Initial import.

(Portage version: 2.1_pre4-r1)

6 files changed, 248 insertions, 0 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
new file mode 100644
index 000000000000..9bcc3f3b3b2e
--- /dev/null
+++ b/sci-chemistry/vmd/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/vmd
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.1 2006/02/10 15:33:08 markusle Exp $
+
+*vmd-1.8.3 (10 Feb 2006)
+
+  10 Feb 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.3-config-gentoo.patch, +metadata.xml, +vmd-1.8.3.ebuild:
+  Initial import.
+
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
new file mode 100644
index 000000000000..3a3b6d69eabb
--- /dev/null
+++ b/sci-chemistry/vmd/Manifest
@@ -0,0 +1,15 @@
+MD5 1206c48a2d3bc4f2d3475bbce47bd469 ChangeLog 290
+RMD160 73525344c19588906d003b30423b761b92bfcf26 ChangeLog 290
+SHA256 65c369e1a0c1265f1e83f51dc5b860db8e2ca8b901362eb7a659a5a3b2b129a5 ChangeLog 290
+MD5 369e1a4fc4a190880b7bcd1847da843f files/digest-vmd-1.8.3 244
+RMD160 99396b8dda8d7fc4a45c128cde3773103be4c5a4 files/digest-vmd-1.8.3 244
+SHA256 afb2b7701f35aeaedd2191351e44ba399d7c2b449edfd8b3d9adac47fd266734 files/digest-vmd-1.8.3 244
+MD5 c2f7407b24ab8fee80f913a2b31e79f5 files/vmd-1.8.3-config-gentoo.patch 2849
+RMD160 6bfdf7aa6f19839578b9dd08833f5af9a934514a files/vmd-1.8.3-config-gentoo.patch 2849
+SHA256 ee812af9c130d93b795c3f6967a1cc84a03fd56c16fcf9308636c3285a86ed73 files/vmd-1.8.3-config-gentoo.patch 2849
+MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272
+RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272
+SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272
+MD5 2b69ecef38ecc334c3a688de2feb96ed vmd-1.8.3.ebuild 3356
+RMD160 ec3cc716ab8e95228d2879aef14e6e3e5d43ad3e vmd-1.8.3.ebuild 3356
+SHA256 297976234eadd7ab620bd5261fe348fb1ce5b91eb0a2bd04813827e38943b39c vmd-1.8.3.ebuild 3356
diff --git a/sci-chemistry/vmd/files/digest-vmd-1.8.3 b/sci-chemistry/vmd/files/digest-vmd-1.8.3
new file mode 100644
index 000000000000..3a9d77d8371e
--- /dev/null
+++ b/sci-chemistry/vmd/files/digest-vmd-1.8.3
@@ -0,0 +1,3 @@
+MD5 8fb3fa55a54bcc3e41dbbd53c1c2cc59 vmd-1.8.3.src.tar.gz 8590337
+RMD160 4ad1b58721005ef85f580f437c032c28f6d786f1 vmd-1.8.3.src.tar.gz 8590337
+SHA256 36fb014004a765e54bbcd6608ef8738c808355268fd05dce618bc498d1f29c3e vmd-1.8.3.src.tar.gz 8590337
diff --git a/sci-chemistry/vmd/files/vmd-1.8.3-config-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.3-config-gentoo.patch
new file mode 100644
index 000000000000..879e00f9b678
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.3-config-gentoo.patch
@@ -0,0 +1,73 @@
+diff -Naur vmd-1.8.3/configure vmd-1.8.3-patched/configure
+--- vmd-1.8.3/configure	2005-02-16 05:44:22.000000000 +0000
++++ vmd-1.8.3-patched/configure	2005-12-18 20:49:49.000000000 +0000
+@@ -13,10 +13,10 @@
+ $install_name = "vmd";
+ 
+ # Directory where VMD startup script is installed, should be in users' paths.
+-$install_bin_dir="/usr/local/bin";
++$install_bin_dir="gentoo-bindir";
+ 
+ # Directory where VMD files and executables are installed
+-$install_library_dir="/usr/local/lib/$install_name";
++$install_library_dir="gentoo-libdir/$install_name";
+ 
+ 
+ # optionally override hard-coded defaults above with environment variables
+@@ -371,8 +371,8 @@
+ 
+ ################ Plugin options
+ #
+-$plugin_dir	= "../plugins";
+-$molfile_dir = "$plugin_dir/$config_arch/molfile";
++$plugin_dir	= "gentoo-plugindir";
++$molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
+ $plugin_include = "-I$plugin_dir/include -I$molfile_dir";
+ $plugin_library = "-L$molfile_dir";
+ $plugin_libs    = "-lmolfile_plugin";
+@@ -472,8 +472,8 @@
+ ################ FLTK GUI
+ $fltk_defines     = "-DVMDGUI -DVMDFLTK";
+ $fltk_dir         = "$vmd_library_dir/fltk";
+-$fltk_include     = "-I$fltk_dir/include";
+-$fltk_library     = "-L$fltk_dir/$config_arch";
++$fltk_include     = "-Igentoo-fltk-include";
++$fltk_library     = "-Lgentoo-fltk-libs";
+ $fltk_libs        = "-lfltk -lX11";
+ #@fltk_cc          = ('forms_ui.c');
+ @fltk_ccpp        = ( 'ColorFltkMenu.C',
+@@ -805,9 +805,9 @@
+ ###################
+ $python_defines     = "-DVMDPYTHON";
+ $python_dir         = "$vmd_library_dir/python";
+-$python_include     = "-I$python_dir/lib_$config_arch/include/python2.2";
+-$python_library     = "-L$python_dir/lib_$config_arch/lib/python2.2/config";
+-$python_libs        = "-lpython2.2 -lpthread";
++$python_include     = "-Igentoo-python-include";
++$python_library     = "-Lgentoo-python-lib";
++$python_libs        = "-lgentoo-python-link -lpthread";
+ @python_h           = ('PythonTextInterp.h',
+                        'VMDTkinterMenu.h',
+ 		       'py_commands.h',
+@@ -1335,8 +1335,8 @@
+     $opengl_libs        = "-lGL -lGLU"; 
+     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
+ 
+-    $arch_cc          = "gcc";
+-    $arch_ccpp        = "g++";
++    $arch_cc          = "gentoo-gcc";
++    $arch_ccpp        = "gentoo-g++";
+     # test hack to statically link libstd++
+     # $arch_ccpp        = "gcc";
+     $arch_depend_flag = "-MM";
+@@ -1345,8 +1345,8 @@
+     $arch_shcppopts   = "-fPIC";
+     $arch_shldopts    = "";
+ 
+-    $arch_opt_flag    = "-fno-for-scope -Wall -Wno-deprecated -O3 -march=i586 -fomit-frame-pointer";
+-    $arch_copts       = "-Wall -Wno-deprecated -O3 -march=i586 -fomit-frame-pointer";
++    $arch_opt_flag    = "gentoo-cflags";
++    $arch_copts       = "gentoo-cflags";
+ 
+     if ($config_static) {
+       $arch_lopts       = "-static";
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
new file mode 100644
index 000000000000..f86602893b1c
--- /dev/null
+++ b/sci-chemistry/vmd/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/vmd/vmd-1.8.3.ebuild b/sci-chemistry/vmd/vmd-1.8.3.ebuild
new file mode 100644
index 000000000000..29add240fbda
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.3.ebuild
@@ -0,0 +1,138 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.3.ebuild,v 1.1 2006/02/10 15:33:08 markusle Exp $
+
+inherit eutils toolchain-funcs python
+
+DESCRIPTION="Visual Molecular Dynamics"
+LICENSE="vmd"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="${P}.src.tar.gz"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="hardened"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	|| ( x11-libs/libXft virtual/x11 )
+	virtual/opengl
+	x11-libs/fltk
+	=dev-lang/tcl-8.4*
+	=dev-lang/tk-8.4*
+	>=dev-lang/python-2.3
+	hardened? ( sys-apps/paxctl )"
+
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${SRC_URI} from"
+	einfo "${VMD_DOWNLOAD}"
+	einfo "after agreeing to the license and then move it to "
+	einfo "${DISTDIR}"
+	echo
+}
+
+src_unpack() {
+	unpack ${A}
+
+	# apply LINUX-arch patches to gamess makesfiles
+	epatch "${FILESDIR}"/${P}-config-gentoo.patch
+
+
+	# prepare the plugins 
+
+	cd "${WORKDIR}"/plugins
+
+	sed -e "s/CC = gcc/CC = $(tc-getCC)/" \
+	    -e "s/CXX = g++/CXX = $(tc-getCXX)/" \
+		-e "s/COPTO = -o /COPTO = -fPIC -o /" \
+		-e "s/LOPTO = -o /LOPTO = -fPIC -o /" \
+		-e "s/CCFLAGS = -O2 -Wall/CCFLAGS = ${CFLAGS}/" \
+		-e "s/CXXFLAGS = -O2 -Wall/CXXFLAGS = ${CXXFLAGS}/" \
+	    -i Make-arch || die "Failed to set up plugins Makefile"
+
+	# prepare vmd itself
+
+	cd "${S}"
+
+	sed -e "s:gentoo-bindir:${D}/usr/bin:" \
+		-e "s:gentoo-libdir:${D}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust install paths"
+
+
+	sed -e "s:gentoo-gcc:$(tc-getCC):" \
+		-e "s:gentoo-g++:$(tc-getCXX):" \
+		-e "s:gentoo-cflags:${CFLAGS}:" \
+		-i configure || die "Failed to adjust C compiler/flags"
+
+
+	sed -e "s:gentoo-plugindir:${WORKDIR}/plugins:" \
+		-i configure || die "Failed to set up linking to plugin files"
+
+	sed -e "s:gentoo-fltk-include:/usr/include/fltk-1.1:" \
+		-e "s:gentoo-fltk-libs:/usr/$(get_libdir)/fltk-1.1:" \
+		-i configure || die "failed setting up fltk"
+
+
+	# get installed python version
+	python_version
+	local PY="python${PYVER}"
+
+	sed -e "s:gentoo-python-include:/usr/include/${PY}:" \
+		-e "s:gentoo-python-lib:/usr/$(get_libdir)/${PY}:" \
+		-e "s:gentoo-python-link:${PY}:" \
+		-i configure || die "failed setting up python"
+
+
+	local myconfig="LINUX OPENGL FLTK TK TCL PTHREADS PYTHON"
+
+	rm -f configure.options && echo $myconfig >> configure.options
+
+	./configure &> /dev/null || die "failed to configure"
+
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+	make LINUX || die "failed to build plugins"
+
+	# build vmd
+	cd "${S}"/src
+	make || die "failed to build vmd"
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	PLUGINDIR=${D}/usr/$(get_libdir)/${PN}/plugins make distrib || \
+		die "failed to install plugins"
+
+	# install vmd 
+	cd "${S}"/src
+	make install || die "failed to install vmd"
+
+	# install docs
+	cd "${S}"
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in 
+	# /usr/lib
+	cd "${D}"/usr/$(get_libdir)/vmd
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed -e "s:${D}::" -i "${D}"/usr/bin/${PN} \
+		|| die "failed to set up vmd wrapper script"
+
+	# adjust paxctl settings on hardened systems
+	if use hardened; then
+		/sbin/paxctl -pemrxs ${D}/usr/$(get_libdir)/${PN}/${PN}_LINUX
+	fi
+}
+