
+       end
+ EOF
+           #firslty test without -lblas
+-          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
++          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread"
+           echo $test_compile
+           if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
+             # Compilation was okay
+-            echo "... only -llapack needed"
+-            XLAPACK_LIB="-llapack"
++            echo "... only -llapack -lpthread needed"
++            XLAPACK_LIB="-llapack -lpthread"
+             # Set the next two variables so that configure
+             # doesn't try to build netlib libraries
+             LAPACKLIB="lapack"
+@@ -2424,12 +2424,12 @@
+             tryblas=
+           else
+ 	    echo "more than just -llapack needed...."
+-            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
++            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread"
+             echo $test_compile
+             if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+               # Compilation was okay
+-              echo "...-llapack and -lblas were needed"
+-              XLAPACK_LIB="-llapack -lblas"
++              echo "...-llapack, -lpthread and -lblas were needed"
++              XLAPACK_LIB="-llapack -lpthread -lblas"
+               # Set the next two variables so that configure
+               # doesn't try to build netlib libraries
+               LAPACKLIB="lapack blas"
+@@ -2720,8 +2720,8 @@
+       STOP
+       END
+ EOF
+-                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
+-                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
++                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
++                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
+                 echo $test_compile
+                 if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+                   have_lapack=yes
+@@ -2738,7 +2738,7 @@
+                   LAPACKDIR="$testdir"
+                   echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
+ 		  #
+-		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
++		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread"
+                   #
+                   # Test to see if we need BLAS too
+                   # Do this by trying to compile a test program
+@@ -2750,8 +2750,8 @@
+                   if test -f testlsame ; then
+                     rm -f testsame testlsame.o
+                   fi
+-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
+-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
++                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread"
++                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread"
+                   echo $test_compile
+                   if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
+                     have_blas=yes
+@@ -2830,8 +2830,8 @@
+       STOP
+       END
+ EOF
+-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
+-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
++                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
++                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
+                   echo $test_compile
+                   if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
+                     have_blas=yes
+@@ -3033,7 +3033,7 @@
+         if test -f testlsame ; then
+           rm -f testsame testlsame.o
+         fi
+-        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB"
++        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread"
+         echo $test_compile
+         if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
+           echo "Found LSAME in lib$BLASLIB"
+@@ -3046,7 +3046,7 @@
+         if test -f testxerbla ; then
+           rm -f testxerbla testxerbla.o
+         fi
+-        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB"
++        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread"
+         echo $test_compile
+         if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then
+           # Found lsame
+@@ -3080,7 +3080,7 @@
+     cd ../..
+     #
+     lapackdir=lib/lapack
+-    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB"
++    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread"
+ # netlib lapack is in fortran, so we may need the fortran libraries when
+ # we are linking using the C or C++ compilers
+     case $system in 
diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
new file mode 100644
index 0000000..3bf5a06
--- /dev/null
+++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5/lib/clipper/configure.orig	2006-01-07 16:54:13.000000000 -0800
++++ ccp4-5.99.5/lib/clipper/configure	2006-01-07 16:54:31.000000000 -0800
+@@ -21751,7 +21751,7 @@
+ 
+ if test "x$mccp4_prefix" != x; then
+  # ie. mccp4=thing was given (thing is what we're checking for)
+- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include"
++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4"
+  ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4"
+ else
+  # treat as standard lib/include
diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
new file mode 100644
index 0000000..34d6197
--- /dev/null
+++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Makefile.in	2006-01-06 12:31:02.000000000 -0800
++++ ccp4-5.99.5/x-windows/Makefile.in	2006-01-06 12:31:30.000000000 -0800
+@@ -158,6 +158,7 @@
+ install_obj = ipdisp.exe hklview xdldataman xdlmapman \
+ rotgen ipmosflm
+ install: all
++	mkdir -p $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
diff --git a/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 b/sci-chemistry/ccp4/files/digest-ccp4-5.99.5
new file mode 100644
index 0000000..f00d379
--- /dev/null
+++ b/sci-chemistry/ccp4/files/digest-ccp4-5.99.5
@@ -0,0 +1,2 @@
+MD5 1dc37afc2597bceaabd971ba20d86ac3 ccp4-core.tar.gz 59156210
+MD5 ac745815cdff2c4c719e9171f029b3ba phaser-cctbx.tar.gz 17821731
diff --git a/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch b/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch
new file mode 100644
index 0000000..721b235
--- /dev/null
+++ b/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch
@@ -0,0 +1,21 @@
+--- ccp4-5.99.5.orig/src/Makefile.in	2006-01-05 22:52:56.000000000 -0800
++++ ccp4-5.99.5/src/Makefile.in	2006-01-05 22:55:58.000000000 -0800
+@@ -57,7 +57,7 @@
+ 
+ PDB_EXTRACT_TARGETS = pdb_extract extract pdb_extract_sf
+ 
+-all : $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) $(PDB_EXTRACT_SUITE) ccp4mapwish phaser
++all : $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) ccp4mapwish phaser
+ 
+ .PHONY : all install instsome clean realclean distclean
+ 
+@@ -67,9 +67,6 @@
+ 	-for i in $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) $(JAVATARGETS); do \
+ 	  test -s $$i  &&  $(INSTALL_PROGRAM) `pwd`/$$i $(bindir)/$$i || true ;\
+ 	done
+-	for i in $(PDB_EXTRACT_TARGETS); do \
+-	  test -s harvest_app_/pdb_extract/bin/$$i  &&  $(INSTALL_PROGRAM) harvest_app_/pdb_extract/bin/$$i $(bindir)/$$i || true ;\
+-	done
+ 	if test -f ccp4mapwish_/Makefile; then \
+ 	   cd ccp4mapwish_; $(MAKE) -i $(MFLAGS) $@; \
+ 	else true; fi
diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
new file mode 100644
index 0000000..8da54fd
--- /dev/null
+++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
@@ -0,0 +1,19 @@
+--- ccp4-5.99.5.orig/x-windows/Makefile.in	2005-12-05 03:06:57.000000000 -0800
++++ ccp4-5.99.5/x-windows/Makefile.in	2005-12-05 03:07:23.000000000 -0800
+@@ -35,7 +35,7 @@
+ #
+ # all
+ #
+-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm
++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm
+ #
+ # xdl_view
+ #
+@@ -161,7 +161,6 @@
+ 	$(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir)
+ 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) install
+-	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
+ 	cd $(rotgen_dir); $(MAKE) install
+ 	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
+ 	cd $(xdlview_dir); $(MAKE) install
diff --git a/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch b/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch
new file mode 100644
index 0000000..21f3053
--- /dev/null
+++ b/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch
@@ -0,0 +1,14 @@
+--- ccp4-5.99.5.orig/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py	2006-01-06 21:48:09.000000000 -0800
++++ ccp4-5.99.5/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py	2006-01-06 21:46:24.000000000 -0800
+@@ -756,8 +756,9 @@
+     else:
+       action = self.write_bin_sh_dispatcher
+       ext = ""
+-      try: os.chmod(source_file, 0755)
+-      except OSError: pass
++      if source_file != self.python_exe:
++        try: os.chmod(source_file, 0755)
++        except OSError: pass
+     target_file_ext = target_file + ext
+     remove_or_rename(target_file_ext)
+     try: action(source_file, target_file_ext)
diff --git a/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch
new file mode 100644
index 0000000..24504d9
--- /dev/null
+++ b/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch
@@ -0,0 +1,87 @@
+--- ccp4-5.99.5.orig/configure	2005-12-05 02:03:51.000000000 -0800
++++ ccp4-5.99.5/configure	2005-12-05 02:03:54.000000000 -0800
+@@ -604,45 +604,45 @@
+ #     echo "! Beware -- the $system installation isn't properly tested." ; }
+ syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
+ 
+-if test -z "$onlylibs" ; then 
+-   for i in CCP4_SCR BINSORT_SCR; do
+-     if ( eval test -d \$$i || eval mkdir \$$i ) ; then :
+-     else
+-       eval echo "! No directory \$$i and can\'t create it."
+-       echo "  Check the value of $i."
+-       badvar=1
+-     fi
+-   done
+-
+-   for i in libdir bindir; do
+-     if ( eval test -d \$$i || eval mkdir \$$i ) ; then :
+-     else
+-       eval echo "! No directory \$$i and can\'t create it."
+-       echo "  Check the argument of --$i."
+-       badvar=1
+-     fi
+-   done
+-
+-   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
+-     if test -d $i || mkdir $i; then :
+-     else
+-       eval echo "! No directory $i and can\'t create it."
+-       badvar=1
+-     fi
+-   done
+-else
+-   # Kludge to fool the "Makefile" target in the top-level CCP4
+-   # Makefile into not trying to remake src/Makefile.in
+-   for i in $srcdir/src $srcdir/lib/src ; do
+-     if test -d $i || mkdir $i; then
+-       if ! test -f $i/Makefile.in ; then
+-         echo
+-         echo "onlylibs: making dummy file $i/Makefile.in"
+-	 touch $i/Makefile.in
+-       fi
+-     fi
+-   done
+-fi
++#if test -z "$onlylibs" ; then 
++#   for i in CCP4_SCR BINSORT_SCR; do
++#     if ( eval test -d \$$i || eval mkdir \$$i ) ; then :
++#     else
++#       eval echo "! No directory \$$i and can\'t create it."
++#       echo "  Check the value of $i."
++#       badvar=1
++#     fi
++#   done
++#
++#   for i in libdir bindir; do
++#     if ( eval test -d \$$i || eval mkdir \$$i ) ; then :
++#     else
++#       eval echo "! No directory \$$i and can\'t create it."
++#       echo "  Check the argument of --$i."
++#       badvar=1
++#     fi
++#   done
++#
++#   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
++#     if test -d $i || mkdir $i; then :
++#     else
++#       eval echo "! No directory $i and can\'t create it."
++#       badvar=1
++#     fi
++#   done
++#else
++#   # Kludge to fool the "Makefile" target in the top-level CCP4
++#   # Makefile into not trying to remake src/Makefile.in
++#   for i in $srcdir/src $srcdir/lib/src ; do
++#     if test -d $i || mkdir $i; then
++#       if ! test -f $i/Makefile.in ; then
++#         echo
++#         echo "onlylibs: making dummy file $i/Makefile.in"
++#	 touch $i/Makefile.in
++#       fi
++#     fi
++#   done
++#fi
+ 
+ ### sanity checks
+ 
diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
new file mode 100644
index 0000000..7813141
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:12.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:41.000000000 -0800
+@@ -37,6 +37,7 @@
+ 	${F77} ${FFLAGS} -o $@ $<
+ 
+ ipmosflm:	${OBJS}
++		mkdir -p ${DPSBIN}
+ 		${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \
+                 -o ${DPSBIN}/ipmosflm ${LDFLAGS}
+ 
diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
new file mode 100644
index 0000000..ae4b763
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:42:19.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:43:35.000000000 -0800
+@@ -132,7 +132,7 @@
+ #
+ # CBF library
+ #
+-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
+ 	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+ 	$(AR) cr $@ *.o
+ 	$(RANLIB) $@
diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
new file mode 100644
index 0000000..97607b6
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:09.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:30.000000000 -0800
+@@ -76,6 +76,7 @@
+ 
+ # local version of libdps_index.a
+ ${LIB}/dps_index.a: ${IOBJS} ${HOBJS}
++	mkdir -p ${LIB}
+ 	ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS}
+ 
+ ${LIB}/libpeak.a: 
diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
new file mode 100644
index 0000000..eac1b9f
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:48:47.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:49:02.000000000 -0800
+@@ -42,6 +42,7 @@
+ 	$(LOCALLIBS) $(LIBS) 
+ 
+ index: $(IOBJS) 
++	mkdir -p $(LIBDIR)
+ 	${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS)
+ 	chmod 644 $(LIBDIR)/libdps_index.a
+ 
diff --git a/sci-chemistry/ccp4/files/make-phaser-bindir.patch b/sci-chemistry/ccp4/files/make-phaser-bindir.patch
new file mode 100644
index 0000000..cdf1460
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-phaser-bindir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/src/phaser/ccp4_build	2006-01-06 15:56:22.000000000 -0800
++++ ccp4-5.99.5/src/phaser/ccp4_build	2006-01-06 15:55:49.000000000 -0800
+@@ -65,6 +65,7 @@
+ ./install $phaseropts --static_libraries --component="phaser" --target="exe/phaser"
+ 
+ # Install in CCP4 bindir
++mkdir -p $bindir
+ cp phaser-$PHASER_VERSION/build/$PHASER_MTYPE/exe/phaser $bindir
+ 
+ echo " "
diff --git a/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch b/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch
new file mode 100644
index 0000000..8011c3f
--- /dev/null
+++ b/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch
@@ -0,0 +1,15 @@
+--- ccp4-5.99.5.orig/src/phaser/conf/configure-options	2006-01-06 11:27:28.000000000 -0800
++++ ccp4-5.99.5/src/phaser/conf/configure-options	2006-01-06 11:26:29.000000000 -0800
+@@ -33,9 +33,9 @@
+   set font_dirs = ''
+   set strip_command = 'strip'
+   set wxpython_env = ''
+-  if ( "$PHASER_MTYPE" == "intel-linux" ) then
+-    setenv LD_ASSUME_KERNEL 2.4.1
+-  endif
++#  if ( "$PHASER_MTYPE" == "intel-linux" ) then
++#    setenv LD_ASSUME_KERNEL 2.4.1
++#  endif
+ else if ( "$PHASER_MTYPE" == "alpha-tru64" ) then
+   set python_configure = '--with-cxx=cxx'
+   set libpng_arch = 'dec'
diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
new file mode 100644
index 0000000..3e1a8b0
--- /dev/null
+++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5.orig/configure	2006-01-06 11:45:43.000000000 -0800
++++ ccp4-5.99.5/configure	2006-01-06 11:46:53.000000000 -0800
+@@ -3210,7 +3210,7 @@
+ #ccp4 setup
+   xopts="${xopts} --with-ccp4=${srcdir}"
+ #interface setup
+-  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
++  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
+   echo   
+   echo "********* CLIPPER CONFIGURATION ***********"
+   echo
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
new file mode 100644
index 0000000..44f281a
--- /dev/null
+++ b/sci-chemistry/coot/Manifest
@@ -0,0 +1,36 @@
+MD5 73492ab7c15201eb04ec25e684c40768 coot-0.0.33.ebuild 1738
+RMD160 c2ee74255ab0b5a01580fcb3c915ef2893abfc8f coot-0.0.33.ebuild 1738
+SHA256 3a90f07be537bb769bd0eb4e6c784beddd93affcaa3781d564dae70df025b2bc coot-0.0.33.ebuild 1738
+MD5 1cc73d156ed5718782f6055f1b011251 coot-0.1.ebuild 2036
+RMD160 442cd4151270ba62e907ce867a026b046631605f coot-0.1.ebuild 2036
+SHA256 13f4c22a845b16e770126c54c283f4f149c7b60469f9277458376c2733927361 coot-0.1.ebuild 2036
+MD5 848b7861d1b09fd6474ead9f9bdc1d08 files/0.1-fix-build.patch 6879
+RMD160 397f4c9636f3289e9798d9959333eac612b09162 files/0.1-fix-build.patch 6879
+SHA256 eddfe2e6c1cd8ca30353f3dbb25a6b14b3cd0a13b72e03aae90e0ad146b13dce files/0.1-fix-build.patch 6879
+MD5 6873d9a8bf2305521cdeadcfa45c5c98 files/add-mmdb-includedir.patch 551
+RMD160 e3ceb851e986a0938b1bf19203f849a17b106dda files/add-mmdb-includedir.patch 551
+SHA256 151e4e1166de7624c8b5ea2c6e84cbfa840285633ae61aedddb5ac3462b9d008 files/add-mmdb-includedir.patch 551
+MD5 e409414e5b1d9e1413f77c61ef69ece2 files/add-needed-includes-libs.patch 3132
+RMD160 b7aee685e04ed6a4de2de80b6c32fcbef1e62fa7 files/add-needed-includes-libs.patch 3132
+SHA256 42ed6b879cf56dbc702afe84f16e4c7da82ac19b3c17a94480dd20bcb8650b88 files/add-needed-includes-libs.patch 3132
+MD5 f3852c0023f7cc86e1f9589d6818cb89 files/coot-0.1_pre1-coot-fftw-single.patch 1819
+RMD160 e81813f144f5cbc41420720c04be8f9a45aee36a files/coot-0.1_pre1-coot-fftw-single.patch 1819
+SHA256 42bf86db30a9abff3eb9beb595a1dc7cd7e2e2a8f954fdb814683754e42ba653 files/coot-0.1_pre1-coot-fftw-single.patch 1819
+MD5 8fbf12b34d09d505c441d3d0a0264bd8 files/coot-0.1_pre1-scripts-in-bin.patch 490
+RMD160 a6cbbbd217e094eb0ea8f2d486f5a7af757c9e7a files/coot-0.1_pre1-scripts-in-bin.patch 490
+SHA256 d600efff3d02ca902f44b742c6129bcb2e162ff537ae1987fe2e14133ee890f9 files/coot-0.1_pre1-scripts-in-bin.patch 490
+MD5 79d5f3b8f68fe0c7ee1055efaf4933c7 files/digest-coot-0.0.33 214
+RMD160 ac8fe4f98830a804c994d480ae800e90a2e1e353 files/digest-coot-0.0.33 214
+SHA256 d1075a8573ed64b76aede5f4612be5878bf5343eefd1c560f6c10d14827c152c files/digest-coot-0.0.33 214
+MD5 f3c79d65a72ef891cda85959ffdb1f29 files/digest-coot-0.1 771
+RMD160 aafaa2ef744ec91459573ee5e71d601f85093f81 files/digest-coot-0.1 771
+SHA256 fd193c645ece8082b50b61224e4e08050ab2b2415b82c67cd777ea5f317df8da files/digest-coot-0.1 771
+MD5 626ca012306b9c9f81ece8fa6d0478c5 files/glutinit.patch 494
+RMD160 9dfadaa40bd6664a5ea593b7033d58418ff1ab36 files/glutinit.patch 494
+SHA256 00b99f0257fbba7a6164013fd2c45e2cb497bde447859fba183c917f58cd1bec files/glutinit.patch 494
+MD5 07e6d9582f242b8fe91b3b61179bf444 files/setupdir.patch 499
+RMD160 b1009b7207ed9fc4cecbd960a24e1f322a8210e2 files/setupdir.patch 499
+SHA256 872a7e8d1cfa03f4f56967c16f8db8453c2c7b96ed31c69b2b330130da6b8961 files/setupdir.patch 499
+MD5 90602c119834fb507bffef4028b20f3b files/use-fftw-single.patch 1417
+RMD160 f74e61ca89edb8ed268f42a4bd09f101da6d3cd5 files/use-fftw-single.patch 1417
+SHA256 9aa65d58fc08e0bbdae0af921bcbdfac974edd05c038c617eecf9df9bedd3e40 files/use-fftw-single.patch 1417
diff --git a/sci-chemistry/coot/coot-0.0.33.ebuild b/sci-chemistry/coot/coot-0.0.33.ebuild
new file mode 100644
index 0000000..786c8e1
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.0.33.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils autotools
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz
+	http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
+	http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE=""
+RDEPEND=">=sci-libs/gsl-1.3
+	=dev-libs/glib-1.2*
+	=x11-libs/gtkglarea-1.2*
+	virtual/glut
+	virtual/opengl
+	sci-chemistry/ccp4
+	dev-lang/python
+	x11-libs/gtk-canvas
+	dev-lang/python
+	x11-libs/guile-gtk
+	dev-libs/goosh
+	dev-libs/guile-www"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/add-needed-includes-libs.patch
+	epatch ${FILESDIR}/glutinit.patch
+	epatch ${FILESDIR}/setupdir.patch
+	epatch ${FILESDIR}/use-fftw-single.patch
+	cd ${S}
+	eautoconf
+	eautomake
+}
+
+src_compile() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix=/usr \
+		--with-clipper-prefix=/usr \
+		--with-mmdb-prefix=/usr \
+		--with-ssmlib-prefix=/usr \
+		--with-guile=/usr \
+		--with-python=/usr \
+		|| die "econf failed"
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	make DESTDIR=${D} install || die
+	ebegin "Copying reference structures to ${D}/usr/share/coot/"
+	cp -R ${WORKDIR}/reference-structures ${D}/usr/share/coot/
+	eend
+	ebegin "Copying monomer library to ${D}/usr/share/coot/"
+	cp -R ${WORKDIR}/lib ${D}/usr/share/coot/
+	eend
+}
diff --git a/sci-chemistry/coot/coot-0.1.ebuild b/sci-chemistry/coot/coot-0.1.ebuild
new file mode 100644
index 0000000..25a8834
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.1.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils autotools
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz
+	http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
+	http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE=""
+RDEPEND=">=sci-libs/gsl-1.3
+	=dev-libs/glib-1.2*
+	=x11-libs/gtkglarea-1.2*
+	virtual/glut
+	virtual/opengl
+	sci-chemistry/ccp4
+	dev-lang/python
+	x11-libs/gtk-canvas
+	dev-lang/python
+	x11-libs/guile-gtk
+	dev-libs/goosh
+	dev-libs/guile-www"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/${PV}-fix-build.patch
+
+	# Link against single-precision fftw
+	sed -i \
+		-e "s:lfttw:lsfttw:g" \
+		-e "s:lrfttw:lsrfttw:g" \
+		${S}/macros/clipper.m4
+
+	# Don't install setup scripts, they're only needed for nonstandard prefixes
+	sed -i \
+		-e "s:^\(setup.*\):#\1:g" \
+		-e "s:.*\(bin_.*\):\1:g" \
+		${S}/setup/Makefile.am
+
+	cd ${S}
+	AT_M4DIR="macros" eautoreconf
+}
+
+src_compile() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix=/usr \
+		--with-clipper-prefix=/usr \
+		--with-mmdb-prefix=/usr \
+		--with-ssmlib-prefix=/usr \
+		--with-guile=/usr \
+		--with-python=/usr \
+		|| die "econf failed"
+
+	# Parallel build's broken
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	make DESTDIR=${D} install || die
+
+	# Install misses this
+	insinto /usr/share/coot/python
+	doins ${S}/src/coot.py
+
+	ebegin "Copying reference structures to ${D}/usr/share/coot/"
+	cp -R ${WORKDIR}/reference-structures ${D}/usr/share/coot/
+	eend
+	ebegin "Copying monomer library to ${D}/usr/share/coot/"
+	cp -R ${WORKDIR}/lib ${D}/usr/share/coot/
+	eend
+}
diff --git a/sci-chemistry/coot/files/0.1-fix-build.patch b/sci-chemistry/coot/files/0.1-fix-build.patch
new file mode 100644
index 0000000..ddec03d
--- /dev/null
+++ b/sci-chemistry/coot/files/0.1-fix-build.patch
@@ -0,0 +1,124 @@
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/coords/Cartesian.h coot-0.1/coords/Cartesian.h
+--- coot-0.1.orig/coords/Cartesian.h	2005-05-09 15:56:01.000000000 -0700
++++ coot-0.1/coords/Cartesian.h	2006-04-13 17:57:43.000000000 -0700
+@@ -155,6 +155,9 @@
+ 
+    short int is_an_in_triangle(surface_face_data face,  const Cartesian &b,
+ 			       const Cartesian &c); 
++   double  cos_angle_btwn_vecs(const Cartesian &a, const Cartesian &b);
++   float           dot_product(const Cartesian &a, const Cartesian &b);
++   Cartesian     cross_product(const Cartesian &a, const Cartesian &b);
+ 
+ 
+    class CartesianPairInfo { 
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/coot-utils/coot-map-heavy.hh coot-0.1/coot-utils/coot-map-heavy.hh
+--- coot-0.1.orig/coot-utils/coot-map-heavy.hh	2005-11-05 16:43:03.000000000 -0800
++++ coot-0.1/coot-utils/coot-map-heavy.hh	2006-04-13 17:20:24.000000000 -0700
+@@ -83,7 +83,7 @@
+ 	 // searching of the trns components of the rtops.  We use the
+ 	 // molecule size (min_molecule_radius_) to do that.
+ 	 std::vector<std::pair<float, clipper::RTop_orth> >
+-	 fffear_search::filter_by_distance_to_higher_peak(const std::vector<std::pair<float, clipper::RTop_orth> > &vr) const;
++	 filter_by_distance_to_higher_peak(const std::vector<std::pair<float, clipper::RTop_orth> > &vr) const;
+ 	 
+       public:
+ 	 clipper::NXmap<float> nxmap;
+@@ -97,7 +97,7 @@
+ 	 // transformations of the coords need to apply this
+ 	 // translation of the molecule (to be centered round the
+ 	 // origin) before applying the RTop of the (negative) peaks of the fffear map.
+-	 clipper::RTop_orth coot::util::fffear_search::mid_point_transformation() const;
++	 clipper::RTop_orth mid_point_transformation() const;
+       };
+ 
+    }
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/coot-utils/peak-search.hh coot-0.1/coot-utils/peak-search.hh
+--- coot-0.1.orig/coot-utils/peak-search.hh	2005-10-20 04:39:25.000000000 -0700
++++ coot-0.1/coot-utils/peak-search.hh	2006-04-13 17:18:28.000000000 -0700
+@@ -40,7 +40,7 @@
+ 				  const clipper::Xmap<float> &xmap) const;
+ 
+       const std::vector<int>
+-      coot::peak_search::find_protein_to_origin_translations(const std::vector<clipper::Coord_orth> &sampled_protein_coords, const clipper::Xmap<float> &xmap) const;
++      find_protein_to_origin_translations(const std::vector<clipper::Coord_orth> &sampled_protein_coords, const clipper::Xmap<float> &xmap) const;
+       
+       double
+       min_dist_to_protein(const clipper::Coord_orth &point,
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/ligand/dunbrack.hh coot-0.1/ligand/dunbrack.hh
+--- coot-0.1.orig/ligand/dunbrack.hh	2006-03-22 09:44:17.000000000 -0800
++++ coot-0.1/ligand/dunbrack.hh	2006-04-13 18:12:51.000000000 -0700
+@@ -37,7 +37,7 @@
+       double probability_score(double chi_angle, int ichi, const coot::simple_rotamer &rot);
+ 
+       std::vector<coot::simple_rotamer>
+-      coot::dunbrack::get_all_rotamers(const std::string &res_type) const;
++      get_all_rotamers(const std::string &res_type) const;
+       std::pair<short int, double> probability_of_this_rotamer(const std::vector<double> &chi_angles,
+ 							       const std::vector<coot::simple_rotamer> &rots) const;
+       std::vector<std::vector<int> > rotamer_atom_names_to_indices(const std::vector<std::vector<std::string> > &residue_rotamer_atoms, PCAtom *residue_atoms, int n_residue_atoms) const;
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/ligand/helix-placement.hh coot-0.1/ligand/helix-placement.hh
+--- coot-0.1.orig/ligand/helix-placement.hh	2005-10-07 11:56:00.000000000 -0700
++++ coot-0.1/ligand/helix-placement.hh	2006-04-13 18:16:32.000000000 -0700
+@@ -68,12 +68,12 @@
+       void build_on_N_end(minimol::fragment *m, float min_density_limit) const;
+       void build_on_C_end(minimol::fragment *m, float min_density_limit) const;
+       minimol::residue
+-      helix_placement::build_N_terminal_ALA(const clipper::Coord_orth &prev_n,
++      build_N_terminal_ALA(const clipper::Coord_orth &prev_n,
+                                             const clipper::Coord_orth &prev_ca,
+                                             const clipper::Coord_orth &prev_c,
+ 					    int seqno) const;
+       minimol::residue
+-      helix_placement::build_C_terminal_ALA(const clipper::Coord_orth &prev_n,
++      build_C_terminal_ALA(const clipper::Coord_orth &prev_n,
+                                             const clipper::Coord_orth &prev_ca,
+                                             const clipper::Coord_orth &prev_c,
+ 					    int seqno) const;
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/ligand/residue_by_phi_psi.hh coot-0.1/ligand/residue_by_phi_psi.hh
+--- coot-0.1.orig/ligand/residue_by_phi_psi.hh	2005-09-15 03:56:01.000000000 -0700
++++ coot-0.1/ligand/residue_by_phi_psi.hh	2006-04-13 18:07:06.000000000 -0700
+@@ -58,7 +58,7 @@
+ 							  short int do_rigid_body_refinement);
+ 
+      minimol::fragment
+-     coot::residue_by_phi_psi::make_2_res_joining_frag(const std::string &chain_id,
++     make_2_res_joining_frag(const std::string &chain_id,
+ 						       const phi_psi_pair &pp1,
+ 						       const phi_psi_pair &pp2,
+ 						       int seqnum,
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/src/graphics-info.h coot-0.1/src/graphics-info.h
+--- coot-0.1.orig/src/graphics-info.h	2006-03-27 01:12:01.000000000 -0800
++++ coot-0.1/src/graphics-info.h	2006-04-13 18:02:41.000000000 -0700
+@@ -657,7 +657,7 @@
+    }
+ 
+    // 
+-   static short int graphics_info_t::use_graphics_interface_flag; 
++   static short int use_graphics_interface_flag; 
+ 
+    // Display size
+    static int graphics_x_size;
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/src/molecule-class-info.h coot-0.1/src/molecule-class-info.h
+--- coot-0.1.orig/src/molecule-class-info.h	2006-03-30 23:25:04.000000000 -0800
++++ coot-0.1/src/molecule-class-info.h	2006-04-13 18:02:09.000000000 -0700
+@@ -395,7 +395,7 @@
+ 
+    // change chain id internal function
+    std::pair<int, std::string>
+-   molecule_class_info_t::change_chain_id_with_residue_range(const std::string &from_chain_id,
++   change_chain_id_with_residue_range(const std::string &from_chain_id,
+ 							     const std::string &to_chain_id,
+ 							     int start_resno,
+ 							     int end_resno);
+diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/src/rama_plot.hh coot-0.1/src/rama_plot.hh
+--- coot-0.1.orig/src/rama_plot.hh	2006-03-30 23:25:06.000000000 -0800
++++ coot-0.1/src/rama_plot.hh	2006-04-13 18:02:24.000000000 -0700
+@@ -289,7 +289,7 @@
+    // SelResidue is guaranteed to have 3 residues (there is no protection
+    // for that in this function).
+    std::pair<short int, coot::phi_psi_t>
+-   coot::rama_plot::get_phi_psi(PCResidue *SelResidue) const;
++   get_phi_psi(PCResidue *SelResidue) const;
+ 
+ 
+    void map_mouse_pos(double x, double y);
diff --git a/sci-chemistry/coot/files/add-mmdb-includedir.patch b/sci-chemistry/coot/files/add-mmdb-includedir.patch
new file mode 100644
index 0000000..cab1f64
--- /dev/null
+++ b/sci-chemistry/coot/files/add-mmdb-includedir.patch
@@ -0,0 +1,11 @@
+--- coot-0.0.33.orig/configure	2005-06-30 05:45:06.000000000 -0700
++++ coot-0.0.33/configure	2006-01-07 20:03:08.000000000 -0800
+@@ -10417,7 +10417,7 @@
+  # when MMDB and dependencies get installed - we infact, include both
+  # directories.
+  #
+- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/src"
++ ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb -I$mmdb_prefix/src"
+  #
+  # Similarly for mmdb, the uninstalled library position is simply in
+  # $mmdb_prefix, but the installed is in the standard prefixed subdirectory.
diff --git a/sci-chemistry/coot/files/add-needed-includes-libs.patch b/sci-chemistry/coot/files/add-needed-includes-libs.patch
new file mode 100644
index 0000000..bbf8c59
--- /dev/null
+++ b/sci-chemistry/coot/files/add-needed-includes-libs.patch
@@ -0,0 +1,56 @@
+diff -urN -x Makefile -x autom4te.cache -x configure -x libtool -x make.log -x src -x setup coot-0.0.33.orig/aclocal.m4 coot-0.0.33/aclocal.m4
+--- coot-0.0.33.orig/aclocal.m4	2005-06-30 05:45:04.000000000 -0700
++++ coot-0.0.33/aclocal.m4	2006-01-08 06:38:18.000000000 -0800
+@@ -5330,7 +5330,7 @@
+ 	# --gtkcanvas-prefix=/some/thing
+ 	#
+ 
+- GTKCANVAS_CFLAGS="-DHAVE_GTK_CANVAS -I$gtkcanvas_prefix/include $IMLIB_CFLAGS"
++ GTKCANVAS_CFLAGS="-DHAVE_GTK_CANVAS -I$gtkcanvas_prefix/include -I$gtkcanvas_prefix/include/gnome-1.0 $IMLIB_CFLAGS"
+  #
+  # Similarly for gtkcanvas, the uninstalled library position is simply in
+  # $gtkcanvas_prefix, but the installed is in the standard prefixed subdirectory.
+@@ -5731,7 +5731,7 @@
+  # when MMDB and dependencies get installed - we infact, include both
+  # directories.
+  #  
+- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/src"
++ ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb -I$mmdb_prefix/src"
+  #
+  # Similarly for mmdb, the uninstalled library position is simply in
+  # $mmdb_prefix, but the installed is in the standard prefixed subdirectory.
+@@ -5805,7 +5805,7 @@
+ 
+ if test x$with_ssmlib_prefix != x; then
+ 
+-   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB -I$with_ssmlib_prefix/include"
++   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB -I$with_ssmlib_prefix/include -I$with_ssmlib_prefix/include/ssm"
+    MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
+   
+ else 
+@@ -5857,7 +5857,7 @@
+  # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
+  # when clipper and dependencies get installed.
+  #  
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
++ CLIPPER_CXXFLAGS="-I$clipper_prefix/include/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
+ # -I$clipper_prefix/cctbx
+  
+  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
+@@ -5868,14 +5868,14 @@
+  # HACK! FIXME
+  # added lz, we should have proper autoconf check for this.
+  #
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
++ CLIPPER_LDOPTS="-L$clipper_prefix/lib  -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
+ else
+  # the compiler looks in the "standard" places for clipper.  In real life,
+  # it would be quite unlikely that clipper would be installed in /usr/include, 
+  # /usr/lib etc. so this code will not usually find the right dependencies.
+  CLIPPER_CXXFLAGS=""
+- CLIPPER_LDOPTS="-lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
++ CLIPPER_LDOPTS=" -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
+ fi
+ 
+ AC_MSG_CHECKING([for Clipper])
diff --git a/sci-chemistry/coot/files/coot-0.1_pre1-coot-fftw-single.patch b/sci-chemistry/coot/files/coot-0.1_pre1-coot-fftw-single.patch
new file mode 100644
index 0000000..f1b0d3e
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.1_pre1-coot-fftw-single.patch
@@ -0,0 +1,22 @@
+diff -urN coot-0.1.0-pre-1.orig/aclocal.m4 coot-0.1.0-pre-1/aclocal.m4
+--- coot-0.1.0-pre-1.orig/aclocal.m4	2006-01-01 05:37:20.000000000 -0800
++++ coot-0.1.0-pre-1/aclocal.m4	2006-01-08 10:01:37.000000000 -0800
+@@ -5826,15 +5826,15 @@
+  # HACK! FIXME
+  # added lz, we should have proper autoconf check for this.
+  #
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lccp4c $MMDB_LIBS -lrfftw -lfftw -lz -lm"
++ CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm"
++ CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lccp4c $MMDB_LIBS -lsrfftw -lsfftw -lz -lm"
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
+ else
+  # the compiler looks in the "standard" places for clipper.  In real life,
+  # it would be quite unlikely that clipper would be installed in /usr/include, 
+  # /usr/lib etc. so this code will not usually find the right dependencies.
+  CLIPPER_CXXFLAGS=""
+- CLIPPER_LDOPTS="-lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
++ CLIPPER_LDOPTS="-lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm"
+ fi
+ 
+ AC_MSG_CHECKING([for Clipper])
diff --git a/sci-chemistry/coot/files/coot-0.1_pre1-scripts-in-bin.patch b/sci-chemistry/coot/files/coot-0.1_pre1-scripts-in-bin.patch
new file mode 100644
index 0000000..6d64437
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.1_pre1-scripts-in-bin.patch
@@ -0,0 +1,15 @@
+diff -urN coot-0.1.0-pre-1.orig/setup/Makefile.am coot-0.1.0-pre-1/setup/Makefile.am
+--- coot-0.1.0-pre-1.orig/setup/Makefile.am	2005-12-30 11:48:18.000000000 -0800
++++ coot-0.1.0-pre-1/setup/Makefile.am	2006-01-08 10:00:49.000000000 -0800
+@@ -1,8 +1,8 @@
+ # Install in both bin and setup
+-setupdir = $(prefix)/setup
++#setupdir = $(prefix)/setup
+ 
+-# bin_SCRIPTS = coot.csh coot.sh
+-setup_SCRIPTS = coot.csh coot.sh
++bin_SCRIPTS = coot.csh coot.sh
++# setup_SCRIPTS = coot.csh coot.sh
+ 
+ 
+ 
diff --git a/sci-chemistry/coot/files/digest-coot-0.0.33 b/sci-chemistry/coot/files/digest-coot-0.0.33
new file mode 100644
index 0000000..94a28e8
--- /dev/null
+++ b/sci-chemistry/coot/files/digest-coot-0.0.33
@@ -0,0 +1,3 @@
+MD5 22b87da19a1156f281844c84cd9b8375 coot-0.0.33.tar.gz 2227396
+MD5 c09bb6b5524901cb0fde14589546224e reference-structures.tar.gz 6945369
+MD5 88cdbabf47914740f2d13e6960eea3c6 refmac-lib-data-monomers.tar.gz 2163068
diff --git a/sci-chemistry/coot/files/digest-coot-0.1 b/sci-chemistry/coot/files/digest-coot-0.1
new file mode 100644
index 0000000..3ca87e2
--- /dev/null
+++ b/sci-chemistry/coot/files/digest-coot-0.1
@@ -0,0 +1,9 @@
+MD5 f983b327ac7d80446efc38c375873a08 coot-0.1.tar.gz 2618089
+RMD160 f5499d539d1b26510675e72f6ba4d99f3a9d3a40 coot-0.1.tar.gz 2618089
+SHA256 7ccde5f0d719a71986d5329fdbb618f8285373a581a6c00d57d9bd0e0a3e5cf5 coot-0.1.tar.gz 2618089
+MD5 c09bb6b5524901cb0fde14589546224e reference-structures.tar.gz 6945369
+RMD160 0dd9b2057cf5d6b0d060d704231aa7c5518f0b3b reference-structures.tar.gz 6945369
+SHA256 ba0a21e1f7f9065c7dd691e784d6508edc9ffae8b31923e5def5f1cbb7108b06 reference-structures.tar.gz 6945369
+MD5 88cdbabf47914740f2d13e6960eea3c6 refmac-lib-data-monomers.tar.gz 2163068
+RMD160 1443977959247c28cf1e7ad6683d0e72228f4cce refmac-lib-data-monomers.tar.gz 2163068
+SHA256 e4c9f89fd3bc1d3ab74c8270ed187875524800e0b72fb8131e298baa2b555a58 refmac-lib-data-monomers.tar.gz 2163068
diff --git a/sci-chemistry/coot/files/glutinit.patch b/sci-chemistry/coot/files/glutinit.patch
new file mode 100644
index 0000000..7c5a593
--- /dev/null
+++ b/sci-chemistry/coot/files/glutinit.patch
@@ -0,0 +1,20 @@
+diff -urN coot-0.0.33.orig/src/main.cc coot-0.0.33/src/main.cc
+--- coot-0.0.33.orig/src/main.cc	2006-01-08 08:20:58.000000000 -0800
++++ coot-0.0.33/src/main.cc	2006-01-08 08:31:44.000000000 -0800
+@@ -31,6 +31,7 @@
+ 
+ #include <gtk/gtk.h>
+ 
++#include <GL/glut.h> // for glutInit
+ 
+ #include "interface.h"
+ #ifndef HAVE_SUPPORT_H
+@@ -121,6 +122,8 @@
+   textdomain (PACKAGE);
+ #endif
+ 
++  glutInit(&argc, argv);
++
+   // command line
+   command_line_data cld = parse_command_line(argc, argv); 
+   
diff --git a/sci-chemistry/coot/files/setupdir.patch b/sci-chemistry/coot/files/setupdir.patch
new file mode 100644
index 0000000..9b52d70
--- /dev/null
+++ b/sci-chemistry/coot/files/setupdir.patch
@@ -0,0 +1,15 @@
+diff -urN coot-0.0.33.orig/setup/Makefile.am coot-0.0.33/setup/Makefile.am
+--- coot-0.0.33.orig/setup/Makefile.am	2006-01-08 08:20:58.000000000 -0800
++++ coot-0.0.33/setup/Makefile.am	2006-01-08 08:25:34.000000000 -0800
+@@ -1,8 +1,8 @@
+ # Install in both bin and setup
+-setupdir = $(prefix)/setup
++#setupdir = $(prefix)/setup
+ 
+-# bin_SCRIPTS = coot.csh coot.sh
+-setup_SCRIPTS = coot.csh coot.sh
++bin_SCRIPTS = coot.csh coot.sh
++# setup_SCRIPTS = coot.csh coot.sh
+ 
+ EXTRA_DIST = coot.csh coot.sh
+ 
diff --git a/sci-chemistry/coot/files/use-fftw-single.patch b/sci-chemistry/coot/files/use-fftw-single.patch
new file mode 100644
index 0000000..7623187
--- /dev/null
+++ b/sci-chemistry/coot/files/use-fftw-single.patch
@@ -0,0 +1,20 @@
+diff -urN coot-0.0.33.orig/aclocal.m4 coot-0.0.33/aclocal.m4
+--- coot-0.0.33.orig/aclocal.m4	2006-01-08 08:42:52.000000000 -0800
++++ coot-0.0.33/aclocal.m4	2006-01-08 08:43:07.000000000 -0800
+@@ -5868,14 +5868,14 @@
+  # HACK! FIXME
+  # added lz, we should have proper autoconf check for this.
+  #
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib  -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
++ CLIPPER_LDOPTS="-L$clipper_prefix/lib  -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm"
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
+ else
+  # the compiler looks in the "standard" places for clipper.  In real life,
+  # it would be quite unlikely that clipper would be installed in /usr/include, 
+  # /usr/lib etc. so this code will not usually find the right dependencies.
+  CLIPPER_CXXFLAGS=""
+- CLIPPER_LDOPTS=" -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm"
++ CLIPPER_LDOPTS=" -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm"
+ fi
+ 
+ AC_MSG_CHECKING([for Clipper])
diff --git a/sci-chemistry/espresso/Manifest b/sci-chemistry/espresso/Manifest
new file mode 100644
index 0000000..7ebd355
--- /dev/null
+++ b/sci-chemistry/espresso/Manifest
@@ -0,0 +1,6 @@
+MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253
+RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253
+SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253
+MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672
+RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672
+SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672
diff --git a/sci-chemistry/espresso/espresso-3.00.ebuild b/sci-chemistry/espresso/espresso-3.00.ebuild
new file mode 100644
index 0000000..5fc64ee
--- /dev/null
+++ b/sci-chemistry/espresso/espresso-3.00.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+inherit fortran
+
+DESCRIPTION="opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization"
+HOMEPAGE="http://www.pwscf.org/"
+SRC_URI="http://www.pwscf.org/downloads/PWcodes/codes/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="mpi"
+
+RDEPEND="virtual/blas
+	virtual/lapack
+	dev-tcltk/itk"
+DEPEND="${RDEPEND}"
+
+# Doesn't work with gfortran, last tested on 4.1_pre20060210
+FORTRAN="ifc"
+
+src_compile() {
+	# For some reason it uses the same fortran but not mpicc
+	econf \
+		$(use_enable mpi parallel) \
+		F90="${FORTRANC}" \
+		CC="${CC}" \
+		MPICC="${CC}" \
+		|| die "configure failed"
+
+	emake || die "make failed"
+}
+
+src_install() {
+	DESTTREE="/usr" dobin bin/* || die "install failed"
+	dodoc README
+}
diff --git a/sci-chemistry/espresso/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/espresso/files/digest-gtk-gamess-1.04.1
new file mode 100644
index 0000000..410cbec
--- /dev/null
+++ b/sci-chemistry/espresso/files/digest-gtk-gamess-1.04.1
@@ -0,0 +1,3 @@
+MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334
+RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334
+SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334
diff --git a/sci-chemistry/gabedit/Manifest b/sci-chemistry/gabedit/Manifest
new file mode 100644
index 0000000..7ebd355
--- /dev/null
+++ b/sci-chemistry/gabedit/Manifest
@@ -0,0 +1,6 @@
+MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253
+RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253
+SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253
+MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672
+RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672
+SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672
diff --git a/sci-chemistry/gabedit/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/gabedit/files/digest-gtk-gamess-1.04.1
new file mode 100644
index 0000000..410cbec
--- /dev/null
+++ b/sci-chemistry/gabedit/files/digest-gtk-gamess-1.04.1
@@ -0,0 +1,3 @@
+MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334
+RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334
+SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334
diff --git a/sci-chemistry/gabedit/gtk-gamess-1.04.1.ebuild b/sci-chemistry/gabedit/gtk-gamess-1.04.1.ebuild
new file mode 100644
index 0000000..611ff42
--- /dev/null
+++ b/sci-chemistry/gabedit/gtk-gamess-1.04.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+DESCRIPTION="GTK+ frontend to GAMESS"
+HOMEPAGE="http://www.uiowa.edu/~ghemical/gtk-gamess.shtml"
+SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+RDEPEND="=gnome-base/libglade-0*"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	sed -i -e "s:/usr/local/gamess/rungms:/usr/bin/rungms:g" \
+		${S}/src/gg_config.cpp
+}
+
+src_install() {
+	make DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-chemistry/gtk-gamess/Manifest b/sci-chemistry/gtk-gamess/Manifest
new file mode 100644
index 0000000..7ebd355
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/Manifest
@@ -0,0 +1,6 @@
+MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253
+RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253
+SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253
+MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672
+RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672
+SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672
diff --git a/sci-chemistry/gtk-gamess/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/gtk-gamess/files/digest-gtk-gamess-1.04.1
new file mode 100644
index 0000000..410cbec
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/files/digest-gtk-gamess-1.04.1
@@ -0,0 +1,3 @@
+MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334
+RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334
+SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334
diff --git a/sci-chemistry/gtk-gamess/gtk-gamess-1.04.1.ebuild b/sci-chemistry/gtk-gamess/gtk-gamess-1.04.1.ebuild
new file mode 100644
index 0000000..611ff42
--- /dev/null
+++ b/sci-chemistry/gtk-gamess/gtk-gamess-1.04.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+DESCRIPTION="GTK+ frontend to GAMESS"
+HOMEPAGE="http://www.uiowa.edu/~ghemical/gtk-gamess.shtml"
+SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+RDEPEND="=gnome-base/libglade-0*"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	sed -i -e "s:/usr/local/gamess/rungms:/usr/bin/rungms:g" \
+		${S}/src/gg_config.cpp
+}
+
+src_install() {
+	make DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-chemistry/king/Manifest b/sci-chemistry/king/Manifest
new file mode 100644
index 0000000..634cdd7
--- /dev/null
+++ b/sci-chemistry/king/Manifest
@@ -0,0 +1,6 @@
+MD5 0ced5ad56d8c926ee1844540db04c881 files/digest-king-1.50.060207 259
+RMD160 d54139758f02dec90e337acc79644e80c6b3b3b4 files/digest-king-1.50.060207 259
+SHA256 ae9e09a316344c91fdd47a54059a84d51a64803133a4410f337b5f28b7293686 files/digest-king-1.50.060207 259
+MD5 c9c012d4f9ae9dd3128ab7a493942d1d king-1.50.060207.ebuild 1022
+RMD160 e062415da3b1dcce08b515b893516409fea25d4c king-1.50.060207.ebuild 1022
+SHA256 71e54d92199fe2b9c2221069593873e293e4876ec668aec0044ae21b6fd9a401 king-1.50.060207.ebuild 1022
diff --git a/sci-chemistry/king/files/digest-king-1.50.060207 b/sci-chemistry/king/files/digest-king-1.50.060207
new file mode 100644
index 0000000..9b9c854
--- /dev/null
+++ b/sci-chemistry/king/files/digest-king-1.50.060207
@@ -0,0 +1,3 @@
+MD5 f8e7974198ab49eca972b2dc9ec6b20c king.1.50.060207.src.zip 13922914
+RMD160 74ff6b60d6ef4ed7bbbb1215fb7740e30c99ddee king.1.50.060207.src.zip 13922914
+SHA256 f6a798978a751b7431da244352ec09de0b1929cf806f9fb160b791fe12d2e0fc king.1.50.060207.src.zip 13922914
diff --git a/sci-chemistry/king/king-1.50.060207.ebuild b/sci-chemistry/king/king-1.50.060207.ebuild
new file mode 100644
index 0000000..48b7e90
--- /dev/null
+++ b/sci-chemistry/king/king-1.50.060207.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+MY_P="${PN}.${PV}"
+DESCRIPTION="An interactive system for 3D graphics (primarily molecular)"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/king.php"
+SRC_URI="http://kinemage.biochem.duke.edu/ftpsite/pub/software/${PN}/${MY_P}.src.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+RDEPEND="virtual/jre"
+DEPEND="${RDEPEND}
+	dev-java/ant-core
+	virtual/jdk"
+
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+	unpack ${A}
+	cd ${WORKDIR}
+
+	for i in king chiropraxis driftwood; do
+		mv ${i}* $i
+	done
+}
+
+src_compile() {
+	ant build || die "ant build failed"
+}
+
+src_install() {
+	dojar king.jar || die "dojar failed"
+	dodoc doc/* || die "dodoc failed"
+	dohtml *.html || die "dohtml failed"
+	cat << EOF >> ${T}/king
+#!/bin/sh
+java -jar /usr/share/king/lib/king.jar
+EOF
+
+	DESTTREE="/usr" dobin ${T}/king
+}
diff --git a/sci-chemistry/maid/CVS/Entries b/sci-chemistry/maid/CVS/Entries
new file mode 100644
index 0000000..865c984
--- /dev/null
+++ b/sci-chemistry/maid/CVS/Entries
@@ -0,0 +1,5 @@
+D/files////
+/metadata.xml/1.1/Thu Dec 15 20:31:24 2005//
+/ChangeLog/1.3/Thu Dec 15 21:06:31 2005//
+/maid-20011112.ebuild/1.3/Thu Dec 15 21:06:31 2005//
+/Manifest/1.4/Thu Dec 15 21:06:37 2005//
diff --git a/sci-chemistry/maid/CVS/Repository b/sci-chemistry/maid/CVS/Repository
new file mode 100644
index 0000000..f75bd84
--- /dev/null
+++ b/sci-chemistry/maid/CVS/Repository
@@ -0,0 +1 @@
+gentoo-x86/sci-chemistry/maid
diff --git a/sci-chemistry/maid/CVS/Root b/sci-chemistry/maid/CVS/Root
new file mode 100644
index 0000000..c108e17
--- /dev/null
+++ b/sci-chemistry/maid/CVS/Root
@@ -0,0 +1 @@
+spyderous@cvs.gentoo.org:/var/cvsroot
diff --git a/sci-chemistry/maid/ChangeLog b/sci-chemistry/maid/ChangeLog
new file mode 100644
index 0000000..6bfd435
--- /dev/null
+++ b/sci-chemistry/maid/ChangeLog
@@ -0,0 +1,20 @@
+# ChangeLog for sci-chemistry/maid
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/ChangeLog,v 1.3 2005/12/15 21:06:31 spyderous Exp $
+
+  15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; maid-20011112.ebuild:
+  Fix SRC_URI.
+
+  15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; maid-20011112.ebuild:
+  Fix license. The author informed me by email that it's intended to be freely
+  distributed, modified and redistributed.
+
+*maid-20011112 (15 Dec 2005)
+
+  15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/fix-compilation.patch, +files/fix-warnings.patch, +metadata.xml,
+  +maid-20011112.ebuild:
+  MAID does automatic fitting of protein X-ray crystallography electron
+  density maps. It can correctly build about 60% of alpha carbons on
+  medium-resolution maps and about 80% on high-resolution maps.
+
diff --git a/sci-chemistry/maid/Manifest b/sci-chemistry/maid/Manifest
new file mode 100644
index 0000000..1489427
--- /dev/null
+++ b/sci-chemistry/maid/Manifest
@@ -0,0 +1,15 @@
+MD5 f2e1b0a0da29465b1b1f29bb3343e08b ChangeLog 895
+RMD160 9d3a38aa52e54035d13b4992dfead92b62f1d8f8 ChangeLog 895
+SHA256 f34fdd7d59c25194a4ab6153b2de22e2dc99a44806514aea73ea3b918d25c629 ChangeLog 895
+MD5 e427165dea82055785c9497e5ca3a85d files/digest-maid-20011112 518
+RMD160 02f506efa14ca843e5f0058e26515b315020e06c files/digest-maid-20011112 518
+SHA256 19a701e406c26fd88bc916e4ad7660c3955639f3fd6f5a59e282ae74604bc7f2 files/digest-maid-20011112 518
+MD5 bcc6fdf88e85ccb7f3a06ef3dd9011b7 files/fix-warnings.patch 17141
+RMD160 b10d94b75c684b3ac506c28dfdd70ec8fb000fc1 files/fix-warnings.patch 17141
+SHA256 338e595a56ea1592221f833ab368afa672b4571460a9d46667871ded7cf8e5c1 files/fix-warnings.patch 17141
+MD5 f65ff5531e9788cf6f87c30a61fa7994 maid-20011112.ebuild 1411
+RMD160 22fa1a82f1bd377ad09f453bfdbca337f3282598 maid-20011112.ebuild 1411
+SHA256 8dfe7c93bb6a5ec536e9c6be0091b8954db03e8c2a4690caf71aa70782fdac38 maid-20011112.ebuild 1411
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
diff --git a/sci-chemistry/maid/files/CVS/Entries b/sci-chemistry/maid/files/CVS/Entries
new file mode 100644
index 0000000..f049271
--- /dev/null
+++ b/sci-chemistry/maid/files/CVS/Entries
@@ -0,0 +1,4 @@
+/digest-maid-20011112/1.1/Thu Dec 15 20:31:19 2005//
+/fix-compilation.patch/1.1/Thu Dec 15 20:31:19 2005//
+/fix-warnings.patch/1.1/Thu Dec 15 20:31:19 2005//
+D
diff --git a/sci-chemistry/maid/files/CVS/Repository b/sci-chemistry/maid/files/CVS/Repository
new file mode 100644
index 0000000..e2903d0
--- /dev/null
+++ b/sci-chemistry/maid/files/CVS/Repository
@@ -0,0 +1 @@
+gentoo-x86/sci-chemistry/maid/files
diff --git a/sci-chemistry/maid/files/CVS/Root b/sci-chemistry/maid/files/CVS/Root
new file mode 100644
index 0000000..c108e17
--- /dev/null
+++ b/sci-chemistry/maid/files/CVS/Root
@@ -0,0 +1 @@
+spyderous@cvs.gentoo.org:/var/cvsroot
diff --git a/sci-chemistry/maid/files/digest-maid-20011112 b/sci-chemistry/maid/files/digest-maid-20011112
new file mode 100644
index 0000000..039bb50
--- /dev/null
+++ b/sci-chemistry/maid/files/digest-maid-20011112
@@ -0,0 +1,6 @@
+MD5 aad12e496bed15581342d206282f03e6 maid-fix-compilation.patch.bz2 5044
+RMD160 fd196923baff07836bebd8cdd463b4f72a12cc87 maid-fix-compilation.patch.bz2 5044
+SHA256 17a2dda71af96d45f57c1cbf500bad1d1aca596cc4da4eee481b4bb62207d7be maid-fix-compilation.patch.bz2 5044
+MD5 23066037ad06f256d26e61a69d91c84a maid_unix_12nov01.tar.gz 480609
+RMD160 fcfcd63e2c68afb43ba576430aac23d5fbee419d maid_unix_12nov01.tar.gz 480609
+SHA256 4dcf2c2945a97efa7dcea8e89a2b3d65c8daf0f44705e11305c426854db5eaa0 maid_unix_12nov01.tar.gz 480609
diff --git a/sci-chemistry/maid/files/fix-warnings.patch b/sci-chemistry/maid/files/fix-warnings.patch
new file mode 100644
index 0000000..b4f48d2
--- /dev/null
+++ b/sci-chemistry/maid/files/fix-warnings.patch
@@ -0,0 +1,419 @@
+diff -ur glmaid_dist.orig/assignseq.c++ glmaid_dist/assignseq.c++
+--- glmaid_dist.orig/assignseq.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/assignseq.c++	2005-12-15 08:36:47.000000000 -0800
+@@ -2630,9 +2630,9 @@
+    if(ibestden <= 1) // 0.8 or 1.0
+        *maxngap = geo.maxngap;
+    else if(ibestden ==2) // 1.2
+-       *maxngap = 1.5*geo.maxngap;
++       *maxngap = (int) (1.5*geo.maxngap);
+    else if (ibestden >2) // 1.4 or 1.6
+-       *maxngap = 2.0 *geo.maxngap;   
++       *maxngap = (int) (2.0 *geo.maxngap);   
+  }
+ #endif
+ 
+diff -ur glmaid_dist.orig/bone.c++ glmaid_dist/bone.c++
+--- glmaid_dist.orig/bone.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/bone.c++	2005-12-15 08:31:26.000000000 -0800
+@@ -815,7 +815,7 @@
+    }
+ 
+ 
+-   bonemin = bone1.minden*maidfile.denscale;  // lower limit  used to make bone (round down) 
++   bonemin = (int) (bone1.minden*maidfile.denscale);  // lower limit  used to make bone (round down) 
+ fprintf(fpout,"bonemin = %d\n",bonemin);
+    defineiden(bone1,iden,den1,bonemin); // set point on boundary = REMOVE
+    bsort(den1,bone1,sortv,bonemin,sortnum,&maxsize);  // sort density into bins; sort[i] is vector of 1 ..... max
+diff -ur glmaid_dist.orig/checkfit.c++ glmaid_dist/checkfit.c++
+--- glmaid_dist.orig/checkfit.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/checkfit.c++	2005-12-15 08:22:14.000000000 -0800
+@@ -2977,7 +2977,7 @@
+    *maxden = -1000.0;
+    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
+    for(k=0;k<=2;k++)
+-       ir[k]=fd[k]+0.5; /*round  to integer*/
++       ir[k]=(int) (fd[k]+0.5); /*round  to integer*/
+    for(ii=ir[0]-2;ii<=ir[0]+2;ii++){
+      if( (ii>=1)&& (ii<=den1.amax[0]-den1.amin[0]-1) )
+         for(jj=ir[1]-2;jj<=ir[1]+2;jj++)
+diff -ur glmaid_dist.orig/extend2.c++ glmaid_dist/extend2.c++
+--- glmaid_dist.orig/extend2.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/extend2.c++	2005-12-15 08:24:45.000000000 -0800
+@@ -363,7 +363,7 @@
+    nend[3]=geo.nend[1]+3;
+ #if 1  // Works well in most cases
+    mrot[0]= 2*nrot;
+-   mrot[1]= 1.5*nrot;
++   mrot[1]= (int) (1.5*nrot);
+    mrot[2]= nrot;
+    mrot[3]= nrot;
+ #endif
+diff -ur glmaid_dist.orig/extendfit.c++ glmaid_dist/extendfit.c++
+--- glmaid_dist.orig/extendfit.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/extendfit.c++	2005-12-15 08:26:43.000000000 -0800
+@@ -4024,7 +4024,7 @@
+ ext.usenfits = 3;//  I do not think this makes any difference since it reset in other routines -Number of unassigned connected that must be linked to assigne seq. value
+    geo.deldist = sqrt( dot(den1.delx,den1.delx) ); // length of den1.delx vector = 1.445 for shad , res = 2.5
+    if(geo.deldist < 1.445)
+-      geo.gnmax = 7*(1.445/geo.deldist) +1;
++      geo.gnmax = (int) (7*(1.445/geo.deldist) +1);
+    else
+       geo.gnmax = 7;
+    geo.maxugap = 8;  //Maximum gap allowed to connect unassigned fits
+diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++
+--- glmaid_dist.orig/fit.c++	2005-12-15 08:15:43.000000000 -0800
++++ glmaid_dist/fit.c++	2005-12-15 08:36:24.000000000 -0800
+@@ -65,7 +65,7 @@
+ tordata.torconst=torconstorig;
+ tordata2.torconst=torconstorig;   
+ tordata.rfor=rfororig; //-BE CAREFUL - MUST BE SURE rfororig defined/geo.maxside = origmaxside;   
+-geo.maxside = origmaxside;   
++geo.maxside = (int) origmaxside;   
+     if (&client_data) {
+         XtRemoveWorkProc (work_id);
+     }
+diff -ur glmaid_dist.orig/initialize.c++ glmaid_dist/initialize.c++
+--- glmaid_dist.orig/initialize.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/initialize.c++	2005-12-15 08:34:02.000000000 -0800
+@@ -300,7 +300,7 @@
+                            nless=nless+1;
+                            dds= -MAXCHAR+1;
+                       }
+-                      den1.den[i][j][k]=dds;
++                      den1.den[i][j][k]=(signed) dds;
+ 		     }
+ 		}
+ 	}
+Files glmaid_dist.orig/initialize.o and glmaid_dist/initialize.o differ
+diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++
+--- glmaid_dist.orig/mapmenu.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/mapmenu.c++	2005-12-15 08:35:53.000000000 -0800
+@@ -430,7 +430,7 @@
+ {
+   int i;
+      for(i=0;i<3;i++)
+-     map.crange[i] = fcontradius[item_no]/map.delx[i];
++     map.crange[i] = (int) (fcontradius[item_no]/map.delx[i]);
+ //printf("map radius = %d\n",map.crange[0]);
+ }
+ 
+diff -ur glmaid_dist.orig/math.c++ glmaid_dist/math.c++
+--- glmaid_dist.orig/math.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/math.c++	2005-12-15 08:31:55.000000000 -0800
+@@ -51,9 +51,9 @@
+   z=xx[2]/den1.cvz;
+   y=(xx[1]-z*den1.cvy)/den1.singam;
+   x=xx[0]-y*den1.cosgam-z*den1.cosbe;
+-  ijk[0]=x/den1.delx[0] - den1.amin[0];
+-  ijk[1]=y/den1.delx[1] - den1.amin[1];
+-  ijk[2]=z/den1.delx[2] - den1.amin[2];
++  ijk[0]=(int) (x/den1.delx[0] - den1.amin[0]);
++  ijk[1]=(int) (y/den1.delx[1] - den1.amin[1]);
++  ijk[2]=(int) (z/den1.delx[2] - den1.amin[2]);
+ }
+ 
+ void imcv(struct griddata& den1,int xi[3],float sx[3])  /*convert from  integer xi,xj (grid point)
+diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++
+--- glmaid_dist.orig/menu.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/menu.c++	2005-12-15 08:35:15.000000000 -0800
+@@ -321,7 +321,7 @@
+ {
+    int i;  
+    sc.cubecol[0] += 0.01;
+-   i= sc.cubecol[0];
++   i= (int) sc.cubecol[0];
+    sc.cubecol[0]= sc.cubecol[0]-i;;
+    draw_screen(client_data);
+     return False; // Runs continually
+@@ -987,14 +987,14 @@
+     int i;
+ 
+     for(i=0;i<=2;i++) // Use default contour radius
+-          den1.crange[i]=sc.contourradius/den1.delx[i];
++          den1.crange[i]=(int) (sc.contourradius/den1.delx[i]);
+     den1.contonoff = -1;
+     den1.selectcontonoff = -1;
+     for(i=0;i<3;i++)
+        den1.color[i]=bluev[i];
+     den1.conlevel = sc.conlevel*maidfile.denscale;  // Set contourleve to default value
+     // Allocate arrays for contour routines
+-    den1.ntri = NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2]); // Scale ntri relative del = 1
++    den1.ntri = (int) (NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2])); // Scale ntri relative del = 1
+ printf("Allocating arrays for contour routines  ntriangles = %d\n",den1.ntri);
+     imat2(den1.tri,den1.ntri,9);
+ printf("   Done\n");
+diff -ur glmaid_dist.orig/pdbtolev.c++ glmaid_dist/pdbtolev.c++
+--- glmaid_dist.orig/pdbtolev.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/pdbtolev.c++	2005-12-15 08:27:19.000000000 -0800
+@@ -645,7 +645,7 @@
+ {
+     int i,j,natot,bi;
+     float  bsqr;
+-    natot=subst[snum].pos[0][0]; /*total # of atoms*/
++    natot=(int) subst[snum].pos[0][0]; /*total # of atoms*/
+     bsqr=tsqr(bondlength);
+     for(i=1;i<=natot;i++)
+        cmat[i][0]=0; /*initally no connections to i*/
+diff -ur glmaid_dist.orig/rankside.c++ glmaid_dist/rankside.c++
+--- glmaid_dist.orig/rankside.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/rankside.c++	2005-12-15 08:33:32.000000000 -0800
+@@ -201,13 +201,13 @@
+ #endif
+      tbad = fit.ibad[resn][a1] + fit.ibad[resn][a2] +fit.ibad[resn][a3];
+      if(tbad==0)
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      if(tbad ==1)
+-         return 1+iadd;
++         return 1+(int) iadd;
+      if(tbad==2)  
+-         return 2+iadd;
++         return 2+(int) iadd;
+      if(tbad==3)  
+-         return 4+iadd;
++         return 4+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+@@ -245,11 +245,11 @@
+         iadd = iadd+1;
+ #endif
+      if(fit.ibad[resn][a1]==0 ) 
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      else if( fit.ibad[resn][a2]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if( fit.ibad[resn][a3]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+@@ -285,11 +285,11 @@
+         iadd = iadd+1;
+ #endif
+      if(fit.ibad[resn][a1]==0 ) 
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      else if( fit.ibad[resn][a2]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if( fit.ibad[resn][a3]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+@@ -316,11 +316,11 @@
+      if(valden> 1.1*ringden) //change2
+         iadd = iadd+1;
+      if(fit.ibad[resn][a1]==0 ) 
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      else if( fit.ibad[resn][a2]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if( fit.ibad[resn][a3]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+Files glmaid_dist.orig/rankside.o and glmaid_dist/rankside.o differ
+diff -ur glmaid_dist.orig/refine.c++ glmaid_dist/refine.c++
+--- glmaid_dist.orig/refine.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/refine.c++	2005-12-15 08:26:15.000000000 -0800
+@@ -67,8 +67,8 @@
+ */
+ {
+    int ix,rnd;
+-   ix = floor(x);
+-   rnd = nn*(x-ix) + 0.5;
++   ix = (int) floor(x);
++   rnd = (int) (nn*(x-ix) + 0.5);
+    printf("nn = %d x = %5.3f  rnd = %d  Grid point %5.3f\n",nn,x,rnd,ix+(float)rnd/nn);
+    return rnd;
+ }
+@@ -82,8 +82,8 @@
+    int k;
+ 
+    for(k=0;k<=2;k++){
+-      ivec[k] = floor(fvec[k]);
+-      ival[k] = nn*(fvec[k]-ivec[k]) + 0.5;
++      ivec[k] = (int) floor(fvec[k]);
++      ival[k] = (int) (nn*(fvec[k]-ivec[k]) + 0.5);
+    }
+ }   
+ 
+@@ -115,9 +115,9 @@
+    }
+    for(k=0;k<=2;k++)
+        gzd.dvec[gzd.num][k] =ivec[k];
+-   gzd.den[gzd.num] = scalechar* exp(-rad*rad/bfact) +0.5; // mult by 100 and round
++   gzd.den[gzd.num] = (int) (scalechar* exp(-rad*rad/bfact) +0.5); // mult by 100 and round
+    for(k=0;k<=2;k++)
+-       gzd.forv[gzd.num][k] = 4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact;   
++       gzd.forv[gzd.num][k] = (int) (4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact);   
+ }
+ 
+ void assignforce(gzdhead)
+@@ -421,7 +421,7 @@
+    gzd[0].num = 0; 
+    oneatomgrid(den1,geo,ivec0,cenpos,gzd[0],bfact,countfunc);
+    printf("totnum = %d\n",gzd[0].num);
+-   maxgzd = gzd[0].num = 1.5*gzd[0].num; // increase by 15%
++   maxgzd = gzd[0].num = (int) (1.5*gzd[0].num); // increase by 15%
+    allocategzd(gzd[0].num);
+    del = 1.0/NDIV;
+    for(i=0;i<=NDIV;i++){
+diff -ur glmaid_dist.orig/sphere.c++ glmaid_dist/sphere.c++
+--- glmaid_dist.orig/sphere.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/sphere.c++	2005-12-15 08:36:06.000000000 -0800
+@@ -95,7 +95,7 @@
+        fclose(fp);
+     } // spherefile opened
+     sc.isphere = maidfile.nsphere; // set active sphere to last read
+-    sc.drawspheres =1.0;
++    sc.drawspheres =1;
+     if (widget = XtNameToWidget (spheremenu,"button_0")) //DEFAULT:  Turn off check box for label on/off button
+             XtVaSetValues (widget, XmNset,TRUE, NULL);
+ }
+diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++
+--- glmaid_dist.orig/tordyn.c++	2005-12-15 08:13:32.000000000 -0800
++++ glmaid_dist/tordyn.c++	2005-12-15 08:28:27.000000000 -0800
+@@ -337,8 +337,8 @@
+     xtof(den1,apos,fd);
+ /* New version, interpolates all neighbors*/
+     for(k=0;k<=2;k++){
+-       ir[k]=fd[k]; /*round down*/
+-       irh[k]=fd[k]+0.5; /*round to next 1/2*/
++       ir[k]=(int) fd[k]; /*round down*/
++       irh[k]=(int) (fd[k]+0.5); /*round to next 1/2*/
+        if( (ir[k]<1)|| (irh[k]>den1.amax[k]-den1.amin[k]-1) ){
+ //         if(verbose>=1)
+          if(verbose>=2) // 30nov00 - do not print this line
+@@ -683,7 +683,7 @@
+    atomden = 0;
+    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
+    for(kc=0;kc<=2;kc++)
+-       ir[kc]=fd[kc]; /*round down to integer*/
++       ir[kc]=(int) fd[kc]; /*round down to integer*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ir[k]<2)|| (ir[k]>den1.amax[k]-den1.amin[k]-2) ){
+          if(verbose>=2)
+@@ -2898,7 +2898,7 @@
+ //printf("oneside = %d geopos6(x) = geo.pos[geo.nend[0]+oneside][6][0] = %5.3f\n",geo.oneside,geo.pos[geo.nend[0]+geo.oneside][6][0]);
+    }
+    *returnden = bestden;  // return best cterm density
+-   *returnbad = bestbad;
++   *returnbad = (int) bestbad;
+  }// quitcont <5
+  quitrout:;
+  geo.fixend = origfixend; // set back to original value
+diff -ur glmaid_dist.orig/trace.c++ glmaid_dist/trace.c++
+--- glmaid_dist.orig/trace.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/trace.c++	2005-12-15 08:31:07.000000000 -0800
+@@ -1079,7 +1079,7 @@
+ 
+    xtoi(den1,pos[resnum][atomnum],ig);
+    for(k=0;k<=2;k++)
+-     ig[k]=ig[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ig[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ig[k]<2)|| (ig[k]>den1.amax[k]-den1.amin[k]-2) )
+          return 0;
+@@ -1099,7 +1099,7 @@
+ 
+    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
+    for(k=0;k<=2;k++)
+-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
+          if(verbose>=2)
+@@ -1127,7 +1127,7 @@
+ 
+    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
+    for(k=0;k<=2;k++)
+-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
+          if(verbose>=2)
+@@ -1204,7 +1204,7 @@
+ 
+    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
+    for(k=0;k<=2;k++)
+-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( ((ig[k]-geo.setrad)<0)|| ((ig[k]+geo.setrad)>den1.griddim[k]-1) ){
+          if(verbose>=2)
+@@ -2543,7 +2543,7 @@
+    atomden = 0;
+    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
+    for(kc=0;kc<=2;kc++)
+-       ir[kc]=fd[kc]; /*round down to integer*/
++       ir[kc]=(int) fd[kc]; /*round down to integer*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
+ //if(verbose>=2)
+@@ -2569,7 +2569,7 @@
+    atomden = 0;
+    xtof(den1,pos[inum][itype],fd); /* convert from double word to float sccreen*/
+    for(kc=0;kc<=2;kc++)
+-       ir[kc]=fd[kc]; /*round down to integer*/
++       ir[kc]=(int) fd[kc]; /*round down to integer*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
+         if(verbose>=2)
+@@ -3438,7 +3438,7 @@
+     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
+ dist = dist/2.0;
+     thdel = rotdel/dist; // step size of theta rotation
+-    mth =1+ thtot/thdel; // max # of theta steps  - round up
++    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
+     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
+     maxden = -10000.0;
+ for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
+@@ -3455,7 +3455,7 @@
+        }
+        else{
+          delph = rotdel/(dist*sin(th));//the delta phi angle step
+-         mphi = phitot/delph +1; // round up
++         mphi = (int) (phitot/delph) +1; // round up
+          delph = phitot/mphi; // make phitot = mphi*delph 
+        }
+        for(iph = 0;iph<=mphi;iph++){ // the phi step 
+@@ -3545,7 +3545,7 @@
+     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
+ dist = dist/2.0;
+     thdel = rotdel/dist; // step size of theta rotation
+-    mth =1+ thtot/thdel; // max # of theta steps  - round up
++    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
+     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
+     maxden = -10000.0;
+ for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
+@@ -3562,7 +3562,7 @@
+        }
+        else{
+          delph = rotdel/(dist*sin(th));//the delta phi angle step
+-         mphi = phitot/delph +1; // round up
++         mphi = (int) (phitot/delph) +1; // round up
+          delph = phitot/mphi; // make phitot = mphi*delph 
+        }
+        for(iph = 0;iph<=mphi;iph++){ // the phi step 
+@@ -6905,8 +6905,8 @@
+   for(i=0;i<=2;i++)
+     avegrid = avegrid+den1.delx[i];
+   avegrid = avegrid/3.0;
+-  geo.nihel = 0.5 + geo.curdist[1]/(1.414*avegrid); // 0.5 so that rounds to nearest int
+-  geo.nisheet = geo.curdist[2]/(1.414*avegrid);
++  geo.nihel = (int) (0.5 + geo.curdist[1]/(1.414*avegrid)); // 0.5 so that rounds to nearest int
++  geo.nisheet = (int) (geo.curdist[2]/(1.414*avegrid));
+ printf("\nGRID SIZE:  %5.3f %5.3f %5.3f avegrid = %5.3f  nihel = %d\n", 
+       den1.delx[0],den1.delx[1],den1.delx[2],avegrid,geo.nihel);
+ 
+Files glmaid_dist.orig/trace.o and glmaid_dist/trace.o differ
diff --git a/sci-chemistry/maid/maid-20011112.ebuild b/sci-chemistry/maid/maid-20011112.ebuild
new file mode 100644
index 0000000..e6156bd
--- /dev/null
+++ b/sci-chemistry/maid/maid-20011112.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/maid-20011112.ebuild,v 1.3 2005/12/15 21:06:31 spyderous Exp $
+
+inherit eutils toolchain-funcs
+
+MY_PN="${PN}_unix"
+MY_PV="${PV:6:2}nov${PV:2:2}"
+MY_P="${MY_PN}_${MY_PV}"
+DESCRIPTION="Automates the fitting of protein X-ray crystallographic electron density maps"
+HOMEPAGE="http://www.msi.umn.edu/~levitt/"
+SRC_URI="http://www.msi.umn.edu/~levitt/${MY_P}.tar.gz
+	mirror://gentoo/maid-fix-compilation.patch.bz2"
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="X"
+DEPEND="X? ( virtual/motif
+		virtual/glu
+		virtual/opengl
+		|| ( x11-libs/libXt virtual/x11 )
+	)"
+S="${WORKDIR}/glmaid_dist"
+
+src_unpack() {
+	if best_version virtual/opengl | grep mesa; then
+		if ! built_with_use media-libs/mesa motif; then
+			msg="Build media-libs/mesa with USE=motif"
+			eerror "${msg}"
+			die "${msg}"
+		fi
+	fi
+
+	unpack ${A}
+	cd ${S}
+
+	epatch ${DISTDIR}/maid-fix-compilation.patch.bz2
+	epatch ${FILESDIR}/fix-warnings.patch
+
+	if use X; then
+		ln -s makefile_graphics makefile
+	else
+		ln -s makefile_batch makefile
+	fi
+
+	sed -i \
+		-e "s:^Cgeneric = .*:Cgeneric = $(tc-getCXX):g" \
+		-e "s:\(Copt.*\)-O:\1${CFLAGS}:g" \
+		makefile
+}
+
+src_compile() {
+	emake || die "emake failed"
+}
+
+src_install() {
+	dodoc MANUAL*
+	if use X; then
+		dobin maid
+	else
+		dobin maidbatch
+	fi
+}
diff --git a/sci-chemistry/maid/metadata.xml b/sci-chemistry/maid/metadata.xml
new file mode 100644
index 0000000..211b8bd
--- /dev/null
+++ b/sci-chemistry/maid/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/mpqc/ChangeLog b/sci-chemistry/mpqc/ChangeLog
new file mode 100644
index 0000000..00b4646
--- /dev/null
+++ b/sci-chemistry/mpqc/ChangeLog
@@ -0,0 +1,80 @@
+# ChangeLog for sci-chemistry/mpqc
+# Copyright 2002-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/ChangeLog,v 1.8 2005/11/20 18:15:19 markusle Exp $
+
+  20 Nov 2005; Markus Dittrich <markusle@gentoo.org> mpqc-2.3.0.ebuild:
+  Reworked install process to avoid sandbox violations. This fixes bug #113056.
+
+*mpqc-2.3.0 (20 Nov 2005)
+
+  20 Nov 2005; Markus Dittrich <markusle@gentoo.org> metadata.xml,
+  +mpqc-2.3.0.ebuild:
+  New version
+
+  11 Jun 2005; Markus Rothe <corsair@gentoo.org> mpqc-2.2.3.ebuild:
+  Added ~ppc64 and solved bug #62124: ppc64 needs --enable-shared
+
+  24 May 2005; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2-r1.ebuild,
+  mpqc-2.2.3.ebuild:
+  (#54595) Inherit fortran eclass so we require a fortran compiler.
+
+*mpqc-2.2.3 (24 May 2005)
+
+  24 May 2005; Donnie Berkholz <spyderous@gentoo.org>; +mpqc-2.2.3.ebuild:
+  (#92179) Bump. Fix up indentation, use '-i' with sed instead of moving files
+  around, change .gz to .bz2 for distfiles. Add threads USE flag.
+
+  24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +mpqc-2.2.2-r1.ebuild, +mpqc-2.2.2.ebuild:
+  Moved from app-sci/mpqc to sci-chemistry/mpqc.
+
+  02 Oct 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2-r1.ebuild,
+  mpqc-2.2.2.ebuild:
+  Add some die()'s (#54595).
+
+  23 Sep 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2-r1.ebuild:
+  Add previous KEYWORDS as ~arch.
+
+*mpqc-2.2.2-r1 (23 Sep 2004)
+
+  23 Sep 2004; Donnie Berkholz <spyderous@gentoo.org>; +mpqc-2.2.2-r1.ebuild:
+  Update blas and lapack dependencies to the virtuals. This requires a revision
+  bump to fix some issues (#54596, #64200).
+
+  23 Sep 2004; Donnie Berkholz <spyderous@gentoo.org>; -mpqc-2.1.2.ebuild,
+  -mpqc-2.2.0.ebuild:
+  Pull old versions.
+
+  21 Sep 2004; Danny van Dyk <kugelfang@gentoo.org> mpqc-2.2.2.ebuild:
+  Marked stable on amd64.
+
+  27 Jul 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2.ebuild:
+  x86.
+
+  05 Jun 2004; David Holm <dholm@gentoo.org> mpqc-2.2.2.ebuild:
+  Added to ~ppc.
+
+*mpqc-2.2.2 (03 Jun 2004)
+
+  03 Jun 2004; Donnie Berkholz <spyderous@gentoo.org>; +mpqc-2.2.2.ebuild:
+  Version bump (#52646). Should now work on ppc.
+
+  30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.1.2.ebuild,
+  mpqc-2.2.0.ebuild:
+  Change x11-base/xfree dependency to virtual/x11.
+
+  24 Dec 2003; Donnie Berkholz <spyderous@gentoo.org>; :
+  Bad digest. Closing bug #36425.
+
+*mpqc-2.2.0 (14 Dec 2003)
+
+  14 Dec 2003; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.0.ebuild:
+  Version bump.
+
+  02 Nov 2002; Hannes Mehnert <hannes@gentoo.org> mpqc-2.1.2.ebuild:
+  marked stable for x86
+
+*mpqc-2.1.2 (31 Oct 2002)
+
+  31 Oct 2002; Hannes Mehnert <hannes@gentoo.org> mpqc-2.1.2.ebuild,
+  ChangeLog: Initial ebuild.
diff --git a/sci-chemistry/mpqc/Manifest b/sci-chemistry/mpqc/Manifest
new file mode 100644
index 0000000..00705f7
--- /dev/null
+++ b/sci-chemistry/mpqc/Manifest
@@ -0,0 +1,24 @@
+MD5 c68b2c8bf315900df6b742527ea91baa ChangeLog 2790
+RMD160 a2a00124bf0bf524ab124158fdac9a61fc4d2646 ChangeLog 2790
+SHA256 22a3072f0b8e5ee650c0f681ef2eeed44b85e4929606f1cc390b791c4a548b18 ChangeLog 2790
+MD5 ef8f7cc3214e84dfd6bec6d38eacb3a6 files/digest-mpqc-2.2.2 129
+RMD160 c64d3d28a7e28dca50d6dfec3896da2c9f7eb465 files/digest-mpqc-2.2.2 129
+SHA256 6e476007b6bb43d49a3b6ea3faa9966c5993db1a6533a3c4fa76fbb0d000ac71 files/digest-mpqc-2.2.2 129
+MD5 4a8b0c0ea1bc3bafc4302eceff353d0f files/digest-mpqc-2.2.3 131
+RMD160 30931d6bfdd3313f4bbdccdfe1c2eba11a387caf files/digest-mpqc-2.2.3 131
+SHA256 1fead6a0addeb7ea4b67a05dddbb250b76920e612b8db2661fee602f350169a1 files/digest-mpqc-2.2.3 131
+MD5 cdcd9f41ec0e4f8816b9fddf98827723 files/digest-mpqc-2.3.0 64
+RMD160 4ae35f6b7d267a399942757299fef1251094512f files/digest-mpqc-2.3.0 64
+SHA256 621bc9e20c5f2ca9601825d7bb3b6b30498d48b0cc1e6a9493fcd09eade5464c files/digest-mpqc-2.3.0 64
+MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272
+RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272
+SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272
+MD5 e9d844071c64f7af1c83acc43ca9e81b mpqc-2.2.2.ebuild 1410
+RMD160 7dfdf2696d1acd6dfc118782fb177f584bbc2dab mpqc-2.2.2.ebuild 1410
+SHA256 d41bec4f18a51b3d1d5efeadc902be7d2d0c383da66d8c562d230fbb5a0533c1 mpqc-2.2.2.ebuild 1410
+MD5 a23ed54c567aeb218b58c4ebd4bb851e mpqc-2.2.3.ebuild 1446
+RMD160 7e0ba5b1ea804d6d7b30ed21c57760ecbdf30784 mpqc-2.2.3.ebuild 1446
+SHA256 29ac57f509d587ff8b9673ae0d115d83918ec9cff35c90b69abb4fb1c75cb08d mpqc-2.2.3.ebuild 1446
+MD5 e91e2b63a729ccc4d3ef98103c194a8e mpqc-2.3.0.ebuild 2538
+RMD160 76c729f3aaf34d79376ba63c908da738552b9ca1 mpqc-2.3.0.ebuild 2538
+SHA256 acf798dcd6068b2bcdc3f682cbf47342a997b41918967989b91747f5b6ddd36c mpqc-2.3.0.ebuild 2538
diff --git a/sci-chemistry/mpqc/files/digest-mpqc-2.2.2 b/sci-chemistry/mpqc/files/digest-mpqc-2.2.2
new file mode 100644
index 0000000..86aa626
--- /dev/null
+++ b/sci-chemistry/mpqc/files/digest-mpqc-2.2.2
@@ -0,0 +1,2 @@
+MD5 7f5d2e6340aa9eba76a6e37cebc5fb9d mpqc-2.2.2.tar.gz 2061755
+MD5 2602c914c9181e92c77153ce21e13116 mpqc-man-2.2.2.tar.gz 166450
diff --git a/sci-chemistry/mpqc/files/digest-mpqc-2.2.3 b/sci-chemistry/mpqc/files/digest-mpqc-2.2.3
new file mode 100644
index 0000000..782b4a7
--- /dev/null
+++ b/sci-chemistry/mpqc/files/digest-mpqc-2.2.3
@@ -0,0 +1,2 @@
+MD5 893a104bc6119058a6fe102803d0bdb9 mpqc-2.2.3.tar.bz2 1615558
+MD5 4048680d977d336096e57f7721f21c0e mpqc-man-2.2.3.tar.bz2 105008
diff --git a/sci-chemistry/mpqc/files/digest-mpqc-2.3.0 b/sci-chemistry/mpqc/files/digest-mpqc-2.3.0
new file mode 100644
index 0000000..228a600
--- /dev/null
+++ b/sci-chemistry/mpqc/files/digest-mpqc-2.3.0
@@ -0,0 +1 @@
+MD5 91da0edb46e0416e730ae871b2ea57fa mpqc-2.3.0.tar.bz2 2446415
diff --git a/sci-chemistry/mpqc/metadata.xml b/sci-chemistry/mpqc/metadata.xml
new file mode 100644
index 0000000..f866028
--- /dev/null
+++ b/sci-chemistry/mpqc/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <maintainer>
+        <email>markusle@gentoo.org</email>
+        <name>Markus Dittrich</name>
+    </maintainer>
+	<herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/mpqc/mpqc-2.2.2.ebuild b/sci-chemistry/mpqc/mpqc-2.2.2.ebuild
new file mode 100644
index 0000000..ebf8814
--- /dev/null
+++ b/sci-chemistry/mpqc/mpqc-2.2.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/mpqc-2.2.2.ebuild,v 1.2 2004/12/29 16:30:31 ribosome Exp $
+
+DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
+HOMEPAGE="http://www.mpqc.org/"
+SRC_URI="mirror://sourceforge/mpqc/${P}.tar.gz
+	doc? ( mirror://sourceforge/mpqc/${PN}-man-${PV}.tar.gz )"
+
+LICENSE="GPL-2"
+SLOT="0"
+# Should work on x86, amd64 and ppc, at least
+KEYWORDS="x86 ~ppc amd64"
+IUSE="doc X"
+
+DEPEND="sys-devel/flex
+	sci-libs/blas
+	sci-libs/lapack
+	dev-lang/perl
+	X? ( virtual/x11 )"
+
+src_compile() {
+	CFLAGS_SAVE=${CFLAGS}; CXXFLAGS_SAVE=${CXXFLAGS}
+	myconf="${myconf} --prefix=/usr"
+	use X && myconf="${myconf} --x-includes=/usr/X11R6/include \
+	  --x-libraries=/usr/X11R6/lib"
+	./configure ${myconf} || die "configure failed"
+	sed -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS_SAVE}:" \
+	  -e "s:^FFLAGS =.*$:FFLAGS=${CFLAGS_SAVE}:" \
+	  -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS_SAVE}:" \
+	  lib/LocalMakefile > lib/LocalMakefile.foo
+	mv lib/LocalMakefile.foo lib/LocalMakefile
+	emake || die "emake failed"
+}
+
+src_install() {
+	sed -e "s:^prefix=.*$:prefix=${D}/usr:" lib/LocalMakefile \
+	  > lib/LocalMakefile.foo
+	mv lib/LocalMakefile.foo lib/LocalMakefile
+	use doc && doman ${WORKDIR}/${PN}-man-${PV}/man3/*
+	make install install_devel install_inc || die "install failed"
+}
diff --git a/sci-chemistry/mpqc/mpqc-2.2.3.ebuild b/sci-chemistry/mpqc/mpqc-2.2.3.ebuild
new file mode 100644
index 0000000..574eff1
--- /dev/null
+++ b/sci-chemistry/mpqc/mpqc-2.2.3.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/mpqc-2.2.3.ebuild,v 1.3 2005/06/11 16:24:38 corsair Exp $
+
+inherit fortran
+
+DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
+HOMEPAGE="http://www.mpqc.org/"
+SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2
+	doc? ( mirror://sourceforge/mpqc/${PN}-man-${PV}.tar.bz2 )"
+
+LICENSE="GPL-2"
+SLOT="0"
+# Should work on x86, amd64 and ppc, at least
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+IUSE="doc X threads"
+
+DEPEND="sys-devel/flex
+	virtual/blas
+	virtual/lapack
+	dev-lang/perl
+	>=sys-apps/sed-4"
+
+src_compile() {
+	CFLAGS_SAVE=${CFLAGS}; CXXFLAGS_SAVE=${CXXFLAGS}
+	myconf="${myconf} --prefix=/usr"
+	use X \
+		&& myconf="${myconf} --x-includes=/usr/X11R6/include \
+		--x-libraries=/usr/X11R6/lib"
+
+	# only shared will work on ppc64 - bug #62124
+	if use ppc64; then
+		myconf="${myconf} --enable-shared"
+	fi
+
+	./configure \
+		$(use_enable threads) \
+		${myconf} || die "configure failed"
+	sed -i -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS_SAVE}:" \
+		-e "s:^FFLAGS =.*$:FFLAGS=${CFLAGS_SAVE}:" \
+		-e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS_SAVE}:" \
+		lib/LocalMakefile
+	emake || die "emake failed"
+}
+
+src_install() {
+	sed -i -e "s:^prefix=.*$:prefix=${D}/usr:" lib/LocalMakefile
+	use doc && doman ${WORKDIR}/${PN}-man-${PV}/man3/*
+	make install install_devel install_inc || die "install failed"
+}
diff --git a/sci-chemistry/mpqc/mpqc-2.3.0.ebuild b/sci-chemistry/mpqc/mpqc-2.3.0.ebuild
new file mode 100644
index 0000000..65737cc
--- /dev/null
+++ b/sci-chemistry/mpqc/mpqc-2.3.0.ebuild
@@ -0,0 +1,104 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/mpqc-2.3.0.ebuild,v 1.3 2006/01/09 22:29:30 mr_bones_ Exp $
+
+inherit fortran
+
+DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
+HOMEPAGE="http://www.mpqc.org/"
+SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+# Should work on x86, amd64 and ppc, at least
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+IUSE="doc threads tcltk"
+
+DEPEND="sys-devel/flex
+	virtual/blas
+	virtual/lapack
+	dev-lang/perl
+	>=sys-apps/sed-4
+	tcltk? ( dev-lang/tk )
+	doc? ( app-doc/doxygen
+		media-gfx/graphviz )"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# do not install tkmolrender if not requested
+	if ! use tcltk; then
+		sed -e "s:.*/bin/molrender/tkmolrender.*::" \
+			-e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \
+			-e "s:/bin/rm -f tkmolrender::" \
+			-i "./src/bin/molrender/Makefile" \
+			|| die "failed to disable tkmolrender"
+	fi
+}
+
+
+src_compile() {
+	CFLAGS_SAVE=${CFLAGS}; CXXFLAGS_SAVE=${CXXFLAGS}
+	myconf="${myconf} --prefix=/usr"
+
+	# only shared will work on ppc64 - bug #62124
+	if use ppc64; then
+		myconf="${myconf} --enable-shared"
+	fi
+
+	econf \
+		$(use_enable threads) \
+		${myconf} || die "configure failed"
+
+	sed -i -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS_SAVE}:" \
+		-e "s:^FFLAGS =.*$:FFLAGS=${CFLAGS_SAVE}:" \
+		-e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS_SAVE}:" \
+		lib/LocalMakefile
+	emake || die "emake failed"
+}
+
+
+src_test() {
+	cd "${S}"/src/bin/mpqc/validate
+
+	# we'll only run the small test set, since the
+	# medium and large ones take >10h and >24h on my
+	# 1.8Ghz P4M
+	make check0 || die "failed in test routines"
+}
+
+
+
+src_install() {
+	make installroot="${D}" install install_devel install_inc \
+		|| die "install failed"
+
+	dodoc CHANGES CITATION README || die "failed to install docs"
+
+	# make extended docs 
+	if use doc; then
+		cd "${S}"/doc
+		make all || die "failed to generate documentation"
+		doman man/man1/* && doman man/man3/* || \
+			die "failed to install man pages"
+		dohtml -r html/
+	fi
+}
+
+pkg_postinst() {
+	echo
+	einfo "MPQC can be picky with regard to compilation flags."
+	einfo "If during mpqc runs you have trouble converging or "
+	einfo "experience oscillations during SCF interations, "
+	einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS."
+	einfo "Particularly, replacing -march=pentium4 by -march=pentium3"
+	einfo "might help if you encounter problems with correlation "
+	einfo "consistent basis sets."
+	echo
+}
+
+
+
+
+
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
new file mode 100644
index 0000000..83da192
--- /dev/null
+++ b/sci-chemistry/pymol/ChangeLog
@@ -0,0 +1,99 @@
+# ChangeLog for sci-chemistry/pymol
+# Copyright 2002-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.10 2005/12/19 18:55:11 spyderous Exp $
+
+  19 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; pymol-0.98.ebuild:
+  virtual/glut, not media-libs/glut.
+
+  13 Aug 2005; Michael Hanselmann <hansmi@gentoo.org> pymol-0.98.ebuild:
+  Stable on ppc.
+
+  25 Jun 2005; Olivier Fisette <ribosome@gentoo.org> -pymol-0.88.ebuild,
+  pymol-0.98.ebuild:
+  Added to x86. Removed obsolete version.
+
+  17 Jun 2005; Michael Hanselmann <hansmi@gentoo.org> pymol-0.97.ebuild:
+  Stable on ppc.
+
+*pymol-0.98 (18 May 2005)
+
+  18 May 2005; Olivier Fisette <ribosome@gentoo.org> -pymol-0.90.ebuild,
+  -pymol-0.95.ebuild, +pymol-0.98.ebuild:
+  New version: 0.98. Removed obsolete versions.
+
+  13 May 2005; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild:
+  Fixed multilib issue (bug #92103).
+
+  04 May 2005; David Holm <dholm@gentoo.org> pymol-0.97.ebuild:
+  Readded to ~ppc. Please don't remove it without filing a proper bug report.
+
+  06 Feb 2005; Simon Stelling <blubb@gentoo.org> pymol-0.97.ebuild:
+  added ~amd64
+
+*pymol-0.97 (24 Dec 2004)
+
+  24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/header_order.patch, +files/nosplash-gentoo.patch,
+  +files/pymol-gentoo.diff, +files/setup.py-gentoo.patch,
+  +files/setup2.py-gentoo.patch, +pymol-0.88.ebuild, +pymol-0.90.ebuild,
+  +pymol-0.95.ebuild, +pymol-0.97.ebuild:
+  Moved from app-sci/pymol to sci-chemistry/pymol.
+
+  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild:
+  Added to x86.
+
+*pymol-0.97 (26 Jul 2004)
+
+  26 Jul 2004; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild:
+  Version bump suggested by Stéphane Gagné <sgagne@rsvs.ulaval.ca> (bug #58097).
+  Removed header order patch since it is no longer needed.
+
+*pymol-0.95 (20 Apr 2004)
+
+  20 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> pymol-0.95.ebuild,
+  files/header_order.patch:
+  Version bump. Needed a little patch and a change to the setup2.py call (if it
+  does not find the modules, it will create no python.com)
+
+  19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> pymol-0.82.ebuild,
+  pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild:
+  Adding IUSE, cleanup
+
+  03 Mar 2004; Peter Bienstman <pbienst@gentoo.org> pymol-0.90:
+  marked stable on x86
+
+  02 Sep 2003; Alastair Tse <liquidx@gentoo.org> pymol-0.82.ebuild,
+  pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild:
+  moved dev-python/Numeric to dev-python/numeric
+
+*pymol-0.90 (23 Jul 2003)
+
+  23 Jul 2003; George Shapovalov <george@gentoo.org> pymol-0.90, files/setup.py-gentoo.patch :
+  new version + fix for setup.py, (#24967)
+  thanks to Ben Cornett <acornet@emory.edu> for the update
+
+*pymol-0.88 (29 Jun 2003)
+
+  19 Jun 2003; George Shapovalov <george@gentoo.org> pymol-0.88.ebuild, files/{digest-pymol-0.88,nosplash-gentoo.patch,setup2.py-gentoo.patch} :
+  new version (#22235)
+  now uses distutils for python
+  thanks to Todd Geders <geders@purdue.edu> for update notification 
+  and Ben Cornett <acornet@emory.edu>  for "distutilized" ebuild submission
+
+*pymol-0.86 (05 Feb 2003)
+
+  05 Feb 2003; George Shapovalov <george@gentoo.org> pymol-0.86.ebuild, files/digest-pymol-0.86 :
+  new version, (#13531)
+  removed -funroll-loops from CFLAGS
+
+*pymol-0.82 (17 July 2002)
+
+  19 Oct 2002; Daniel Ahlberg <aliz@gentoo.org> pymol-0.82.ebuild :
+  Updated to mirror://sourceforge in SRC_URI.
+
+  17 July 2002; George Shapovalov <george@gentoo.org> pymol-0.82.ebuild, files/digest-pymol-0.82, ChangeLog :
+
+  Inital release,
+  molecular visualization package
+  
+  ebuild submitted by Ben Cornett <acornet@emory.edu>
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
new file mode 100644
index 0000000..40dcc55
--- /dev/null
+++ b/sci-chemistry/pymol/Manifest
@@ -0,0 +1,27 @@
+MD5 b6605c26bd0098518434bb02aec53a68 ChangeLog 3719
+RMD160 520116b287065463171c79202250eab0d14644ce ChangeLog 3719
+SHA256 a50073ea82a1685ba15d39a2c5c06e3e45c7541b85cbd06c72899200ca3ac9fd ChangeLog 3719
+MD5 925dc45d0ae6070f5506dffc1d100975 files/digest-pymol-0.99_rc6 247
+RMD160 505a34a7bebbbdd2c60913ea3ec7cd41164eeaff files/digest-pymol-0.99_rc6 247
+SHA256 c6ec27d34304ab8e1d2d24f80537f9b63d14e6e915776434e158eecfa1060aac files/digest-pymol-0.99_rc6 247
+MD5 1a6ba582a7928c370c8dfe44c8867e7c files/header_order.patch 905
+RMD160 0a4e2b2f95e2ace2ad21d27740bef5308a4990d5 files/header_order.patch 905
+SHA256 1f181350c2d99e31c59baea2f31b5ce27b16bae61ce6c9438d2f0e1e903b4cce files/header_order.patch 905
+MD5 929741dc2da6577e6e99c5542d68dbd5 files/nosplash-gentoo.patch 332
+RMD160 2280fbe9daba8a0d3ca81a3aacfcc55bd06fc7d3 files/nosplash-gentoo.patch 332
+SHA256 5e0761591eeea90bcaa06a72c210a80ba46f2542ff985f8dd893af112254a890 files/nosplash-gentoo.patch 332
+MD5 34d172ef31b5038e071b634d4e645cf1 files/pymol-gentoo.diff 1566
+RMD160 6a566cd0105ba94f9b06be8219c5fbe644281ab9 files/pymol-gentoo.diff 1566
+SHA256 15bdd116551022045c57743f21337c14ca368211a68a2a9763a1a7950f9af9d3 files/pymol-gentoo.diff 1566
+MD5 e42746bf581479c61ff1e7cc5b978edd files/setup.py-gentoo.patch 311
+RMD160 483f63778aa928bf2ce4de99edbc45af98abab8c files/setup.py-gentoo.patch 311
+SHA256 850bae1aef6007f159abf8d2f3ba3342ea5a7aaff8f4798c6829fc879d08d5ed files/setup.py-gentoo.patch 311
+MD5 af2da92225ab57969d18d16ed60324ce files/setup2.py-gentoo.patch 493
+RMD160 2d6bbabc01f6e4eb8ddafb9b0215ece50a639923 files/setup2.py-gentoo.patch 493
+SHA256 dc721d4d3fd557c684ddb1ec43e07e05c38f13750393cd1665148e18c5e6a959 files/setup2.py-gentoo.patch 493
+MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156
+RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156
+SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata.xml 156
+MD5 3662c250200ff906c5f280082f8e24a4 pymol-0.99_rc6.ebuild 1717
+RMD160 94ab430d50ce8c8f40184ebbfe16619c306d7c9f pymol-0.99_rc6.ebuild 1717
+SHA256 1e78941c363700b90d4d0ab2d55df003f3a454b929932e9265b9a5499a870416 pymol-0.99_rc6.ebuild 1717
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.99_rc6 b/sci-chemistry/pymol/files/digest-pymol-0.99_rc6
new file mode 100644
index 0000000..3a46209
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.99_rc6
@@ -0,0 +1,3 @@
+MD5 cb29385ab523f648d4db47a222b1d03e pymol-0_99rc6-src.tgz 4198816
+RMD160 e9dc568dd38fffd37f306adf7e7a109d81dd4477 pymol-0_99rc6-src.tgz 4198816
+SHA256 d56bebc1316fd3442c54dee5bc4b2979041943bf50a9b34b44839595fd1b9a59 pymol-0_99rc6-src.tgz 4198816
diff --git a/sci-chemistry/pymol/files/header_order.patch b/sci-chemistry/pymol/files/header_order.patch
new file mode 100644
index 0000000..e11f31b
--- /dev/null
+++ b/sci-chemistry/pymol/files/header_order.patch
@@ -0,0 +1,36 @@
+--- layer0/MyPNG.c	2004-01-30 00:40:33.000000000 +0100
++++ layer0/MyPNG.c.new	2004-04-20 16:05:35.399498139 +0200
+@@ -14,17 +14,8 @@
+ Z* -------------------------------------------------------------------
+ */
+ 
+-#include"os_predef.h"
+-#include"os_std.h"
+-
+-#include"Base.h"
+-#include "MyPNG.h"
+-#include"MemoryDebug.h"
+-#include "Setting.h"
+-
+ #ifdef _HAVE_LIBPNG
+-#include<png.h>
+-
++#include <png.h>
+  /* The png_jmpbuf() macro, used in error handling, became available in
+   * libpng version 1.0.6.  If you want to be able to run your code with older
+   * versions of libpng, you must define the macro yourself (but only if it
+@@ -37,6 +28,14 @@
+ 
+ #endif
+ 
++#include"os_predef.h"
++#include"os_std.h"
++
++#include"Base.h"
++#include "MyPNG.h"
++#include"MemoryDebug.h"
++#include "Setting.h"
++
+ int MyPNGWrite(char *file_name,unsigned char *p,unsigned int width,unsigned int height)
+ {
+ #ifdef _HAVE_LIBPNG
diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
new file mode 100644
index 0000000..202a7cf
--- /dev/null
+++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch
@@ -0,0 +1,8 @@
+--- modules/pymol/invocation.py.orig	2003-06-11 13:40:13.000000000 -0400
++++ modules/pymol/invocation.py	2003-06-11 13:40:29.000000000 -0400
+@@ -179,5 +179,3 @@
+ 
+          else:
+             options.deferred.append(a)
+-      if options.show_splash and not options.no_gui:
+-         options.deferred.insert(0,"_do__ cmd.splash(1)")
diff --git a/sci-chemistry/pymol/files/pymol-gentoo.diff b/sci-chemistry/pymol/files/pymol-gentoo.diff
new file mode 100644
index 0000000..8b4b2ba
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-gentoo.diff
@@ -0,0 +1,53 @@
+--- Rules.linux	Sun Mar 31 03:06:22 2002
++++ Rules.make	Tue May 21 15:42:31 2002
+@@ -12,14 +12,13 @@
+ XLIB_DIR = -L/usr/X11R6/lib
+ XINC_DIR = -I/usr/X11R6/include
+ #--- Python
+-PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python
++PYTHON_EXE = /usr/bin/python
+ PYTHON_LIB =
+ PYTHON_LIB_DIR = 
+-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \
+-	-I$(PYMOL_PATH)/ext/include/python2.1/Numeric
++PYTHON_INC_DIR = -I/usr/include/python2.2  -I/usr/include/python2.2/Numeric
+ #--- Other external dependencies
+-EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include
+-EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib
++EXT_INC_DIR = 
++EXT_LIB_DIR = 
+ #---------------------------------------------------------------------
+ #
+ #- Build for LINUX as an importable module ---------------------------
+@@ -48,7 +47,7 @@
+ #
+ #- Choose One --------------------------------------------------------
+ #--- Workaround for XFree86/DRI linux dll problem for module build
+-BUGS = -D_DRI_WORKAROUND
++DEFS += -D_DRI_WORKAROUND
+ #---
+ #BUGS =
+ #---------------------------------------------------------------------
+@@ -58,7 +57,7 @@
+ #PNG = -D_HAVE_LIBPNG 
+ #ZLIB = 
+ #--- Libpng2 available but needs zlib 
+-PNG = -D_HAVE_LIBPNG 
++DEFS += -D_HAVE_LIBPNG 
+ ZLIB = -lz
+ #--- Libpng2 not available
+ #PNG = 
+@@ -77,12 +76,7 @@
+ PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \
+    -I../layer3 -I../layer4 -I../layer5 
+ 
+-C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \
+-   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS)
+-
+-CFLAGS = $(C_FLAGS)
+-
+-
++C_FLAGS := $(CFLAGS) $(PYTHON_INC_DIR) $(XINC_DIR) $(DEFS)
+ 
+ 
+ 
diff --git a/sci-chemistry/pymol/files/setup.py-gentoo.patch b/sci-chemistry/pymol/files/setup.py-gentoo.patch
new file mode 100644
index 0000000..d675596
--- /dev/null
+++ b/sci-chemistry/pymol/files/setup.py-gentoo.patch
@@ -0,0 +1,10 @@
+--- pymol-0.90/setup.py 2003-04-26 21:22:14.000000000 -0400
++++ pymol-0.90.new/setup.py     2003-07-21 09:39:51.000000000 -0400
+@@ -71,6 +71,7 @@
+    "layer0/Map.c",
+    "layer0/Match.c",
+    "layer0/Matrix.c",
++   "layer0/MemoryCache.c",
+    "layer0/MemoryDebug.c",
+    "layer0/MyPNG.c",
+    "layer0/Parse.c",
diff --git a/sci-chemistry/pymol/files/setup2.py-gentoo.patch b/sci-chemistry/pymol/files/setup2.py-gentoo.patch
new file mode 100644
index 0000000..1d387ea
--- /dev/null
+++ b/sci-chemistry/pymol/files/setup2.py-gentoo.patch
@@ -0,0 +1,17 @@
+--- setup2.py.orig	2003-06-10 19:12:35.000000000 -0400
++++ setup2.py	2003-06-10 19:11:46.000000000 -0400
+@@ -12,6 +12,14 @@
+ import sys
+ from distutils import dir_util,file_util
+ 
++import os.path
++pmlibs = os.path.join(os.environ['D'],
++                      sys.prefix[1:],
++                      'lib/python%s' % sys.version[:3],
++                      'site-packages')
++sys.path.insert(0, pmlibs)
++
++
+ if sys.platform=='win32':
+    launch_script = "pymol.bat"
+ elif sys.platform=='cygwin':
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
new file mode 100644
index 0000000..b229aec
--- /dev/null
+++ b/sci-chemistry/pymol/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-0.99_rc6.ebuild b/sci-chemistry/pymol/pymol-0.99_rc6.ebuild
new file mode 100644
index 0000000..d1827c5
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-0.99_rc6.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.98.ebuild,v 1.4 2005/12/19 18:55:11 spyderous Exp $
+
+inherit distutils eutils multilib
+
+MY_PV=${PV/_}
+MY_S_P="${PN}-${MY_PV}"
+MY_PV=${MY_PV/./_}
+MY_P="${PN}-${MY_PV}"
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="mirror://sourceforge/pymol/${MY_P}-src.tgz"
+
+LICENSE="PSF-2.2"
+IUSE=""
+SLOT="0"
+KEYWORDS="~amd64 ppc x86"
+
+DEPEND="dev-lang/python
+	dev-python/pmw
+	dev-python/numeric
+	dev-lang/tk
+	media-libs/libpng
+	sys-libs/zlib
+	virtual/glut"
+S="${WORKDIR}/${MY_S_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though.
+	[[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		${S}/setup.py
+}
+
+src_install() {
+	python_version
+
+	distutils_src_install
+	cd ${S}
+	
+	#The following three lines probably do not do their jobs and should be
+	#changed
+	PYTHONPATH="${D}/usr/$(get_libdir)/site-packages" ${python} setup2.py
+
+	# Make our own wrapper
+cat >> ${T}/pymol << EOF
+#!/bin/sh
+PYMOL_PATH=/usr/lib/python${PYVER}/site-packages/pymol
+PYMOL_DATA="/usr/share/pymol/data"
+PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+export PYMOL_PATH PYMOL_DATA PYMOL_SCRIPTS
+${python} \${PYMOL_PATH}/__init__.py \$*
+EOF
+	
+	exeinto /usr/bin
+	doexe ${T}/pymol
+	dodoc DEVELOPERS CHANGES
+
+	mv examples ${D}/usr/share/doc/${PF}/
+
+	dodir /usr/share/pymol
+	mv test ${D}/usr/share/pymol/
+	mv data ${D}/usr/share/pymol/
+	mv scripts ${D}/usr/share/pymol/
+}
diff --git a/sci-chemistry/schakal/Manifest b/sci-chemistry/schakal/Manifest
new file mode 100644
index 0000000..7ebd355
--- /dev/null
+++ b/sci-chemistry/schakal/Manifest
@@ -0,0 +1,6 @@
+MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253
+RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253
+SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253
+MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672
+RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672
+SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672
diff --git a/sci-chemistry/schakal/schakal-99.ebuild b/sci-chemistry/schakal/schakal-99.ebuild
new file mode 100644
index 0000000..ac9dada
--- /dev/null
+++ b/sci-chemistry/schakal/schakal-99.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+# This is an incredibly ugly UI, but it can create beautiful graphics.
+# Ebuild not yet in a working state, but very close. src_install() just needs
+# finishing.
+
+inherit fortran toolchain-funcs
+
+DESCRIPTION="Program for the graphical representation of molecular and solid-state structure models"
+HOMEPAGE="http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/schakal.html"
+SRC_URI="http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/sch${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+RDEPEND="|| ( ( x11-libs/libXaw
+			x11-terms/xterm
+		)
+		virtual/x11
+	)"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+FORTRAN="gfortran"
+
+src_unpack() {
+	unpack ${A}
+	sed -i \
+		-e "s:^\(MACHINE=\).*:\1LINUX:g" \
+		-e "s:^\(F77=\).*:\1${FORTRANC}:g" \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(C_FLAGS = \).*:\1${CFLAGS} -DFILEPROMPT:g" \
+		${S}/makefile.x
+	sed -i \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		${S}/makefile.fsb
+	sed -i \
+		-e 's~^jot.*~xterm -e ${EDITOR:-/bin/nano} $*~g' \
+		${S}/editt.sh
+	epatch ${FILESDIR}/fix-xs-character-escapes.patch
+}
+
+src_compile() {
+	emake -f makefile.x || die "make.x failed"
+
+	# Do file selection box by hand -- taken from mfilepr script
+	mkdir file_selection_box
+	cd file_selection_box
+	mv ../file*.* .
+	mv ../makefile.fsb .
+	emake -f makefile.fsb || die "make.fsb failed"
+	cp fileprompt ../
+	cd ..
+
+}
+
+src_install() {
+	doexe ${S}/uschak ${S}/sch99x ${S}/fileprompt ${S}/printm
+
+	insinto /usr/lib/schakal
+	# create all the dat, scf, sif etc dirs with stuff in them
+}
+
+pkg_postinst() {
+	einfo "You may also wish to download the tutorial from"
+	einfo "http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/tutorial.pdf"
+}
diff --git a/sci-chemistry/tinker/ChangeLog b/sci-chemistry/tinker/ChangeLog
new file mode 100644
index 0000000..2300ccb
--- /dev/null
+++ b/sci-chemistry/tinker/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for sci-chemistry/tinker
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.2 2005/12/03 20:29:18 spyderous Exp $
+
+  03 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; tinker-4.2.ebuild:
+  Note that tinker script has hardcoded blackdown in it. This is needed
+  because java-config's exit codes return 0, even on failure.
+
+*tinker-4.2 (03 Dec 2005)
+
+  03 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml,
+  +tinker-4.2.ebuild:
+  (#35945) New molecular mechanics package. Heavily modified ebuild based on
+  that of Jeremy Warren <jwarren@cheesefoam.dyndns.org>.
+
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
new file mode 100644
index 0000000..54d514d
--- /dev/null
+++ b/sci-chemistry/tinker/Manifest
@@ -0,0 +1,12 @@
+MD5 8bb9b767a5eb6c8e9b18e4956f614744 ChangeLog 679
+RMD160 4fdd4abd2cf01a883c0103fbe79fab82a629f751 ChangeLog 679
+SHA256 0c538893547f95ecb36d0b826d9d9d6c7bb61eab5446fc58c756df1a551a7c65 ChangeLog 679
+MD5 c336619e5cd4eb1ef174a15514c99a88 files/digest-tinker-4.2 59
+RMD160 417dc19396cb5a4a4b6ffb67fbbd2f75dc58f0d5 files/digest-tinker-4.2 59
+SHA256 85b0f4ec639f8ec3037abd8ea96cef7747983ee1252b105fb9c848c654c950ce files/digest-tinker-4.2 59
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
+MD5 0ff4f27045feca24fdc0d7ef4d0eed6f tinker-4.2.ebuild 3538
+RMD160 f1522c64af702e4d9fd9e7f0fc10516035fe954c tinker-4.2.ebuild 3538
+SHA256 6f493b1f8f3f35814f6e91729e8d7e131ba65bcc66966fa6955ad54daf1329d3 tinker-4.2.ebuild 3538
diff --git a/sci-chemistry/tinker/files/digest-tinker-4.2 b/sci-chemistry/tinker/files/digest-tinker-4.2
new file mode 100644
index 0000000..3381b74
--- /dev/null
+++ b/sci-chemistry/tinker/files/digest-tinker-4.2
@@ -0,0 +1 @@
+MD5 5618d8a373896f00e452b137200223fd tinker.tar.gz 8177555
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
new file mode 100644
index 0000000..211b8bd
--- /dev/null
+++ b/sci-chemistry/tinker/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/tinker/tinker-4.2.ebuild b/sci-chemistry/tinker/tinker-4.2.ebuild
new file mode 100644
index 0000000..d3adad8
--- /dev/null
+++ b/sci-chemistry/tinker/tinker-4.2.ebuild
@@ -0,0 +1,135 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-4.2.ebuild,v 1.2 2005/12/03 20:29:18 spyderous Exp $
+
+inherit fortran toolchain-funcs
+
+FORTRAN="ifc g77"
+
+DESCRIPTION="TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM.  A Java based visualization front end is included."
+HOMEPAGE="http://dasher.wustl.edu/tinker/"
+SRC_URI="ftp://dasher.wustl.edu/pub/tinker.tar.gz"
+IUSE="X"
+LICENSE="Tinker"
+SLOT="0"
+KEYWORDS="~x86"
+
+DEPEND="X? (
+			|| ( dev-java/blackdown-java3d-bin
+			dev-java/sun-java3d-bin )
+		)"
+S="${WORKDIR}/tinker/source"
+
+src_compile() {
+	if use X; then
+		COMPGUI="./compgui.make"
+		LINK="./linkgui.make"
+		if use ppc-macos; then
+			cp ../jar/macosx/sockets.c .
+		else
+			cp ../jar/linux/sockets.c .
+		fi
+	else
+		LINK="./link.make"
+	fi
+
+	COMPILE="./compile.make"
+	LIBRARY="./library.make"
+
+	# Need to make sure all of the appropriate config files are in place
+	# for the build.
+	# This should be easily customizable for other Fortran compilers, e.g. pg77.
+	if use ppc-macos; then
+		cp ../apple/gnu/* .
+	elif [ "${FORTRANC}" = "ifc" ]; then
+		cp ../linux/intel/* .
+	elif [ "${FORTRANC}" = "g77" ]; then
+		cp ../linux/gnu/* .
+	fi
+
+	cp ../make/* .
+
+	# Prep build scripts
+	if use X; then
+		sed -i \
+			-e "s:-O3:${CFLAGS}:" \
+			-e "s:gcc:$(tc-getCC):" \
+			${COMPGUI}
+		local JAVA_HOME=$(java-config --jdk-home)
+		local JAVA_LIB_PATH="${JAVA_HOME}/jre/lib/i386/client"
+		ln -s ${JAVA_LIB_PATH}/libjvm.so
+		sed -i -e "s:/local/java/j2sdk1.4.2_05:${JAVA_HOME}:g" ${COMPGUI}
+		sed -i -e "s:g77:${FORTRANC}:g" ${LINK}
+	fi
+	# Default to -O2 if FFLAGS is unset
+	sed -i -e "s:-O3 -ffast-math:${FFLAGS:- -O2}:" ${COMPILE}
+	sed -i -e "s:g77:${FORTRANC}:g" ${COMPILE}
+
+	# Prep executable script - the one packaged with the distro is b0rked
+	if use X; then
+		echo 'java -jar /usr/lib/tinker/ffe.jar -Djava.library.path=$(java-config -i blackdown-java3d-bin) -cp $(java-config -p blackdown-java3d-bin)' > tinker
+	fi
+
+	einfo "Compiling ..."
+	if use X; then
+		${COMPGUI} || die "GUI compile failed"
+	fi
+	${COMPILE} || die "compile failed"
+	einfo "Building libraries ..."
+	${LIBRARY} || die "library creation failed"
+	einfo "Linking ..."
+	${LINK} || die "link failed"
+}
+
+src_install() {
+	exeinto /usr/bin
+
+	dodoc \
+		${WORKDIR}/tinker/doc/*.txt \
+		${WORKDIR}/tinker/doc/release-4.2 \
+		${WORKDIR}/tinker/doc/*.pdf
+
+	if use X; then
+		if use ppc-macos; then
+			dolib.so ${WORKDIR}/tinker/jar/macosx/libffe.jnilib
+		else
+			dolib.so ${WORKDIR}/tinker/jar/linux/libffe.so
+		fi
+	fi
+
+	dolib.a libtinker.a
+
+	insinto /usr/lib/tinker
+	if use X; then
+		doins ${WORKDIR}/tinker/jar/ffe.jar
+	fi
+
+	for EXE in *.x; do
+		newexe ${EXE} ${EXE%.x}
+	done
+
+	# superpose overlaps with ccp4, so don't install it locally
+	rm -f ${D}/usr/bin/superpose
+
+	if use X; then
+		doexe tinker
+	fi
+
+	docinto example
+	dodoc ${WORKDIR}/tinker/example/*
+	docinto test
+	dodoc ${WORKDIR}/tinker/test/*
+
+	doexe ${WORKDIR}/tinker/perl/mdavg
+
+	insinto /usr/share/tinker/params
+	doins ${WORKDIR}/tinker/params/*
+}
+
+pkg_postinst() {
+	einfo "Tinker binaries installed to ${ROOT}usr/bin."
+	einfo "Parameter files installed to ${ROOT}usr/share/tinker/params."
+	einfo "Call the Java X front-end, Force-Field Explorer, with 'tinker.'"
+	einfo "It doesn't seem to detect installed Java3D yet, fixes welcome."
+	einfo "You must edit ${ROOT}usr/bin/tinker if you aren't using Blackdown."
+}
diff --git a/sci-chemistry/yaehmop/Manifest b/sci-chemistry/yaehmop/Manifest
new file mode 100644
index 0000000..7ebd355
--- /dev/null
+++ b/sci-chemistry/yaehmop/Manifest
@@ -0,0 +1,6 @@
+MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253
+RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253
+SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253
+MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672
+RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672
+SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672
diff --git a/sci-chemistry/yaehmop/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/yaehmop/files/digest-gtk-gamess-1.04.1
new file mode 100644
index 0000000..410cbec
--- /dev/null
+++ b/sci-chemistry/yaehmop/files/digest-gtk-gamess-1.04.1
@@ -0,0 +1,3 @@
+MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334
+RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334
+SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334
diff --git a/sci-chemistry/yaehmop/gtk-gamess-1.04.1.ebuild b/sci-chemistry/yaehmop/gtk-gamess-1.04.1.ebuild
new file mode 100644
index 0000000..611ff42
--- /dev/null
+++ b/sci-chemistry/yaehmop/gtk-gamess-1.04.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
+
+DESCRIPTION="GTK+ frontend to GAMESS"
+HOMEPAGE="http://www.uiowa.edu/~ghemical/gtk-gamess.shtml"
+SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+RDEPEND="=gnome-base/libglade-0*"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	sed -i -e "s:/usr/local/gamess/rungms:/usr/bin/rungms:g" \
+		${S}/src/gg_config.cpp
+}
+
+src_install() {
+	make DESTDIR="${D}" install || die "install failed"
+}
author	Donnie Berkholz <donnie@supernova.(none)>	2006-04-17 22:30:24 -0700
committer	Donnie Berkholz <donnie@supernova.(none)>	2006-04-17 22:30:24 -0700
commit	b084e8250f714a5d67587f1d43f40d5774d25643 (patch)
tree	bc819fff34c32bd0c8c4c68df3a846f0b47316ca /sci-chemistry
download	dberkholz-b084e8250f714a5d67587f1d43f40d5774d25643.tar.gz dberkholz-b084e8250f714a5d67587f1d43f40d5774d25643.tar.bz2 dberkholz-b084e8250f714a5d67587f1d43f40d5774d25643.zip