merge

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci * 'master' of git://git.overlays.gentoo.org/proj/sci: (95 commits) Some scripts are in the wrong place [sci-libs/fftw] added static-libs useflag (Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit) [sci-libs/pfft] added static-libs useflag (Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit) [sci-libs/nfft] initial commit (Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit) [sci-libs/pfft]: initial commit (Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit) [sci-libs/fftw] Added alpha version to test mpi interface (Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit) [dev-tex/revtex] Upstream bumped the patch level without renaming the file... (Portage version: 2.1.8.3/git/Linux i686) (Unsigned Manifest commit) mpir version bump Local bump of sci-mathematics/axiom-201005 Version Bump Moved to the tree. See bug #79082. [dev-vcs/mercurial-server] updated elog messages (Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit) sci-mathematics/normaliz bump to 2.5 Add missing factory headers for libsingular. Imort all my fixes to singular from the sage-on-gentoo overlay. Import Christopher's version of factory migrated to the autotools-utils eclass from the sage-on-gentoo overlay. Version Bump Fixed patch sci-geosciences/swmm: Version bump. Version bump. ... Conflicts: sci-chemistry/dssp2pdb/Manifest
author: Justin Lecher (jlec) <jlec@j-schmitz.net> 2010-09-13 12:36:50 +0200
committer: Justin Lecher (jlec) <jlec@j-schmitz.net> 2010-09-13 12:36:50 +0200
commit: 4ef17bec150af02f808505f6d2159a7dbb5cdaaa (patch)
tree: 0ead9485c93e271cb0f8d06276a9f6f59dfd518d /sci-chemistry
parent: Keyworded for *-linux (diff)
parent: Some scripts are in the wrong place (diff)
download: sci-4ef17bec150af02f808505f6d2159a7dbb5cdaaa.tar.gz
sci-4ef17bec150af02f808505f6d2159a7dbb5cdaaa.tar.bz2
sci-4ef17bec150af02f808505f6d2159a7dbb5cdaaa.zip
31 files changed, 1100 insertions, 816 deletions
diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest
new file mode 100644
index 000000000..872d0931b
--- /dev/null
+++ b/sci-chemistry/avogadro/Manifest
@@ -0,0 +1,22 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+EBUILD avogadro-9999.ebuild 1154 RMD160 72ab78f9f875fc54aded8d3453328f4c8f0f9619 SHA1 26434ea38782a15b42ff6d4eb6685f04795e1b63 SHA256 7cecb5f75ae42d570d7ba84a07f82e459e9e4ede4ba09bf233280caf7cc2b466
+MISC metadata.xml 600 RMD160 d3559123f9438a9d0a49783ebb38027f91492e8d SHA1 f0dc9728b4196c6b09e8a0c4fdb02cd9f692cda4 SHA256 298cc4b9c2fc652f167bf9ae6e9faec1cfd1aa41a276295f4d1a6814912b58af
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+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+=q3nR
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/avogadro/avogadro-9999.ebuild b/sci-chemistry/avogadro/avogadro-9999.ebuild
new file mode 100644
index 000000000..a69d3b534
--- /dev/null
+++ b/sci-chemistry/avogadro/avogadro-9999.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/avogadro/avogadro-1.0.1.ebuild,v 1.1 2010/05/21 15:33:28 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="python? 2:2.5"
+
+inherit cmake-utils eutils python git
+
+DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL"
+HOMEPAGE="http://avogadro.sourceforge.net/"
+EGIT_REPO_URI="git://github.com/cryos/avogadro.git"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="+glsl python"
+
+RDEPEND=">=sci-chemistry/openbabel-2.2.3
+	>=x11-libs/qt-gui-4.5.3:4
+	>=x11-libs/qt-opengl-4.5.3:4
+	x11-libs/gl2ps
+	glsl? ( >=media-libs/glew-1.5.0	)
+	python? (
+		>=dev-libs/boost-1.35
+		>=dev-libs/boost-1.35.0-r5[python]
+		dev-python/numpy
+		dev-python/sip
+	)"
+DEPEND="${RDEPEND}
+	>=dev-cpp/eigen-2.0.9
+	>=dev-util/cmake-2.6.2"
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_configure() {
+	local mycmakeargs
+	mycmakeargs="${mycmakeargs}
+		-DENABLE_THREADGL=FALSE
+		-DENABLE_RPATH=OFF
+		-DENABLE_UPDATE_CHECKER=OFF
+		$(cmake-utils_use_enable glsl GLSL)
+		$(cmake-utils_use_enable python PYTHON)"
+
+	cmake-utils_src_configure
+}
diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml
new file mode 100644
index 000000000..4f8df4c8f
--- /dev/null
+++ b/sci-chemistry/avogadro/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>cryos@gentoo.org</email>
+  </maintainer>
+  <longdescription>
+    Avogadro is an advanced molecular editor designed for cross-platform use in
+	computational chemistry, molecular modeling, bioinformatics, materials
+	science, and related areas. It offers flexible rendering and a powerful
+	plugin architecture.
+  </longdescription>
+  <use>
+    <flag name="glsl">Enable glsl features via GLEW.</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-chemistry/bist/ChangeLog b/sci-chemistry/bist/ChangeLog
new file mode 100644
index 000000000..543e6afd1
--- /dev/null
+++ b/sci-chemistry/bist/ChangeLog
@@ -0,0 +1,30 @@
+# ChangeLog for sci-chemistry/bist
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  22 Aug 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
+  Moved from sunrise to sci overlay.
+
+  25 Sep 2009; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
+  +bist-0.5.1-r1.ebuild, +files/bist-0.5.1-bracket.patch,
+  -files/wrap_bracket_dialog-amd64.patch, -bist-0.5.1.ebuild,
+  +files/bist-0.5.1-install.patch:
+  Fixed installation of plugins, help files, molecule library,
+  internationalization, man page, desktop file, and icon.
+
+  21 Sep 2009; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
+  -bist-0.4.7.ebuild, +bist-0.5.1.ebuild:
+  Version bump and upgrade of the ebuild to EAPI=2
+
+  20 Sep 2009; Thomas Sachau (Tommy[D]) <tommy@gentoo.org>
+  bist-0.4.7.ebuild:
+  Drop dependency on gcc
+
+  06 Oct 2008; Tomáš Chvátal <tomas.chvatal@gmail.com> bist-0.4.7.ebuild:
+  Fix Depend/Rdepend issue about gcc
+
+  30 Sep 2008; Giuseppe Marco Randazzo <gmrandazzo@gmail.com>
+  +files/wrap_bracket_dialog-amd64.patch, +bist-0.4.7.ebuild, +metadata.xml:
+  New Ebuild sci-chemistry/bist for bug 239172 thanks to Giuseppe Marco
+  Randazzo aka zeld
+
diff --git a/sci-chemistry/bist/Manifest b/sci-chemistry/bist/Manifest
new file mode 100644
index 000000000..a5ff6b6ec
--- /dev/null
+++ b/sci-chemistry/bist/Manifest
@@ -0,0 +1,26 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX bist-0.5.1-bracket.patch 379 RMD160 4d9d835a8c189862ec53f069862069a005b4c4ff SHA1 7c6ec5afb2bf2f1d6bc4ed931c5dbf03fe2abb98 SHA256 3fd94f204a237d3b00c2fd86b45259f65ac31606ebfe7ab076c3e24f8f855671
+AUX bist-0.5.1-install.patch 4074 RMD160 35136ca7aa40e34c543efae3def45ced6d9d2886 SHA1 fc69c1a111ca724409674a35b40d7bc342b99388 SHA256 b94add3bed813222d29f4156668668c3296f6d817eb8f097709fcabd37d5ae67
+DIST bist-0.5.1.tar.gz 766731 RMD160 a848cf778c9096239ca964dce352eeeab1ee4dc2 SHA1 22fd8186ef3a4fcc2776a3cf5b57ca78bfb4ab69 SHA256 78809230e2bcfffefaf8f95d85740d94cf2d10b4dd0d746f28cf1e82e4fc6cd5
+EBUILD bist-0.5.1-r1.ebuild 694 RMD160 a2b89ddcb1739df0f8ba9ecbfb437604f43fdb52 SHA1 dbfc9b9482d687ffbd7d86afc912f11585140621 SHA256 2d1a05d6bc8ad7e62b1e6cdde75d006cbc12d7aa2595c9ad4d3668833af6fd61
+MISC ChangeLog 1179 RMD160 09e71b55f8d994d4fec7f640cacf6ca8cdf25c79 SHA1 d60db59280ec2d855eb0888cfd772ed3ff641e4e SHA256 da7f51562f12111b0f707b85d39178c35191fe0f79e28c3facada9b4f3c99185
+MISC metadata.xml 1221 RMD160 a53092870d168cb265d2eef41a1556975b161846 SHA1 4c7dd7b7dfc788161a06815502785e1b6f2d9f7a SHA256 3469c6fb0fedd54e56f8961a7e1b6fc6aa23a6ace1d18b89a4a87ef2748fe164
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+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+=8rwF
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/bist/bist-0.5.1-r1.ebuild b/sci-chemistry/bist/bist-0.5.1-r1.ebuild
new file mode 100644
index 000000000..2a31a618c
--- /dev/null
+++ b/sci-chemistry/bist/bist-0.5.1-r1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit eutils base
+
+DESCRIPTION="Bist, the chemical drawing tool"
+HOMEPAGE="http://www.autistici.org/interzona/index.php?mod=03_Bist"
+SRC_URI="http://www.autistici.org/interzona/ftrack.php?url=sections/06_Download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="net-misc/curl
+	dev-libs/expat
+	>=x11-libs/fltk-1.1.7:1.1
+	sci-libs/gsl
+	>=sci-chemistry/openbabel-2.2.0
+	>=media-libs/plotutils-2.5"
+
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	use amd64 && epatch "${FILESDIR}/${P}-bracket.patch"
+	epatch "${FILESDIR}/${P}-install.patch"
+}
diff --git a/sci-chemistry/bist/files/bist-0.5.1-bracket.patch b/sci-chemistry/bist/files/bist-0.5.1-bracket.patch
new file mode 100644
index 000000000..86a587e6a
--- /dev/null
+++ b/sci-chemistry/bist/files/bist-0.5.1-bracket.patch
@@ -0,0 +1,11 @@
+--- pluginclude/wrap_bracket_dialog.hpp.orig	2008-09-30 10:45:56.000000000 +0200
++++ pluginclude/wrap_bracket_dialog.hpp	2008-09-30 10:46:07.000000000 +0200
+@@ -10,7 +10,7 @@
+ #if SIZEOF_INT_P == 8
+ #define WRAP_BRACKET_SIZE_USER_DATA_MENU long int
+ #else
+-#define WRAP_BRACKET_SIZE_USER_DATA_MENU unsigned int
++#define WRAP_BRACKET_SIZE_USER_DATA_MENU unsigned long
+ #endif
+ 
+ 
diff --git a/sci-chemistry/bist/files/bist-0.5.1-install.patch b/sci-chemistry/bist/files/bist-0.5.1-install.patch
new file mode 100644
index 000000000..b349b0d5b
--- /dev/null
+++ b/sci-chemistry/bist/files/bist-0.5.1-install.patch
@@ -0,0 +1,80 @@
+diff -r -u bist-0.5.1.orig/Makefile.in bist-0.5.1/Makefile.in
+--- bist-0.5.1.orig/Makefile.in	2009-04-04 12:04:44.000000000 +0200
++++ bist-0.5.1/Makefile.in	2009-09-23 23:59:37.000000000 +0200
+@@ -16,12 +16,7 @@
+ 
+ SRC_DIR =./src/
+ INC_DIR=./include/
+-LIB_DIR=@LIB_DIR_CONFIG_PATH@
+-LIB_DIR_DEBIAN=@LIB_DIR_CONFIG@
+-
+-ifneq ($(strip ${exec_prefix}),)
+-LIB_DIR=${LIB_DIR_DEBIAN}
+-endif
++LIB_DIR=@libdir@
+ 
+ 
+ 
+@@ -186,33 +181,29 @@
+ 	rm -f *.o
+ 	rm -f plugin/*.so
+ install:
+-	install -D -o root -g root -m 0755 -s $(ELF) $(prefix)/bin/$(ELF)
+-	install -D -o root -g root -m 0644  bist.png $(prefix)/share/pixmap/bist.png
+-	install -D -o root -g root -m 0644  bist.desktop $(prefix)/share/applications/bist.desktop
++	install -D -o root -g root -m 0755 -s $(ELF) $(DESTDIR)/$(prefix)/bin/$(ELF)
++	install -D -o root -g root -m 0644  bist.png $(DESTDIR)/$(prefix)/share/pixmaps/bist.png
++	install -D -o root -g root -m 0644  bist.desktop $(DESTDIR)/$(prefix)/share/applications/bist.desktop
+ 	find rings -type d -exec install -D -o root \
+-	 -g root -m 0755 -d $(prefix)/share/$(ELF)-$(VERSION)/\{\} \;
++	 -g root -m 0755 -d $(DESTDIR)/$(prefix)/share/$(ELF)-$(VERSION)/\{\} \;
+ 	find rings ! -type d -exec install -D -o root -g root \
+-	-m 0644 \{\} $(prefix)/share/$(ELF)-$(VERSION)/\{\} \;
+-	install -D -o root -g root -m 0755 -d   $(prefix)/share/doc/$(ELF)-$(VERSION)
+-	install -D -o root -g root -m 0644 doc/*.*  $(prefix)/share/doc/$(ELF)-$(VERSION)/
+-	install -D -o root -g root -m 0644 TODO  $(prefix)/share/doc/$(ELF)-$(VERSION)/
+-	install -D -o root -g root -m 0644 BUGS  $(prefix)/share/doc/$(ELF)-$(VERSION)/
+-	install -D -o root -g root -m 0644 README  $(prefix)/share/doc/$(ELF)-$(VERSION)/
+-	./mkinstalldirs $(LIB_DIR)/$(ELF)-$(VERSION)/plugin
+-	install -D -o root -g root -m 0644 plugin/*.so $(LIB_DIR)/$(ELF)-$(VERSION)/plugin/
+-	./mkinstalldirs $(prefix)/share/locale/$(ELF)-$(VERSION)
+-	cp -R po/* $(prefix)/share/locale/$(ELF)-$(VERSION)/
+-	./mkinstalldirs $(prefix)/share/man/man1/
++	-m 0644 \{\} $(DESTDIR)/$(prefix)/share/$(ELF)-$(VERSION)/\{\} \;
++	install -D -o root -g root -m 0755 -d   $(DESTDIR)/$(prefix)/share/doc/$(ELF)-$(VERSION)
++	install -D -o root -g root -m 0644 doc/*.*  $(DESTDIR)/$(prefix)/share/doc/$(ELF)-$(VERSION)/
++	install -D -o root -g root -m 0644 TODO  $(DESTDIR)/$(prefix)/share/doc/$(ELF)-$(VERSION)/
++	install -D -o root -g root -m 0644 BUGS  $(DESTDIR)/$(prefix)/share/doc/$(ELF)-$(VERSION)/
++	install -D -o root -g root -m 0644 README  $(DESTDIR)/$(prefix)/share/doc/$(ELF)-$(VERSION)/
++	./mkinstalldirs $(DESTDIR)/$(LIB_DIR)/$(ELF)-$(VERSION)/plugin
++	install -D -o root -g root -m 0644 plugin/*.so $(DESTDIR)/$(LIB_DIR)/$(ELF)-$(VERSION)/plugin/
++	./mkinstalldirs $(DESTDIR)/$(prefix)/share/locale
++	find po -name "*.po" -exec rm -v \{\} \;
++	rm -v po/LINGUAS po/bist.pot
++	cp -R po/* $(DESTDIR)/$(prefix)/share/locale/
++	./mkinstalldirs $(DESTDIR)/$(prefix)/share/man/man1/
+ 	gzip -c --best ./doc/man/$(ELF).1 > ./doc/man/$(ELF).1.gz
+-	install -D -o root -g root -m 0644 ./doc/man/$(ELF).1.gz $(prefix)/share/man/man1/
++	install -D -o root -g root -m 0644 ./doc/man/$(ELF).1.gz $(DESTDIR)/$(prefix)/share/man/man1/
+ 	rm -f ./doc/man/$(ELF).1.gz
+ 
+-uninstall:
+-	rm -Rf $(prefix)/bin/$(ELF)-$(VERSION)
+-	rm -Rf $(prefix)/share/$(ELF)-$(VERSION)
+-	rm -Rf $(prefix)/share/doc/$(ELF)-$(VERSION)
+-	rm -Rf $(LIB_DIR)/$(ELF)-$(VERSION)/
+-	rm -f $(prefix)/share/man/man1/$(ELF).1.gz
+ dist: distclean
+ 	./rmcvs.py
+ 	cd .. ; tar -c $(ELF) | gzip --best >  $(TARNAME)-$(VERSION).tar.gz
+diff -r -u bist-0.5.1.orig/include/config_path.h.in bist-0.5.1/include/config_path.h.in
+--- bist-0.5.1.orig/include/config_path.h.in	2009-04-04 12:04:42.000000000 +0200
++++ bist-0.5.1/include/config_path.h.in	2009-09-23 23:29:35.000000000 +0200
+@@ -12,6 +12,6 @@
+ #define VERSION             "@VERSION@"
+ 
+ #define PLUGIN_PATH_HOME    "/.bist/plugin/"
+-#define PLUGIN_PATH_SHARED  "@LIB_DIR_CONFIG_PATH@/@ELF@-@VERSION@/plugin/"
++#define PLUGIN_PATH_SHARED  "@libdir@/@ELF@-@VERSION@/plugin/"
+ 
+ #define ELF_ABS_PATH          "@prefix@/bin/@ELF@"
diff --git a/sci-chemistry/bist/metadata.xml b/sci-chemistry/bist/metadata.xml
new file mode 100644
index 000000000..d6a2d376f
--- /dev/null
+++ b/sci-chemistry/bist/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer><email>maintainer-wanted@gentoo.org</email></maintainer>
+<longdescription>
+Bist stands for bidimensional structures (in italian it sounds like "beast" in english ) and is a chemical drawing tool. It is focused on organic chemistry but it may be useful also for chemists or teacher as well.
+Bist support many of the formalism used to describe molecoles structures like single bond, double bond, stereospecific bond, charges, resonance arrows, lone pairs etc...
+It can export both postscript and png formats.
+This version is now integrated with openbabel API so virtually all the formats this library can accept should be a valid input for bist too.
+Currently portability is not my goal so only GNU/Linux platform is supported. However any effort in this direction is appreciated so feel free to ask me about any porting question. Please remember that bist is actually in a beta stage of development so i strongly suggest you to not using it except for testing or hacking purpose. Bist is free software released under GNU GPL version 3
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/dssp2pdb/ChangeLog b/sci-chemistry/dssp2pdb/ChangeLog
index 5447ee59c..372996faa 100644
--- a/sci-chemistry/dssp2pdb/ChangeLog
+++ b/sci-chemistry/dssp2pdb/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Jul 2010; Justin Lecher <jlec@gentoo.org> dssp2pdb-0.03.ebuild:
+  Keyworded for *-linux prefix
+
 *dssp2pdb-0.03 (15 Jan 2010)
 
   15 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/dssp2pdb/Manifest b/sci-chemistry/dssp2pdb/Manifest
deleted file mode 100644
index cafafcdb4..000000000
--- a/sci-chemistry/dssp2pdb/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST dssp2pdb-0.03.tar 10240 RMD160 eab385645aec1016045ea536ff4805423b90687e SHA1 e950f5c2e2cac69e58af7d6cf41b025b4faf61bd SHA256 4ec79fdd7223a6125d5ab221438ca9d9747e293c37bcfc5b67981e678280ec61
-EBUILD dssp2pdb-0.03.ebuild 447 RMD160 fe1dd4311c6d7debe5d2037824aeba1eb1d8e7d2 SHA1 4cf28851ac38eb83af0c63f8526bd91859074ede SHA256 e34f83d7fe93e2d5831af04abf1d38990fd67c159b6e110b6bc1a2dc6a8bbe62
-MISC ChangeLog 268 RMD160 afc894ff81f91a1411c68d79c6e57ba7f75a50a8 SHA1 ee02dfcbc82cd317d5908e184ed7d42081305bbe SHA256 d429a365a74a50dc80ffa34bb8fd7c99b11ee28b43c1efd76e14e1dd1bb2d4c6
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7726449b3..f8aa6364f 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,33 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-4.5.1 (02 Sep 2010)
+
+  02 Sep 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-4.5_beta3.ebuild, +gromacs-4.5.1.ebuild:
+  version bump
+
+*gromacs-4.5_beta3 (11 Aug 2010)
+
+  11 Aug 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.9999.ebuild,
+  -gromacs-4.5_beta2.ebuild, +gromacs-4.5_beta3.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Add epatch_user
+
+*gromacs-4.5_beta2 (02 Aug 2010)
+
+  02 Aug 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-4.5_beta1.ebuild, +gromacs-4.5_beta2.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Version bump + new manual
+
+*gromacs-4.5.9999 (31 Jul 2010)
+*gromacs-4.5_beta1 (31 Jul 2010)
+
+  31 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.5_beta1.ebuild, +gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Version bump
+
   24 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   ffamber officialy shipped with gromacs from now on
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 8e5c23b01..ae8bee182 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,15 +3,19 @@ Hash: SHA1
 
 DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
+DIST gromacs-4.5.1.tar.gz 10300446 RMD160 b28973526859359c84ba5d4fe2a5018b158f932b SHA1 4352565278e39fb619208950780d8cb0b470a200 SHA256 c565e469d2ee495fe67b227179af1740a49ef78321978417cd818b6d4bdae233
 DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
-EBUILD gromacs-4.0.9999.ebuild 9240 RMD160 8d6f31dcde6297f7d06f410b5d9ee5c321cf3824 SHA1 7ecc1f13330ef172b23a0b36f9047fa38451fc3d SHA256 ed0c4fe69bfa803cb73be3d14a73c6affaa8e175e5b58405dc8f9fa706546eee
-EBUILD gromacs-9999.ebuild 7119 RMD160 06ffdd882fce711e9c3d170d5880993ec62d643f SHA1 83748e3e65eae35a9d9a763444bce097a9b4e9f1 SHA256 6d75d252800b4ab6aea4e2c82b52378a17a66f898d9222b86aa3d687966d67d0
-MISC ChangeLog 4834 RMD160 f8297200737f6b7dd99104d683d671333e52bf4e SHA1 09c76f712a052115f22a38769ac745b775662bce SHA256 de84d0da3b17eae88b6d527ea05b59f686029ff36004528fc9dbfc0ef2923913
+DIST manual-4.5-beta2.pdf 2317594 RMD160 3936ca2ec810ae2e74c57f19a993fda8152bedcd SHA1 d995be380e6453056330c5f5bfed95fbf4cb554f SHA256 fdeb0cd0be5244cdfddc17a643199ddf043e0a9d37811998300df86541483c61
+EBUILD gromacs-4.0.9999.ebuild 9253 RMD160 b1d0cc7e6e51a718fd01d72947b3e2e22059a0d2 SHA1 888c75e12238560e741bc9e2a4198cfee2ab3701 SHA256 3da8f43fd21df44375cf03b1fe46c594aa51c2f72307c4a9eec9747330d54a8d
+EBUILD gromacs-4.5.1.ebuild 7428 RMD160 a2205a735fa14d34a98bc88ee2dbf20153966c2e SHA1 8a927e5217eaf9c57c25bcefe8a315600c4d261e SHA256 9264000e86e930d26e38ab53d460754ff461965de1817c3b2c6c70d6414a9124
+EBUILD gromacs-4.5.9999.ebuild 7467 RMD160 84ca2c188addeb9823b6c5da01138c14b85f4277 SHA1 6f713d3d098b6b49bb3769f3c5bb835d1c4b8bb9 SHA256 aedbbe05bf932418e237c1ac5f9a77c03559eafdf60f0cecc082ce6834f07878
+EBUILD gromacs-9999.ebuild 7851 RMD160 a92cfefd23992e1e49e72b0d7e850ecc7715bcd4 SHA1 7d9bea15ca33e677e5c461dbb3627112522d7e5f SHA256 c0a561f207198a58a8f6d507ba943a10af40b4a6f01c5f230a86d05db528c582
+MISC ChangeLog 5658 RMD160 b18635eae8b4777ab5a73f443200500508b1e72c SHA1 e0b8a4d90a4aee0a0956817f9df077766a5b8601 SHA256 94464b430f371acb24ca4efc7776d5a7dc745af98a6260cec74e1542a40e123c
 MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd4a32d896b7a2586667bc684d46f9daf8693 SHA256 177885ec674e8630a9c9451a0e0a35fc83615b39b387a67002e27f1b0d6b19b2
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAkxMnFQACgkQy0OE/ans1/l7dwCfZFEwQj4Re6jIV5haPvomLdtO
-PWkAn3KMtVvQyrfIJBM9tuzTnM7FIOAI
-=lqsP
+iEYEARECAAYFAkyAClwACgkQy0OE/ans1/n//wCeMK0y3ywpEF+cOLLHnka7Yobr
+4REAn2C1rQTSt/9IBgSzgfxV0Vu19uFS
+=5ItK
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
index 86bf31062..3c02f87a5 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
@@ -69,6 +69,7 @@ src_prepare() {
 	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
 		|| die "Failed to fixup demo script."
 
+	epatch_user
 	eautoreconf
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" single"
diff --git a/sci-chemistry/gromacs/gromacs-4.5.1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
new file mode 100644
index 000000000..f210a8dc0
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
@@ -0,0 +1,259 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+MANUAL_PV="4.5-beta2"
+
+inherit autotools bash-completion eutils fortran multilib toolchain-funcs
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +threads +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+QA_EXECSTACK="usr/lib/libgmx.so.*
+	usr/lib/libgmx_d.so.*"
+
+use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
+
+pkg_setup() {
+	if use fkernels; then
+		FORTRAN="g77 gfortran ifc"
+		fortran_pkg_setup
+	else
+		FORTRANC=""
+	fi
+}
+
+src_prepare() {
+
+	( use single-precision || use double-precision ) || \
+		die "Nothing to compile, enable single-precision and/or double-precision"
+
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	if use static; then
+		use X && die "You cannot compile a static version with X support, disable X or static"
+		use xml && die "You cannot compile a static version with xml support
+		(see bug #306479), disable xml or static"
+	fi
+	epatch_user
+	eautoreconf
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" single"
+	use double-precision && GMX_DIRS+=" double"
+	for x in ${GMX_DIRS}; do
+		mkdir "${S}-${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
+		use mpi || continue
+		mkdir "${S}-${x}_mpi" || die
+	done
+}
+
+src_configure() {
+	local myconf
+	local myconfsingle
+	local myconfdouble
+	local suffixdouble
+
+	#leave all assembly options enabled mdrun is smart enough to deside itself
+	#there so no gentoo on bluegene!
+	myconf="${myconf} --disable-bluegene"
+
+	#from gromacs configure
+	if ! use fftw; then
+		ewarn "WARNING: The built-in FFTPACK routines are slow."
+		ewarn "Are you sure you don\'t want to use FFTW?"
+		ewarn "It is free and much faster..."
+	fi
+
+	if [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		myconf="${myconf} --enable-fortran"
+	else
+		myconf="${myconf} --disable-fortran"
+	fi
+
+	# if we need external blas
+	if use blas; then
+		export LIBS="${LIBS} -lblas"
+		myconf="${myconf} $(use_with blas external-blas)"
+	fi
+
+	# if we need external lapack
+	if use lapack; then
+		export LIBS="${LIBS} -llapack"
+		myconf="${myconf} $(use_with lapack external-lapack)"
+	fi
+
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		#gmx build static libs by default
+		myconf="${myconf} --disable-shared $(use_enable static all-static)"
+	else
+		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
+	fi
+
+	myconf="--datadir="${EPREFIX}"/usr/share \
+			--bindir="${EPREFIX}"/usr/bin \
+			--libdir="${EPREFIX}"/usr/$(get_libdir) \
+			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
+			$(use_with gsl) \
+			$(use_with X x) \
+			$(use_with xml) \
+			$(use_enable threads) \
+			${myconf}"
+
+	#if we build single and double - double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffixdouble="_d"
+	else
+		suffixdouble=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
+	myconfsingle="${myconf} --enable-float --program-suffix=''"
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		cd "${S}-${x}"
+		local p=myconf${x}
+		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		einfo "Compiling for ${x} precision"
+		emake || die "emake for ${x} precision failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake mdrun || die "emake mdrun for ${x} precision failed"
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${S}-${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -f "${ED}"/usr/bin/completion.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL README
+	if use doc; then
+		dodoc "${DISTDIR}/manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+pkg_postinst() {
+	env-update && source /etc/profile
+	elog
+	elog "Please read and cite:"
+	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	elog "http://dx.doi.org/10.1021/ct700301q"
+	elog
+	bash-completion_pkg_postinst
+	elog
+	elog $(g_luck)
+	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
+	elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
new file mode 100644
index 000000000..fac433946
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -0,0 +1,261 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+MANUAL_PV="4.5-beta2"
+
+EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+EGIT_BRANCH="release-4-5-patches"
+
+inherit autotools bash-completion eutils fortran git multilib toolchain-funcs
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +threads +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+QA_EXECSTACK="usr/lib/libgmx.so.*
+	usr/lib/libgmx_d.so.*"
+
+use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
+
+pkg_setup() {
+	if use fkernels; then
+		FORTRAN="g77 gfortran ifc"
+		fortran_pkg_setup
+	else
+		FORTRANC=""
+	fi
+}
+
+src_prepare() {
+
+	( use single-precision || use double-precision ) || \
+		die "Nothing to compile, enable single-precision and/or double-precision"
+
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	if use static; then
+		use X && die "You cannot compile a static version with X support, disable X or static"
+		use xml && die "You cannot compile a static version with xml support
+		(see bug #306479), disable xml or static"
+	fi
+	epatch_user
+	eautoreconf
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" single"
+	use double-precision && GMX_DIRS+=" double"
+	for x in ${GMX_DIRS}; do
+		mkdir "${S}-${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
+		use mpi || continue
+		mkdir "${S}-${x}_mpi" || die
+	done
+}
+
+src_configure() {
+	local myconf
+	local myconfsingle
+	local myconfdouble
+	local suffixdouble
+
+	#leave all assembly options enabled mdrun is smart enough to deside itself
+	#there so no gentoo on bluegene!
+	myconf="${myconf} --disable-bluegene"
+
+	#from gromacs configure
+	if ! use fftw; then
+		ewarn "WARNING: The built-in FFTPACK routines are slow."
+		ewarn "Are you sure you don\'t want to use FFTW?"
+		ewarn "It is free and much faster..."
+	fi
+
+	if [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 4.1 anyway
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+		myconf="${myconf} --enable-fortran"
+	else
+		myconf="${myconf} --disable-fortran"
+	fi
+
+	# if we need external blas
+	if use blas; then
+		export LIBS="${LIBS} -lblas"
+		myconf="${myconf} $(use_with blas external-blas)"
+	fi
+
+	# if we need external lapack
+	if use lapack; then
+		export LIBS="${LIBS} -llapack"
+		myconf="${myconf} $(use_with lapack external-lapack)"
+	fi
+
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		#gmx build static libs by default
+		myconf="${myconf} --disable-shared $(use_enable static all-static)"
+	else
+		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
+	fi
+
+	myconf="--datadir="${EPREFIX}"/usr/share \
+			--bindir="${EPREFIX}"/usr/bin \
+			--libdir="${EPREFIX}"/usr/$(get_libdir) \
+			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
+			$(use_with gsl) \
+			$(use_with X x) \
+			$(use_with xml) \
+			$(use_enable threads) \
+			${myconf}"
+
+	#if we build single and double - double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffixdouble="_d"
+	else
+		suffixdouble=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
+	myconfsingle="${myconf} --enable-float --program-suffix=''"
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		cd "${S}-${x}"
+		local p=myconf${x}
+		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		einfo "Compiling for ${x} precision"
+		emake || die "emake for ${x} precision failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake mdrun || die "emake mdrun for ${x} precision failed"
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${S}-${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		cd "${S}-${x}"
+		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -f "${ED}"/usr/bin/completion.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL README
+	if use doc; then
+		dodoc "${DISTDIR}/manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+pkg_postinst() {
+	env-update && source /etc/profile
+	elog
+	elog "Please read and cite:"
+	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	elog "http://dx.doi.org/10.1021/ct700301q"
+	elog
+	bash-completion_pkg_postinst
+	elog
+	elog $(g_luck)
+	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
+	elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 0dcac3d92..07aae9e98 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -14,8 +14,7 @@ inherit autotools bash-completion eutils fortran git multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -58,12 +57,19 @@ src_prepare() {
 	( use single-precision || use double-precision ) || \
 		die "Nothing to compile, enable single-precision and/or double-precision"
 
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
 	if use static; then
 		use X && die "You cannot compile a static version with X support, disable X or static"
 		use xml && die "You cannot compile a static version with xml support
 		(see bug #306479), disable xml or static"
 	fi
-
+	epatch_user
 	eautoreconf
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" single"
@@ -189,6 +195,11 @@ src_compile() {
 		cd "${S}-${x}"
 		einfo "Compiling for ${x} precision"
 		emake || die "emake for ${x} precision failed"
+		if use doc && [ -z "$OPTDIR" ]; then
+			cd src/contrib
+			emake options || die "emake options failed"
+			OPTDIR="${PWD}"
+		fi
 		use mpi || continue
 		cd "${S}-${x}_mpi"
 		emake mdrun || die "emake mdrun for ${x} precision failed"
@@ -230,10 +241,16 @@ src_install() {
 		|| die "Failed to fixup demo script."
 
 	cd "${S}"
-	dodoc AUTHORS INSTALL README
+	dodoc AUTHORS INSTALL* README*
 	if use doc; then
-		dodoc "${DISTDIR}/manual-4.0.pdf"
 		dohtml -r "${ED}usr/share/gromacs/html/"
+		insinto /usr/share/gromacs
+		doins "admin/programs.txt"
+		ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
+		doins "${T}"/programs.list
+		cd "${OPTDIR}" || die "cd "${OPTDIR}" failed"
+		../../libtool --mode=install cp options "${ED}"/usr/bin/g_options \
+			|| die "install of g_options failed"
 	fi
 	rm -rf "${ED}usr/share/gromacs/html/"
 }
@@ -250,4 +267,7 @@ pkg_postinst() {
 	elog $(g_luck)
 	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
 	elog
+	if use doc; then
+		elog "Live Gromacs manual is available from app-doc/gromacs-manual"
+	fi
 }
diff --git a/sci-chemistry/mgltools/ChangeLog b/sci-chemistry/mgltools/ChangeLog
index b94dfa41f..3816d10ba 100644
--- a/sci-chemistry/mgltools/ChangeLog
+++ b/sci-chemistry/mgltools/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/mgltools
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Aug 2010; Justin Lecher <jlec@gentoo.org> mgltools-1.5.4.ebuild:
+  Fixed SRC_URI
+
   19 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   mgltools-1.5.4.ebuild:
   need tk USE for imaging
diff --git a/sci-chemistry/mgltools/Manifest b/sci-chemistry/mgltools/Manifest
index 6fb3c143c..d23c15413 100644
--- a/sci-chemistry/mgltools/Manifest
+++ b/sci-chemistry/mgltools/Manifest
@@ -1,4 +1,14 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST mgltools_source_1.5.4.tar.gz 21591865 RMD160 faa158477c4e9156ee5fd23b89251e5bedbd689d SHA1 3b3056a75cd944a4aa46771e09916a4e85052b88 SHA256 d0c614e167512bd19127c741cb2d9860443c097f7ccf0bbe244c0b155e59a9c2
-EBUILD mgltools-1.5.4.ebuild 1070 RMD160 9f71733be0d49be5247778b956d136cfe3eaff73 SHA1 954c8f667b4a9d32fb97db95a241d3ae1a2fca81 SHA256 c7779b3a7db2a343736c0ec51c7275560934e49dc7c8684e5570d4b1cc984fd2
-MISC ChangeLog 380 RMD160 c7912b316aa056d9c3ef732b2c94391c55af791b SHA1 b90e7d041a5829efacdb7ae6a07468bcac612012 SHA256 543a5a53dc925fc084b08158a41d514fe34daabc31467e58b4ce28975a1d7b08
+EBUILD mgltools-1.5.4.ebuild 1208 RMD160 4fbbfe07816b55b301c1121f5800ee1a03e95480 SHA1 6fd0902f8f321dbe7b832b4d12387a3c4c0916f8 SHA256 ba88ee81ed57aaf9033665f6f9670a4d6bc7a8655cb35490e478cff42abf0378
+MISC ChangeLog 467 RMD160 16cd2904439e08b4184b7203c81b419e7e29148e SHA1 f3b6e7c86c213574e574f9c1c959e5edeccee489 SHA256 1eec2123df8f76340db18a927b6faa385a11eb7675002b33e936a3184594400a
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkx7+cMACgkQgAnW8HDreRZ5vwCdHl28txiWlkozGbyQreBL9tY/
+VLMAoMDt+eKnMLkZdUaTpxpB67MhoEy+
+=LpO+
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/mgltools/mgltools-1.5.4.ebuild b/sci-chemistry/mgltools/mgltools-1.5.4.ebuild
index b61f846c1..0024777b3 100644
--- a/sci-chemistry/mgltools/mgltools-1.5.4.ebuild
+++ b/sci-chemistry/mgltools/mgltools-1.5.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -11,7 +11,10 @@ PLUGINS="autodocktools bhtree cmolkit dejavu geomutils gle mglutil molkit networ
 DESCRIPTION="Software to visualization and analysis of molecular structures"
 HOMEPAGE="http://mgltools.scripps.edu/"
 #SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz"
-SRC_URI="http://dev.gentooexperimental.org/~jlec/distfiles/mgltools_source_${PV}.tar.gz"
+SRC_URI="
+	http://dev.gentooexperimental.org/~jlec/distfiles/mgltools_source_${PV}.tar.gz
+	http://91.191.147.225/~jlec/distfiles/mgltools_source_${PV}.tar.gz
+	http://dev.gentoo.org/~jlec/distfiles/mgltools_source_${PV}.tar.gz"
 
 LICENSE="MGLTOOLS"
 SLOT="0"
diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog
index d31d54cae..277e5c70a 100644
--- a/sci-chemistry/nmrpipe/ChangeLog
+++ b/sci-chemistry/nmrpipe/ChangeLog
@@ -2,6 +2,37 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*nmrpipe-5.4.2010.250.17.50-r1 (13 Sep 2010)
+
+  13 Sep 2010; Justin Lecher <jlec@gentoo.org>
+  -nmrpipe-5.4.2010.250.17.50.ebuild, +nmrpipe-5.4.2010.250.17.50-r1.ebuild:
+  Some scripts are in the wrong place
+
+*nmrpipe-5.4.2010.250.17.50 (10 Sep 2010)
+
+  10 Sep 2010; Justin Lecher <jlec@gentoo.org>
+  -files/5.4.2010.221.16.40-lib.patch, -nmrpipe-5.4.2010.221.16.40.ebuild,
+  +files/5.4.2010.250.17.50-lib.patch, +nmrpipe-5.4.2010.250.17.50.ebuild:
+  Version Bump
+
+*nmrpipe-5.4.2010.221.16.40 (04 Sep 2010)
+
+  04 Sep 2010; Justin Lecher <jlec@gentoo.org>
+  -files/5.0.2010.190.16.49-lib.patch, -nmrpipe-5.0.2010.190.16.49.ebuild,
+  +files/5.4.2010.221.16.40-lib.patch, +nmrpipe-5.4.2010.221.16.40.ebuild:
+  Version Bump
+
+  04 Sep 2010; Justin Lecher <jlec@gentoo.org>
+  -files/5.0.2010.176.15.02-lib.patch, +files/5.0.2010.190.16.49-lib.patch,
+  files/env-nmrpipe-new, metadata.xml:
+  Fixed patch
+
+*nmrpipe-5.0.2010.190.16.49 (12 Jul 2010)
+
+  12 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  -nmrpipe-5.0.2010.176.15.02.ebuild, +nmrpipe-5.0.2010.190.16.49.ebuild:
+  Version BUmp
+
 *nmrpipe-5.0.2010.176.15.02 (28 Jun 2010)
 
   28 Jun 2010; Justin Lecher <jlec@gentoo.org>
diff --git a/sci-chemistry/nmrpipe/Manifest b/sci-chemistry/nmrpipe/Manifest
index 914a431e3..e4540b32c 100644
--- a/sci-chemistry/nmrpipe/Manifest
+++ b/sci-chemistry/nmrpipe/Manifest
@@ -1,22 +1,22 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX 5.0.2010.176.15.02-lib.patch 997 RMD160 09e9dbed8e1e2e4964bdf381a15b556d0ea9f3bb SHA1 881a3554f21fb23973e0b8a31b59cff495f5edbb SHA256 011aea3e38ef3eb650be7b5d6274913bbb4f5367838f4bb86f97556ad247b57f
+AUX 5.4.2010.250.17.50-lib.patch 997 RMD160 09e9dbed8e1e2e4964bdf381a15b556d0ea9f3bb SHA1 881a3554f21fb23973e0b8a31b59cff495f5edbb SHA256 011aea3e38ef3eb650be7b5d6274913bbb4f5367838f4bb86f97556ad247b57f
 AUX env-nmrpipe-new 597 RMD160 6948506b9106af33ecd1d7aefce5bb1b9a1f3e1d SHA1 df74a34eab52ed3b4007cf2a33a8b2ccacf50938 SHA256 9cdf0ebfb771c04ff8e38b94ad29cd18e349f76ee6604e07d4b7567621c6be46
-DIST NMRPipeX.tZ 123739972 RMD160 5005df92b9a0c1b07ca0fcdad88f0e4cfa189702 SHA1 546f989dd79ff971e2c4c9fa4cd043825c9708a5 SHA256 99cd8fe1b53724c536651ddda66a2f00720b9fea4e08c48bc5d24128ee860c05
+DIST NMRPipeX.tZ 117311973 RMD160 b169778c5aed623f9216ba7e1f81eb433043c91b SHA1 74644f328e775bd26281e46a6841e8479d76178d SHA256 a8d852da6debe608d702468b1b67a810e505b2e67cf7a793ac4ac9c802420477
 DIST acme.tar.Z 11681951 RMD160 fdcf35fab1b63ddda55288b1b2ed0f82c8299bef SHA1 5093f92a4d7e4173bc056b6b1922a6da8e6bbf0c SHA256 5713452a1461e636f0de48e5ce3476fc0ae60b3f78a0288744f45e455f3445d9
-DIST binval.com 3654 RMD160 60f7b8e13ef48dc22822beb2fd107beac25db300 SHA1 fdd8d2a2b9b6f57ad9d2ebac84b15e428478d261 SHA256 0ab49d267a3b947f31024e3eae281101b7002a64a801b36f1671bd79e8ef5a9d
-DIST dyn.tZ 137459867 RMD160 e2656774981984c0a08d826ae1a8f15593612bb5 SHA1 3d0ec4b2eee9c9a167fc65cd16427db032f4340a SHA256 b8502141482b522e3ed5c92e2cf3e3572630fd876751b6e3dffe743039704c0f
+DIST binval.com 3807 RMD160 263195035981216833da16afa4dcea568ba06303 SHA1 d90062ee85c77157e421fd684e32d59a3118c6f9 SHA256 349a6b3b3bac0f82d645a44ee6073b95b9ad9573c548367a3528d32cf0c5694e
+DIST dyn.tZ 137796769 RMD160 9d492341eb6e27cf8864e13751bc2fa3defebd98 SHA1 4b14503e147342a9ce8090e65a57e561a9e8539a SHA256 de369b4eefd9f8a00a8e75ab9eea3c369b40eabbef3833fb5460e4d0a3dca52a
 DIST install.com 36561 RMD160 7a7cae57e470f5637106a895d1a2ace486bb33a9 SHA1 2c296e0aadb14735253891f2cf5a451b98638581 SHA256 af5977a3c165d5552f5fad43a9cd9e303adc72b85011e284e28cc2cdd04bd160
-DIST talos.tZ 36993914 RMD160 4823f0d0357cd93ac326b3912adab82a76a16f90 SHA1 9b3966bd619275ed97d17d9bbc862246aae01641 SHA256 bb130df152e445d7713809e724018c92a46bf1950cfd10c68072af515bbdbebf
+DIST talos.tZ 37070217 RMD160 4a33a947fbcfa21b9f9c47ed51b0737e7c14ad01 SHA1 ae1865e1b56cb73fd4821b000af3773920d9b5d6 SHA256 3a8a5e18ee08bb99134fa2259825c606cdd9ff459c12772d8d4d6cbbcc44feda
 DIST valpha_all.tar 699166720 RMD160 75ebf0a84524212cd25d62ba33f6a5edca05dd20 SHA1 a8be07ac97a826e44ed240946217a50fd3e8ba1e SHA256 3f2ff243e1d0e2508f20ec1ab6108eb986bcc1bc4c9ec79b4ff8ce6584805b0a
-EBUILD nmrpipe-5.0.2010.176.15.02.ebuild 4719 RMD160 26662a5dd8124fdd97390d66db513e6f486d241c SHA1 153e8996bd65294b7ea7c94b410eec38600ce093 SHA256 c969db73a557ec5343767834f061582cab94e9e7ab32dfcc849750e43ef410dd
-MISC ChangeLog 6106 RMD160 6f246c7ebb3fc5c8f0ddadf4dca030f294f00618 SHA1 ff5b749c9735a199fddcb38d93295a35de98f8b9 SHA256 b45799c353cfded59ad1371e1629d3345152c75a196be79c4ea312d0f91bc043
-MISC metadata.xml 263 RMD160 6a7463bafc4f1e7df75d12fc57c693ad582d58fa SHA1 e38c1eecffc0f52395d69359a9e3dd1114bcf550 SHA256 31cd25872ef5bc46e50dd04eb523bd093d07797f39b072177df59690a4fc07a3
+EBUILD nmrpipe-5.4.2010.250.17.50-r1.ebuild 4785 RMD160 15247937be92830e8cb1df188a1c9d868eb9d6af SHA1 a947c8302dddaded500709e5d03a83fd8a40d304 SHA256 ea59dabd1479e8252247f873cdbadc815c9412adb27887bce949a58c41681895
+MISC ChangeLog 7184 RMD160 a46414ded0a64b7f7302ab2f7871ab0c6fc4807b SHA1 50b24e22e94f2cfe276aff3e478b80495b1651df SHA256 c396b1dc45320013f7850e8820f1ee93b70195c22f245e68a9d6c5e8d7d87b0c
+MISC metadata.xml 249 RMD160 789eca813b850a4619f671586826b824098ec47b SHA1 554c0cc8335f6d6410f6f504bf032a7c6de36c89 SHA256 c3f71fe107b700acc3c21923ed360604cfd47ac3181d9ed7605a0472250a8064
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAkwoXDYACgkQgAnW8HDreRbKYwCfYntP/MCjQWbLph/IlvmmCPB6
-m/sAoKe72JwsoYwO1ATMRe2/kpk0ylrv
-=Ot0w
+iEYEARECAAYFAkyN/JIACgkQgAnW8HDreRaxvACgqFHdaAwBJRshfl2nRAP//9Cp
+rPoAn3Izb6zm7bDQLayqpzf/30BRGol2
+=hnNS
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/nmrpipe/files/5.0.2010.176.15.02-lib.patch b/sci-chemistry/nmrpipe/files/5.4.2010.250.17.50-lib.patch
index 91abd611d..91abd611d 100644
--- a/sci-chemistry/nmrpipe/files/5.0.2010.176.15.02-lib.patch
+++ b/sci-chemistry/nmrpipe/files/5.4.2010.250.17.50-lib.patch
diff --git a/sci-chemistry/nmrpipe/metadata.xml b/sci-chemistry/nmrpipe/metadata.xml
index 27e626a3f..8487320ca 100644
--- a/sci-chemistry/nmrpipe/metadata.xml
+++ b/sci-chemistry/nmrpipe/metadata.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>maintainer-wanted</herd>
+	<herd>sci</herd>
 	<maintainer>
 		<email>jlec@gentoo.org</email>
 		<name>Justin Lecher</name>
diff --git a/sci-chemistry/nmrpipe/nmrpipe-5.0.2010.176.15.02.ebuild b/sci-chemistry/nmrpipe/nmrpipe-5.4.2010.250.17.50-r1.ebuild
index 9a382d6a5..137a90d75 100644
--- a/sci-chemistry/nmrpipe/nmrpipe-5.0.2010.176.15.02.ebuild
+++ b/sci-chemistry/nmrpipe/nmrpipe-5.4.2010.250.17.50-r1.ebuild
@@ -139,6 +139,9 @@ src_install() {
 		> env-${PN}-new
 	newenvd env-${PN}-new 40${PN} || die "Failed to install env file."
 
+	# Some scripts are on the wrong place
+	cp -vf nmrtxt/*.com com/
+
 	insinto ${NMRBASE}
 	doins -r * || die "Failed to install application."
 
diff --git a/sci-chemistry/simpson/ChangeLog b/sci-chemistry/simpson/ChangeLog
index cd9e2567d..419cb6887 100644
--- a/sci-chemistry/simpson/ChangeLog
+++ b/sci-chemistry/simpson/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*simpson-3.0.1 (11 Aug 2010)
+
+  11 Aug 2010; Justin Lecher <jlec@gentoo.org> -files/2.0.0-gentoo.patch,
+  +simpson-3.0.1.ebuild, +files/3.0.1-gentoo.patch, +files/3.0.1-type.patch,
+  -simpson-2.0.0.ebuild:
+  Version Bump, removed old
+
 *simpson-2.0.0 (11 May 2010)
 
   11 May 2010; Justin Lecher <jlec@gentoo.org> +files/2.0.0-gentoo.patch,
diff --git a/sci-chemistry/simpson/Manifest b/sci-chemistry/simpson/Manifest
index dae36803c..54e47234e 100644
--- a/sci-chemistry/simpson/Manifest
+++ b/sci-chemistry/simpson/Manifest
@@ -1,15 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX 2.0.0-gentoo.patch 20488 RMD160 e35672edc19cad1d51842c03dedbed25bfda3a15 SHA1 0ca15aa3af0f4aec6a19e02bd0932b5e8d5e4146 SHA256 15253e209c6772986f93259546341ec768c7602693fc49224008a859bdf4dc2f
-DIST simpson-2.0.0.tar.gz 1152963 RMD160 c7dd798880b8e77544d015a31ddf1d49f19ace6c SHA1 d81836ff80f10cfe1631cc285a63b95092fddda6 SHA256 8a2af8f51e85dcd3eeb958624edfae10608fd4973b27613ffad69beab6abbde7
-EBUILD simpson-2.0.0.ebuild 977 RMD160 fcb53f922a773d4ac337fd396eea394004e792c6 SHA1 383fdd63ec1558e27cf6f60e1ecd2675bfc6ec20 SHA256 21b30f17e3957d11db24bd756935cc5500039ac702ac42e364de5e1a717916f9
-MISC ChangeLog 282 RMD160 da4ff8b8d9d90674382d3d9a3e38c735935a8ed9 SHA1 e41dac2c6c4de9ff56d580b6a5d73c3b1af93340 SHA256 42ffb9faeab125d13249811343b99b05fa52505b2b058802fea681f8ea8c9cc5
+AUX 3.0.1-gentoo.patch 716 RMD160 9c90f3c9deee8a0ff1f583a34fcc1bd3d55fdbbf SHA1 472288c2c041d66aed13212958a765325d5e735f SHA256 cc85cdd872b7f60288037ada586f8373b0b2f6c7dfa9af122d0143c489dbb4df
+AUX 3.0.1-type.patch 2600 RMD160 97b061cfa1a1fd5b3ebc9c7d597135122b552b2d SHA1 6c79eb9e92d40524e326263e218f5d90580753df SHA256 c079575af39c32cd58223be2356b9bed56ad5eb8a75900d06571ee0d2beddc81
+DIST simpson-source-3.0.1.tgz 383619 RMD160 8d596831d5f413cd5c18a984b965e8171a5b5da7 SHA1 7d9f219da1c146642e80350d8ea54570a462118a SHA256 77c5946b4a02b4e743b11dae4514935a2a66f4ed12e700845ccb49ee4c56ed17
+EBUILD simpson-3.0.1.ebuild 925 RMD160 4d98d3513874ea1b978468b6e42102854dbc9a7b SHA1 ff9c6f9174540c466af15a4dd5157f6d5ad9336e SHA256 1bb187ce58c62c396d7a1c85dd5d70d171e5be1422cdfcf22af5a97e1d93712a
+MISC ChangeLog 517 RMD160 d2c39cd8046975fcaf4167659d243df463a5be09 SHA1 f53468c963b83ecb04fd6fa86e1854971e86758a SHA256 0e1a8417d6604617b5fd703b01fec2781c52094aebc730d90b7263c3457b2c1a
 MISC metadata.xml 1238 RMD160 c82938e77f387291d6a1c3bf9b0d802f2878dd12 SHA1 b5738f14922c69e78cfb867acdc65eeea25977bf SHA256 2c13f98be5fa8bdaf21ac86bcd00bbeb8944df5615de0cfce35ae4c00ef4b4d5
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkvpMmUACgkQgAnW8HDreRZjDwCgjgSaSiGgeABI2gN1foqCcy6J
-q+4Ani3Q6KcITpgp9TT+c1B7yfpogKQF
-=y6+x
+iEYEARECAAYFAkxjCPoACgkQgAnW8HDreRbejQCcCMTqtWKthtiNMJSFQXF0e2p9
+8GwAoISRI98e2unpNdlapfEkhFPA4sOu
+=+Sl7
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/simpson/files/2.0.0-gentoo.patch b/sci-chemistry/simpson/files/2.0.0-gentoo.patch
deleted file mode 100644
index c61fe4342..000000000
--- a/sci-chemistry/simpson/files/2.0.0-gentoo.patch
+++ /dev/null
@@ -1,761 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index b4cee2c..ee97cc6 100755
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,6 +1,6 @@
- EXTRA_DIST = autogen.sh div.m4
- 
--SUBDIRS = f2c $(SUBDIR_ADD) simpson cryst
-+SUBDIRS = $(SUBDIR_ADD) simpson cryst
- 
- bindist: bindistdir
- 	-chmod -R a+r $(BINDISTDIR)
-diff --git a/config.h.in b/config.h.in
-index b1e9a27..d078f0b 100644
---- a/config.h.in
-+++ b/config.h.in
-@@ -24,6 +24,12 @@
- /* Disable networking */
- #undef DISABLE_NETWORK
- 
-+/* #undef ENABLE_MINUIT */
-+#undef ENABLE_MINUIT
-+
-+/* #undef ENABLE_SIMMOL */
-+#undef ENABLE_SIMMOL
-+
- /* Compile with Tk support */
- #undef ENABLE_TK
- 
-@@ -33,6 +39,12 @@
- /* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */
- #undef HAVE_DOPRNT
- 
-+/* #undef HAVE_F_EXIT */
-+#undef HAVE_F_EXIT
-+
-+/* #undef HAVE_GETLINE */
-+#undef HAVE_GETLINE
-+
- /* Define to 1 if you have the <inttypes.h> header file. */
- #undef HAVE_INTTYPES_H
- 
-@@ -66,6 +78,9 @@
- /* Define to 1 if you have the <memory.h> header file. */
- #undef HAVE_MEMORY_H
- 
-+/* #undef HAVE_POW_DI */
-+#undef HAVE_POW_DI
-+
- /* Define to 1 if you have the <stdint.h> header file. */
- #undef HAVE_STDINT_H
- 
-@@ -105,9 +120,15 @@
- /* Define to the address where bug reports for this package should be sent. */
- #undef PACKAGE_BUGREPORT
- 
-+/* #undef PACKAGE_DATA_DIR */
-+#undef PACKAGE_DATA_DIR
-+
- /* Define to the full name of this package. */
- #undef PACKAGE_NAME
- 
-+/* #undef PACKAGE_SOURCE_DIR */
-+#undef PACKAGE_SOURCE_DIR
-+
- /* Define to the full name and version of this package. */
- #undef PACKAGE_STRING
- 
-@@ -120,15 +141,27 @@
- /* Make the code multithreaded */
- #undef PARALLEL
- 
-+/* #undef PIVOT_PHASE */
-+#undef PIVOT_PHASE
-+
- /* Define as the return type of signal handlers (`int' or `void'). */
- #undef RETSIGTYPE
- 
--/* Enable serverlogging */
-+/* #undef REVERSEBYTES */
-+#undef REVERSEBYTES
-+
-+/* #undef SECURE_SERVER */
-+#undef SECURE_SERVER
-+
-+/* #undef SERVER_LOGGING */
- #undef SERVER_LOGGING
- 
- /* Define to 1 if you have the ANSI C header files. */
- #undef STDC_HEADERS
- 
-+/* #undef USEPORT64 */
-+#undef USEPORT64
-+
- /* Version number of package */
- #undef VERSION
- 
-diff --git a/configure.in b/configure.in
-index dfc3817..a86da05 100755
---- a/configure.in
-+++ b/configure.in
-@@ -1,7 +1,7 @@
- dnl Process this file with autoconf to produce a configure script.
- AC_INIT(configure.in,minuit/minuit/minuit/d506cm.inc)
- AM_INIT_AUTOMAKE(simpson,2.0.0)
--AM_CONFIG_HEADER(config.h)
-+AC_CONFIG_HEADER(config.h)
- 
- builtin(include,div.m4)
- dnl Checks for host-type.
-@@ -10,7 +10,7 @@ BINDISTDIR=simpson-$VERSION-$host
- AC_SUBST(BINDISTDIR)
- 
- dnl Checks for programs.
--AC_ISC_POSIX
-+AC_SEARCH_LIBS([strerror],[cposix])
- AC_PROG_CC
- AC_PROG_CXX
- AM_PROG_LIBTOOL
-@@ -21,7 +21,7 @@ AC_HEADER_STDC
- AC_PROG_LIBTOOL
- AC_PROG_INSTALL
- AC_PROG_LN_S
--AC_PROG_RANLIB
-+#AC_PROG_RANLIB
- AC_CHECK_PROGS(TAR, gtar tar)
- AC_CHECK_PROGS(F77, g77 f77)
- 
-@@ -30,17 +30,17 @@ AC_CHECK_LIB(m, sqrt)
- AC_CHECK_LIB(g2c, log, have_g2c=1, have_g2c=0)
- if test "$have_g2c" = 1; then
-   LIBG2C=-lg2c
--  AC_CHECK_LIB(g2c, pow_di, AC_DEFINE(HAVE_POW_DI))
-+  AC_CHECK_LIB(g2c, pow_di, AC_DEFINE([HAVE_POW_DI],,[#undef HAVE_POW_DI]))
- fi
- AC_CHECK_LIB(f2c, log, have_f2c=1, have_f2c=0)
- if test "$have_f2c" = 1; then
-   LIBG2C=-lf2c
--  AC_CHECK_LIB(f2c, pow_di, AC_DEFINE(HAVE_POW_DI))
-+  AC_CHECK_LIB(f2c, pow_di, AC_DEFINE([HAVE_POW_DI],,[#undef HAVE_POW_DI]))
- fi
- AC_CHECK_LIB(gfortran, log, have_gfortran=1, have_gfortran=0)
- if test "$have_gfortran" = 1; then
-   LIBG2C=-lgfortran
--  AC_CHECK_LIB(gfortran, pow_di, AC_DEFINE(HAVE_POW_DI))
-+  AC_CHECK_LIB(gfortran, pow_di, AC_DEFINE([HAVE_POW_DI],,[#undef HAVE_POW_DI]))
- fi
- AC_SUBST(LIBG2C)
- AC_CHECK_LIB(g2c, main)
-@@ -61,14 +61,14 @@ AC_SUBST(LIB_SOCKET)
- 
- 
- LIBLAPACK=""
--AC_CHECK_LIB(lapack, zgeev, have_lapack=1, have_lapack=0)
-+AC_CHECK_LIB(lapack, zgeev_, have_lapack=1, have_lapack=0)
- if test "$have_lapack" = 1; then
-   LIBLAPACK=-llapack
- fi
- AC_SUBST(LIBLAPACK)
- 
- LIBBLAS=
--AC_CHECK_LIB(blas, cscal, have_blas=1, have_blas=0)
-+AC_CHECK_LIB(blas, cscal_, have_blas=1, have_blas=0)
- if test "$have_blas" = 1; then
-   LIBBLAS=-lblas
- fi
-@@ -85,7 +85,7 @@ if test "$have_fexit" = 0; then
-   AC_CHECK_LIB(gfortran, f_exit, have_fexit=1, have_fexit=0)
- fi
- if test "$have_fexit" = 1; then
--  AC_DEFINE(HAVE_F_EXIT)
-+  AC_DEFINE(HAVE_F_EXIT,,[#undef HAVE_F_EXIT])
- fi
- 
- AC_CHECK_LIB(g2c, pow_di, have_powdi=1, have_powdi=0)
-@@ -96,11 +96,11 @@ if test "$have_powdi" = 0; then
-   AC_CHECK_LIB(gfortran, pow_di, have_powdi=1, have_powdi=0)
- fi
- if test "$have_fexit" = 1; then
--  AC_DEFINE(HAVE_F_EXIT)
-+  AC_DEFINE([HAVE_F_EXIT],,[#undef HAVE_F_EXIT])
- fi
- 
- dnl Checks for header files.
--#AC_STDC_HEADERS
-+#AC_HEADER_STDC
- #AC_CHECK_HEADERS(malloc.h)
-          
- dnl Checks for typedefs, structures, and compiler characteristics.
-@@ -113,7 +113,7 @@ dnl Checks for library functions.
- AC_TYPE_SIGNAL
- AC_FUNC_VPRINTF
- AC_CHECK_FUNCS(strstr strtod strtol)
--AC_CHECK_FUNC(getline, AC_DEFINE(HAVE_GETLINE))                                 
-+AC_CHECK_FUNC(getline, AC_DEFINE([HAVE_GETLINE],,[#undef HAVE_GETLINE]))                                 
- 
- dnl Use -Wall if we have gcc.
- changequote(,)dnl
-@@ -124,7 +124,13 @@ if test "x$GCC" = "xyes"; then
-   esac
- fi
- changequote([,])dnl
--AC_CYGWIN
-+
-+AC_CANONICAL_HOST
-+case $host_os in
-+  *cygwin* ) CYGWIN=yes;;
-+	 * ) CYGWIN=no;;
-+esac
-+
- AC_OBJEXT
- AC_EXEEXT
- 
-@@ -133,14 +139,14 @@ SC_PATH_TCLCONFIG
- SC_LOAD_TCLCONFIG
- SC_PUBLIC_TCL_HEADERS
- 
--AC_ARG_WITH(tklib, [  --with-tklib            Build with Tk support], enable_tk="no", enable_tk="yes")
-+AC_ARG_ENABLE([tklib], AS_HELP_STRING([--enable-tklib],[Build with Tk support]))
- 
--if test x$enable_tk = xyes; then  
-+AS_IF([test "x$enable_tklib" = "xyes"], [
-   AC_DEFINE([ENABLE_TK], 1, [Compile with Tk support])
-   SC_PATH_TKCONFIG
-   SC_LOAD_TKCONFIG
-   SC_PUBLIC_TK_HEADERS
--fi
-+])
- 
- SUBDIR_ADD=""
- 
-@@ -186,51 +192,42 @@ fi
- AC_ARG_ENABLE(serverlog, [  --enable-serverlog      Enable server logging], enable_serverlog="yes", enable_serverlog="no")
- 
- if test x"${enable_serverlog}" = xyes; then
--  AC_DEFINE([SERVER_LOGGING], 1, [Enable serverlogging])
-+  AC_DEFINE([SERVER_LOGGING], 1, [#undef SERVER_LOGGING])
- fi
- 
- 
--AC_ARG_ENABLE(parallel, [  --enable-parallel       Create multithreaded code], enable_parallel="yes", enable_parallel="no")
-+AC_ARG_ENABLE([parallel], AS_HELP_STRING([--enable-parallel],[Create multithreaded code]))
- 
--if test x"${enable_parallel}" = xyes; then
-+AS_IF([test "x$enable_parallel" = "xyes"], [
-   AC_DEFINE([PARALLEL], 1, [Make the code multithreaded])
--fi
-+])
- 
- 
- 
- 
--AC_ARG_WITH(simplot,[  --without-simplot       Do not compile the SIMPLOT program], simplot="no", simplot="yes")
-+AC_ARG_ENABLE([simplot], AS_HELP_STRING([--enable-simplot],[Do not compile the SIMPLOT program]))
- 
--if test x$simplot = xyes; then
-+AS_IF([test "x$enable_simplot" = "xyes"], [
- 
--    AM_PATH_GTK(1.2.0, ,
--      if test x"${ac_cv_cygwin}" = x"yes" ; then
--      AC_MSG_ERROR(Cannot find GTK: Is gtk-config in path?
--      
--   Optionally use './configure --without-simplot' and compile simplot
--   manually with the makefile 'simplot/Makefile.win32' configured properly.
--   )
--      else
--      AC_MSG_ERROR(Cannot find GTK: Is gtk-config in path?)
--      fi
--    )
-+	PKG_PROG_PKG_CONFIG
-+	PKG_CHECK_MODULES([GTK], [gtk+])
-     dnl Set PACKAGE_DATA_DIR in config.h.
-     if test "x${datadir}" = 'x${prefix}/share'; then
-       if test "x${prefix}" = "xNONE"; then
--        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${ac_default_prefix}/share/${PACKAGE}")
-+        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${ac_default_prefix}/share/${PACKAGE}",[#undef PACKAGE_DATA_DIR])
-       else
--        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${prefix}/share/${PACKAGE}")
-+        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${prefix}/share/${PACKAGE}",[#undef PACKAGE_DATA_DIR])
-       fi
-     else
--      AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${datadir}/${PACKAGE}")
-+      AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${datadir}/${PACKAGE}",[#undef PACKAGE_DATA_DIR])
-     fi
- 
-     dnl Set PACKAGE_SOURCE_DIR in config.h.
-     packagesrcdir=`cd $srcdir && pwd`
--    AC_DEFINE_UNQUOTED(PACKAGE_SOURCE_DIR, "${packagesrcdir}")
-+    AC_DEFINE_UNQUOTED(PACKAGE_SOURCE_DIR, "${packagesrcdir}",[#undef PACKAGE_SOURCE_DIR])
- 
-     SUBDIR_ADD="${SUBDIR_ADD} simplot"
--fi
-+])
- 
- if test -z "$TARGET"; then
-   test -f ./config.guess && TARGET=`sh ./config.guess` 2>/dev/null
-@@ -241,17 +238,26 @@ else
- your target specification; this may cause problems later on...)
- fi
- 
--case $TARGET in
-+AC_CANONICAL_HOST
-+case $host in
- mips-dec-*)	REVERSEBYTES="yes";;
- i386-*)		REVERSEBYTES="yes";;
- i486-*)		REVERSEBYTES="yes";;
- i586-*)		REVERSEBYTES="yes";;
- i686-*)		REVERSEBYTES="yes";;
-+x86_64-*)	REVERSEBYTES="yes"; USEPORT64="yes";;
- *)		REVERSEBYTES="no";;
- esac
-+
-+echo "host is $host"
- echo "Reverse byte order...$REVERSEBYTES"
-+
- if test x$REVERSEBYTES = xyes; then
--  AC_DEFINE_UNQUOTED(REVERSEBYTES, 1)
-+  AC_DEFINE_UNQUOTED([REVERSEBYTES], 1,[#undef REVERSEBYTES])
-+fi
-+# if building on 64bits architecture then change the default port to 3264
-+if test x$USEPORT64 = xyes; then
-+  AC_DEFINE([USEPORT64], 1,[#undef USEPORT64])
- fi
- 
- 
-@@ -268,7 +274,7 @@ if test x$minuit = xyes; then
-       AC_MSG_WARN(You must have a Fortran compiler to compile minuit) 
-     fi
-     SUBDIR_ADD="${SUBDIR_ADD} minuit"
--    AC_DEFINE_UNQUOTED(ENABLE_MINUIT, 1)
-+    AC_DEFINE_UNQUOTED([ENABLE_MINUIT], 1, [#undef ENABLE_MINUIT ])
-     MINUIT_LIB="../minuit/minuit/code/libminuit.a"
- fi
- 
-@@ -276,19 +282,20 @@ AC_ARG_WITH(simmol,   [  --without-simmol         Build with simmol], enable_sim
- 
- if test x$enable_simmol = xyes; then
-   SUBDIR_ADD="${SUBDIR_ADD} simmol"
--  AC_DEFINE_UNQUOTED(ENABLE_SIMMOL,1)
-+  AC_DEFINE_UNQUOTED(ENABLE_SIMMOL,1,[#undef ENABLE_SIMMOL])
- fi
-+AM_CONDITIONAL([ENABLE_SIMBIO], [test x$enable_simmol = xyes])
- 
- AC_ARG_WITH(secureserver,   [  --without-secureserver  Do not overrule dangerous tcl-commands], secure="no", secure="yes")
- 
- if test x$secure = xyes; then
--    AC_DEFINE_UNQUOTED(SECURE_SERVER, 1)
-+    AC_DEFINE_UNQUOTED(SECURE_SERVER, 1,[#undef SECURE_SERVER])
- fi
- 
- AC_ARG_WITH(pivotphasing,   [  --with-pivotphasing     Enable vnmr pivot phasing], pivot="yes", pivot="no")
- 
- if test x$pivot = xyes; then
--    AC_DEFINE_UNQUOTED(PIVOT_PHASE, 1)
-+    AC_DEFINE_UNQUOTED(PIVOT_PHASE, 1,[#undef PIVOT_PHASE])
- fi
- 
- AC_SUBST(SUBDIR_ADD)
-@@ -296,9 +303,8 @@ AC_SUBST(MINUIT_LIB)
- AC_SUBST(GD_LIB)
- AC_SUBST(BUILDLIBSIMPSON)
- 
--AC_OUTPUT([Makefile 
-+AC_CONFIG_FILES([Makefile 
- 	   cryst/Makefile
--	   f2c/Makefile
- 	   simpson/Makefile
- 	   simplot/Makefile
- 	   simmol/Makefile
-@@ -309,5 +315,6 @@ AC_OUTPUT([Makefile
- 	   gd1.4/Makefile
- 	   vnmrtools/Makefile
- 	   ])
-+AC_OUTPUT
- 
- 
-diff --git a/simmol/Makefile.am b/simmol/Makefile.am
-index 4d61920..632feba 100644
---- a/simmol/Makefile.am
-+++ b/simmol/Makefile.am
-@@ -1,7 +1,7 @@
- INCLUDES = $(TCL_INCLUDES) -I../minuit
- LIBS = $(TCL_LIBS)
--CFLAGS=-g -O2 -Wall -DNO_CONST
--CXXFLAGS=-g -O0 -Wall -DNO_CONST
-+AM_CFLAGS=-g -O2 -Wall -DNO_CONST
-+AM_CXXFLAGS=-g -O0 -Wall -DNO_CONST
- bin_PROGRAMS = simmol
- noinst_LIBRARIES = libsimmol.a
- 
-diff --git a/simmol/backbone.cc b/simmol/backbone.cc
-index 88261e0..c3cf714 100644
---- a/simmol/backbone.cc
-+++ b/simmol/backbone.cc
-@@ -23,10 +23,10 @@
- #include <fstream>
- #include <math.h>
- #include <stdlib.h>
--#include <fstream.h>
- #include <ctype.h>
- #include "euler.h"
- #include "molecule.h"
-+using namespace std;
- 
- /* The distances in atomtype.h must be multiplied with 0.004
-    to be converted to Aangstroems */
-diff --git a/simmol/commands.cc b/simmol/commands.cc
-index 8650e1e..d6d3a18 100644
---- a/simmol/commands.cc
-+++ b/simmol/commands.cc
-@@ -31,6 +31,7 @@
- #include "descriptor.h"
- #include "vector3.h"
- #include "molecule.h"
-+using namespace std;
- 
- 
- int tclMload(ClientData data,Tcl_Interp* interp,int argc, char *argv[])
-diff --git a/simmol/complx.h b/simmol/complx.h
-index 631ab10..09a5450 100644
---- a/simmol/complx.h
-+++ b/simmol/complx.h
-@@ -24,7 +24,8 @@
- #define __COMPLX_H
- 
- #include <math.h>
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- 
- #ifdef DEFINE_MATHCONST
- #define M_E             2.7182818284590452354
-diff --git a/simmol/descriptor.cc b/simmol/descriptor.cc
-index 468be77..8e315b4 100644
---- a/simmol/descriptor.cc
-+++ b/simmol/descriptor.cc
-@@ -21,9 +21,10 @@
-     Descriptor is the internal list of allocated molecules.
- */
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include "descriptor.h"
-+using namespace std;
- 
- Descriptor desc;
- 
-diff --git a/simmol/elements.cc b/simmol/elements.cc
-index 817212f..ca321ba 100644
---- a/simmol/elements.cc
-+++ b/simmol/elements.cc
-@@ -19,7 +19,7 @@
-     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  
- */
- #include <iomanip>
--#include <iostream.h>
-+#include <iostream>
- #include <math.h>
- #include <ctype.h>
- #include <stdlib.h>
-@@ -29,6 +29,7 @@
- #include "elements.h"
- #include "tensors.h"
- #include "jcouplings.h"
-+using namespace std;
- 
- 
- int Atom::getsecondary_structuretype()
-@@ -94,7 +95,7 @@ Atom::Atom(const vector<double>& p) : plane(0)
- 
- ostream& operator << (ostream& out, const Atom& atom)
- {
--  char *p;
-+  const char *p;
-   static int atomno = 1;
-   int flags;
-   
-diff --git a/simmol/geomview.cc b/simmol/geomview.cc
-index e0e8eef..831d316 100644
---- a/simmol/geomview.cc
-+++ b/simmol/geomview.cc
-@@ -20,12 +20,13 @@
-     
- */
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include <math.h>
- #include <ctype.h>
- #include "euler.h"
- #include "geomview.h"
-+using namespace std;
- 
- const char *Geomview_begin = 
- "(backcolor \"World\" 1.000000 1.000000 1.000000)\n"
-diff --git a/simmol/geomview.h b/simmol/geomview.h
-index a08d65a..8f78659 100644
---- a/simmol/geomview.h
-+++ b/simmol/geomview.h
-@@ -34,8 +34,9 @@
- #include "container.h"
- #endif
- 
--#include <iostream.h>
--#include <fstream.h>
-+#include <iostream>
-+#include <fstream>
-+using namespace std;
- 
- /* Writes a OOGL object to a file
- 
-diff --git a/simmol/libsimmol.cc b/simmol/libsimmol.cc
-index e11bd90..84cf942 100644
---- a/simmol/libsimmol.cc
-+++ b/simmol/libsimmol.cc
-@@ -20,12 +20,13 @@
-     
- */
- 
--#include <iostream.h> 
-+#include "config.h"
-+#include <iostream> 
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
- #include <tcl.h>
--#include "config.h"
-+using namespace std;
- 
- extern void RegisterCommands_commands(Tcl_Interp* interp);
- extern void RegisterCommands_primitives(Tcl_Interp* interp);
-diff --git a/simmol/main.cc b/simmol/main.cc
-index 0e0c615..f7f724f 100644
---- a/simmol/main.cc
-+++ b/simmol/main.cc
-@@ -20,12 +20,13 @@
-     
- */
- 
--#include <iostream.h> 
-+#include "config.h"
-+#include <iostream> 
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
- #include <tcl.h>
--#include "config.h"
-+using namespace std;
- 
- extern void RegisterCommands_commands(Tcl_Interp* interp);
- extern void RegisterCommands_primitives(Tcl_Interp* interp);
-diff --git a/simmol/make.cc b/simmol/make.cc
-index 3e94d66..c3c4bd2 100644
---- a/simmol/make.cc
-+++ b/simmol/make.cc
-@@ -19,12 +19,11 @@
-     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
- */
- 
--#include <iomanip.h>
-+#include <iomanip>
- #include <strstream>
- #include <fstream>
- #include <math.h>
- #include <stdlib.h>
--#include <fstream.h>
- #include <ctype.h>
- #include <tcl.h>
- #include <string.h>
-@@ -35,6 +34,7 @@
- #include "tensors.h"
- #include "jcouplings.h"
- 
-+using namespace std;
- 
- #define Cos(a) cos((a)*M_PI/360.0)
- #define Sin(a) sin((a)*M_PI/360.0)
-diff --git a/simmol/matrix.h b/simmol/matrix.h
-index a997a61..a58fc56 100644
---- a/simmol/matrix.h
-+++ b/simmol/matrix.h
-@@ -23,8 +23,10 @@
- #ifndef __MATRIX_H	 
- #define __MATRIX_H
- 
--#include <iostream.h>
-+#include <iostream>
-+#include <stdlib.h>
- #include <memory.h>
-+using namespace std;
- 
- 
- template <class T> class matrix {
-diff --git a/simmol/molecule.cc b/simmol/molecule.cc
-index 0500162..c75ad52 100644
---- a/simmol/molecule.cc
-+++ b/simmol/molecule.cc
-@@ -19,12 +19,11 @@
-     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
- */
- 
--#include <iomanip.h>
-+#include <iomanip>
- #include <strstream>
- #include <fstream>
- #include <math.h>
- #include <stdlib.h>
--#include <fstream.h>
- #include <ctype.h>
- #include <tcl.h>
- #include <string.h>
-@@ -34,6 +33,7 @@
- #include "descriptor.h"
- #include "tensors.h"
- #include "jcouplings.h"
-+using namespace std;
- 
- 
- #define Cos(a) cos((a)*M_PI/360.0)
-diff --git a/simmol/primitives.cc b/simmol/primitives.cc
-index 195af7f..df876a5 100644
---- a/simmol/primitives.cc
-+++ b/simmol/primitives.cc
-@@ -28,6 +28,7 @@
- #include "vector3.h"
- #include "euler.h"
- #include "matrix.h"
-+using namespace std;
- 
- #define TYPE_FLOAT  3
- #define TYPE_VECTOR 1
-diff --git a/simmol/spinsys.cc b/simmol/spinsys.cc
-index f811b24..06b4c75 100644
---- a/simmol/spinsys.cc
-+++ b/simmol/spinsys.cc
-@@ -24,12 +24,13 @@
- */
- 
- #include <stdlib.h>
--#include <iostream.h>
--#include <iomanip.h>
-+#include <iostream>
-+#include <iomanip>
- #include <string.h>
- #include <stdio.h>
- #include <assert.h>
- #include "spinsys.h"
-+using namespace std;
- 
- Hash::Hash(int _nlist=101) : nlist(_nlist), curr(0), nnames(0)
- { 
-diff --git a/simmol/spinsys.h b/simmol/spinsys.h
-index d863af0..4dcea0a 100644
---- a/simmol/spinsys.h
-+++ b/simmol/spinsys.h
-@@ -26,8 +26,9 @@
- #ifndef __SPINSYS_H
- #define __SPINSYS_H
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdio.h>
-+using namespace std;
- 
- #include "atomtype.h"
- const int MAX_NUC_LEN = 16;
-diff --git a/simmol/vector3.cc b/simmol/vector3.cc
-index f13c5ea..0376e90 100644
---- a/simmol/vector3.cc
-+++ b/simmol/vector3.cc
-@@ -20,10 +20,11 @@
-     
- */
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include <math.h>
- #include "vector3.h"
-+using namespace std;
- 
- double norm(const vector<double>& v)
- {
-diff --git a/simplot/Makefile.am b/simplot/Makefile.am
-index a36f260..4b34100 100644
---- a/simplot/Makefile.am
-+++ b/simplot/Makefile.am
-@@ -1,6 +1,6 @@
- INCLUDES = @GTK_CFLAGS@ -I../simpson
- 
--CFLAGS=@CFLAGS_STATIC@ @CFLAGS@
-+AM_CFLAGS=@CFLAGS_STATIC@ @CFLAGS@
- LIBS=@LIBS@ @LIBS_STATIC@ $(BZLIB)
- 
- EXTRA_DIST = simplot.glade Makefile.win32 Makefile.osx
-diff --git a/simpson/Makefile.am b/simpson/Makefile.am
-index b19a781..c4caed9 100644
---- a/simpson/Makefile.am
-+++ b/simpson/Makefile.am
-@@ -1,8 +1,8 @@
--INCLUDES = -I../f2c $(TCL_INCLUDES) -I../minuit
-+INCLUDES = -I${incudedir}/f2c $(TCL_INCLUDES) -I../minuit
- TCLSRC=csafit.tcl ftools.tcl main.tcl misc.tcl simpson.tcl rfshapes.tcl
- simbio_TCLSRC=csafit.tcl ftools.tcl misc.tcl simpson.tcl rfshapes.tcl simbio_main.tcl
- 
--CFLAGS=@CFLAGS@ -DNO_CONST
-+AM_CFLAGS=@CFLAGS@ -DNO_CONST
- LIBS=@LIBS@ $(LIB_SOCKET) $(LIBLAPACK) $(LIBBLAS)
- 
- EXTRA_LTLIBRARIES=libsimpson.la
-@@ -52,18 +52,18 @@ simbio_SOURCES = cm.h defs.h ham.h matrix.h sim.h cryst.h tclcmd.h \
-   atom.h rfshapes.h rfshapes.c OCroutines.h OCroutines.c rfprof.c
- 
- simpson_LDADD =  $(GD_LIB) $(LIBG2C) \
--  ../f2c/libf2c.a  $(TCL_LIB_SPEC) $(MINUIT_LIB) -lm
-+  -lf2c  $(TCL_LIB_SPEC) $(MINUIT_LIB) -lm
- 
- simbio_LIBS = @LIBS@ @LIBS_STATIC@
- simbio_LDADD =  $(GD_LIB) \
--  ../f2c/libf2c.a  $(TCL_LIB_SPEC) $(MINUIT_LIB) \
-+  -lf2c  $(TCL_LIB_SPEC) $(MINUIT_LIB) \
-   ../simmol/libsimmol.a -lm $(TK_LIB_SPEC) $(OPENGL_LIB) $(LIBG2C) 
- 
- libsimpson_la_SOURCES = $(simpson_SOURCES) 
- libsimpson_la_CFLAGS = -DLIBSIMPSON
- libsimpson_la_LDFLAGS = -release $(VERSION)
--libsimpson_la_LIBADD = ../gd1.4/libgd.a \
--  ../f2c/libf2c.a ../minuit/minuit/code/libminuit.a
-+libsimpson_la_LIBADD = $(GD_LIB) \
-+  -lf2c -lminuit
- 
- simdps_SOURCES = simdps.c simdpstcl.c
- simdps_LDADD = $(TCL_LIB_SPEC) -lm
-diff --git a/simpson/simpson.c b/simpson/simpson.c
-index e613806..c9975d9 100644
---- a/simpson/simpson.c
-+++ b/simpson/simpson.c
-@@ -85,7 +85,11 @@ void putbits(char *bits,int e)
- 
- #ifndef DISABLE_NETWORK
- 
-+#ifdef USEPORT64
-+#define DEFAULT_PORT 3264
-+#else
- #define DEFAULT_PORT 3265
-+#endif
- #define SIMPSON_ID 15273
- 
- #ifndef STDIN_FILENO
-diff --git a/vnmrtools/Makefile.am b/vnmrtools/Makefile.am
-index 79bb7c5..61084aa 100644
---- a/vnmrtools/Makefile.am
-+++ b/vnmrtools/Makefile.am
-@@ -1,4 +1,4 @@
--EXTRA_DIST = README.vnmrtools create2d create2dph rt2d rt2dph savefid savespe
-+EXTRA_DIST = create2d create2dph rt2d rt2dph savefid savespe
- LIBS= @LIBS@ -lm
- bin_SCRIPTS = create2d create2dph rt2d rt2dph savefid savespe README.vnmrtools
- 
diff --git a/sci-chemistry/simpson/files/3.0.1-gentoo.patch b/sci-chemistry/simpson/files/3.0.1-gentoo.patch
new file mode 100644
index 000000000..61d170f89
--- /dev/null
+++ b/sci-chemistry/simpson/files/3.0.1-gentoo.patch
@@ -0,0 +1,28 @@
+diff --git a/Makefile b/Makefile
+index c5f6fcf..25e328f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -7,8 +7,9 @@ C_OBJS = *.o
+ #INCLUDES = -IC:/Tcl/include -I../CBLAS/src
+ #LIBRARIES = -lm *.dll
+ # LINUX:
+-INCLUDES = -I/usr/include/tcl8.5
+-LIBRARIES = -lm -lgslcblas -llapack -ltcl8.5
++INCLUDES = -I@GENTOO_PORTAGE_EPREFIX@/usr/include/
++BLASLIBS = `pkg-config --libs cblas lapack`
++LIBRARIES = -lm ${BLASLIBS} -ltcl
+ 
+ FLAGS = -c -O3
+ CC = gcc
+@@ -16,9 +17,9 @@ RM = rm
+ TAR = tar
+ 
+ simpson: $(C_OBJS)
+-	$(CC) $(LIBRARIES) $(C_OBJS) -o simpson 
++	$(CC) $(LDFLAGS) -o simpson $(C_OBJS) $(LIBRARIES)
+ $(C_OBJS):
+-	$(CC) $(FLAGS) $(INCLUDES) *.c
++	$(CC) $(CFLAGS) $(INCLUDES) -c *.c
+ clean:
+ 	$(RM) -f *.o simpson
+ dist:
diff --git a/sci-chemistry/simpson/files/3.0.1-type.patch b/sci-chemistry/simpson/files/3.0.1-type.patch
new file mode 100644
index 000000000..3f6cc7023
--- /dev/null
+++ b/sci-chemistry/simpson/files/3.0.1-type.patch
@@ -0,0 +1,110 @@
+diff --git a/OCroutines.c b/OCroutines.c
+index eef6849..60ef56c 100644
+--- a/OCroutines.c
++++ b/OCroutines.c
+@@ -11,6 +11,7 @@
+ #include "iodata.h"
+ #include "tclutil.h"
+ #include "B0inhom.h"
++#include "defs_blas_lapack.h"
+ 
+ /* global variable holding all OC parameters */
+ OCoptPars OCpar;
+diff --git a/contour.c b/contour.c
+index ec5a223..87ae8ee 100644
+--- a/contour.c
++++ b/contour.c
+@@ -242,7 +242,8 @@ DEFINE_CMD(FContour)
+   double lowcolor[3], highcolor[3], xmin, xmax, ymin, ymax;
+   double *levels, x1, y1, x2, y2, cl, r1, r2, fmax;
+   double *xpos, *ypos, **z, iratio, jratio, nlowcolor[3], nhighcolor[3];
+-  char outputfile[256], **av;
++  char outputfile[256];
++  const char **av;
+   FILE *file;
+   FD *fdp;
+   Point *p, **pp;
+diff --git a/ftools.c b/ftools.c
+index 682e475..3c150d6 100644
+--- a/ftools.c
++++ b/ftools.c
+@@ -1434,7 +1434,8 @@ int tclFRms(ClientData data,Tcl_Interp* interp,int argc, char *argv[])
+   double2 *vec,*vec2;
+   double v1,v2;
+   int part;
+-  char **par,**par2,*range;
++  char *range;
++  const char **par,**par2;
+   int i,i1,i2,npar,npar2;
+   double sumrms,sumint;
+ 
+diff --git a/ham.c b/ham.c
+index 5be9dd1..5d36bdc 100644
+--- a/ham.c
++++ b/ham.c
+@@ -34,6 +34,7 @@
+ #include "cm_new.h"
+ #include "ham.h"
+ #include "defs.h"
++#include "defs_blas_lapack.h"
+ 
+ /*
+   Allocation strategy:
+diff --git a/matrix_new.c b/matrix_new.c
+index c0aaad2..2f3f370 100644
+--- a/matrix_new.c
++++ b/matrix_new.c
+@@ -24,6 +24,7 @@
+ 
+ #include <stdlib.h>
+ #include <stdio.h>
++#include <string.h>
+ #include "complx.h"
+ #include "matrix_new.h"
+ 
+diff --git a/new_direct.c b/new_direct.c
+index 24502f2..cc5fd68 100644
+--- a/new_direct.c
++++ b/new_direct.c
+@@ -1,4 +1,5 @@
+ #include "new_direct.h"
++#include "defs_blas_lapack.h"
+ 
+ /* make visible global variable pulse */
+ extern Pulse* puls;
+diff --git a/pulse.c b/pulse.c
+index f40787c..335d225 100644
+--- a/pulse.c
++++ b/pulse.c
+@@ -43,6 +43,7 @@
+ #include "OCroutines.h"
+ #include "B0inhom.h"
+ #include "relax.h"
++#include "defs_blas_lapack.h"
+ 
+ /*
+   tpropstart_usec : the time when the propagator was reset last time
+diff --git a/wigner.c b/wigner.c
+index bacf4b8..1644aaf 100644
+--- a/wigner.c
++++ b/wigner.c
+@@ -27,6 +27,7 @@
+ #include <math.h>
+ #include "complx.h"
+ #include <stdio.h>
++#include <stdlib.h>
+ #include "defs.h"
+ #include "matrix_new.h"
+ //#include "defs_blas_lapack.h"
+diff --git a/zte.c b/zte.c
+index 77dcb87..6025fa4 100644
+--- a/zte.c
++++ b/zte.c
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include "cm_new.h"
+ #include "pulse.h"
++#include "tclutil.h"
+ 
+ typedef struct _ZTEstruct {
+    mv_complx *rho0, *sigma;
diff --git a/sci-chemistry/simpson/simpson-2.0.0.ebuild b/sci-chemistry/simpson/simpson-3.0.1.ebuild
index 9ad3fb6b1..16c6ee870 100644
--- a/sci-chemistry/simpson/simpson-2.0.0.ebuild
+++ b/sci-chemistry/simpson/simpson-3.0.1.ebuild
@@ -4,11 +4,11 @@
 
 EAPI="3"
 
-inherit autotools eutils
+inherit autotools eutils prefix
 
 DESCRIPTION="General-purpose software package for simulation virtually all kinds of solid-state NMR experiments"
 HOMEPAGE="http://bionmr.chem.au.dk/bionmr/software/index.php"
-SRC_URI="http://bionmr.chem.au.dk/download/${PN}/${PV}/${P}.tar.gz"
+SRC_URI="http://www.bionmr.chem.au.dk/download/${PN}/3.0/${PN}-source-${PV}.tgz"
 
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"
@@ -23,22 +23,22 @@ RDEPEND="
 	tk? ( dev-lang/tk )"
 DEPEND="${RDEPEND}"
 
+S="${WORKDIR}"/${PN}-source-${PV}
+
 src_prepare() {
-	rm -rf f2c missing
+	edos2unix Makefile
 	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	eautoreconf
+	epatch "${FILESDIR}"/${PV}-type.patch
+	eprefixify Makefile
 }
 
-src_configure(){
-# Broken
-#		$(use_enable threads parallel) \
-	econf \
-		--disable-parallel \
-		$(use_enable tk tklib) \
-		$(use_enable gtk simplot)
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		|| die
 }
 
 src_install() {
-	emake DESTDIR="${D}" install || die
-	dodoc vnmrtools/README.vnmrtools NEWS README TODO AUTHORS || die
+	dobin ${PN} || die
 }
author	Justin Lecher (jlec) <jlec@j-schmitz.net>	2010-09-13 12:36:50 +0200
committer	Justin Lecher (jlec) <jlec@j-schmitz.net>	2010-09-13 12:36:50 +0200
commit	4ef17bec150af02f808505f6d2159a7dbb5cdaaa (patch)
tree	0ead9485c93e271cb0f8d06276a9f6f59dfd518d /sci-chemistry
parent	Keyworded for *-linux (diff)
parent	Some scripts are in the wrong place (diff)
download	sci-4ef17bec150af02f808505f6d2159a7dbb5cdaaa.tar.gz sci-4ef17bec150af02f808505f6d2159a7dbb5cdaaa.tar.bz2 sci-4ef17bec150af02f808505f6d2159a7dbb5cdaaa.zip