VMD now depends on stride in order to properly display secondary structure information. Also patched a paratool plugin error under tcl-8.4.13.

Package-Manager: portage-2.1.1_pre4-r4

5 files changed, 215 insertions, 23 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 64d86d114d80..b96cf4168098 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,14 @@
 # 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 1.5 2006/04/29 00:39:08 marienz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.6 2006/08/13 17:48:01 markusle Exp $
+
+*vmd-1.8.4-r1 (13 Aug 2006)
+
+  13 Aug 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.4-paratool.patch, +vmd-1.8.4-r1.ebuild:
+  VMD now depends on stride in order to properly display secondary
+  structure information. Also patched a paratool plugin error under
+  tcl-8.4.13.
 
   29 Apr 2006; Marien Zwart <marienz@gentoo.org> Manifest:
   Fix SHA256 digests.
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 657805a4d9df..fed65f2be413 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,33 +1,38 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-AUX vmd-1.8.3-config-gentoo.patch 2849 RMD160 6bfdf7aa6f19839578b9dd08833f5af9a934514a SHA1 bbb8f6045d0a2b7a4f70fdc86aee2fbff1a4cc7a SHA256 ee812af9c130d93b795c3f6967a1cc84a03fd56c16fcf9308636c3285a86ed73 size 2849
+AUX vmd-1.8.3-config-gentoo.patch 2849 RMD160 6bfdf7aa6f19839578b9dd08833f5af9a934514a SHA1 bbb8f6045d0a2b7a4f70fdc86aee2fbff1a4cc7a SHA256 ee812af9c130d93b795c3f6967a1cc84a03fd56c16fcf9308636c3285a86ed73
 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
-AUX vmd-1.8.4-config-gentoo.patch 4246 RMD160 61aa7bff404a775e5e6be01c42654eeb69a7711f SHA1 51e80f1887cb7a00b554359c809a960b22851b57 SHA256 0be5b5d67a5198929b4c3db8c0dfa3a7a69150f02b075d7bafe0255825bdcbb9 size 4246
+AUX vmd-1.8.4-config-gentoo.patch 4246 RMD160 61aa7bff404a775e5e6be01c42654eeb69a7711f SHA1 51e80f1887cb7a00b554359c809a960b22851b57 SHA256 0be5b5d67a5198929b4c3db8c0dfa3a7a69150f02b075d7bafe0255825bdcbb9
 MD5 6325ce1d0cbfe7731240deef3d69efa5 files/vmd-1.8.4-config-gentoo.patch 4246
 RMD160 61aa7bff404a775e5e6be01c42654eeb69a7711f files/vmd-1.8.4-config-gentoo.patch 4246
 SHA256 0be5b5d67a5198929b4c3db8c0dfa3a7a69150f02b075d7bafe0255825bdcbb9 files/vmd-1.8.4-config-gentoo.patch 4246
-AUX vmd-1.8.4-plugin-autopsf.patch 723 RMD160 6ccb492685cdeedc762f16e6f8ba010e2833908a SHA1 a05dd68ac178b75bfdc7c1b4d8b079557837195e SHA256 7230d8f5f4281b7b8615cc7ff60fc3b77432b3ec12cc507f3016566178b07fae size 723
+AUX vmd-1.8.4-paratool.patch 1008 RMD160 40e707894c50fee586b2f3c042086c03c53ca97e SHA1 4c90456cd5bb41de60ed14b7397375d21ab4384f SHA256 e6853e4f260c91777adccac10fde29e1b3f9bec2231f47d15e92ac7d845f178b
+MD5 5885e749cea5fdb0e819d16d48159040 files/vmd-1.8.4-paratool.patch 1008
+RMD160 40e707894c50fee586b2f3c042086c03c53ca97e files/vmd-1.8.4-paratool.patch 1008
+SHA256 e6853e4f260c91777adccac10fde29e1b3f9bec2231f47d15e92ac7d845f178b files/vmd-1.8.4-paratool.patch 1008
+AUX vmd-1.8.4-plugin-autopsf.patch 723 RMD160 6ccb492685cdeedc762f16e6f8ba010e2833908a SHA1 a05dd68ac178b75bfdc7c1b4d8b079557837195e SHA256 7230d8f5f4281b7b8615cc7ff60fc3b77432b3ec12cc507f3016566178b07fae
 MD5 94569757919baac0e2b61400d356cb74 files/vmd-1.8.4-plugin-autopsf.patch 723
 RMD160 6ccb492685cdeedc762f16e6f8ba010e2833908a files/vmd-1.8.4-plugin-autopsf.patch 723
 SHA256 7230d8f5f4281b7b8615cc7ff60fc3b77432b3ec12cc507f3016566178b07fae files/vmd-1.8.4-plugin-autopsf.patch 723
-DIST vmd-1.8.3.src.tar.gz 8590337 RMD160 4ad1b58721005ef85f580f437c032c28f6d786f1 SHA256 36fb014004a765e54bbcd6608ef8738c808355268fd05dce618bc498d1f29c3e size 8590337
-DIST vmd-1.8.4.src.tar.gz 12042149 RMD160 f49a68ae63a607cd37a58d894df2f22d7df55b85 SHA256 29b046767f1efe90d5f3e3dbbdcd4988d5335d1db226405f5ddb9f171c811cac size 12042149
-EBUILD vmd-1.8.3.ebuild 3615 RMD160 2bbeaf3e7ebb73ce89aa4c8d56269790f9900071 SHA1 52d65b2e66a0e0c5aa5fa5dfe3a68ced725f350d SHA256 afb3dc12dfbaab4cd9bcf14e3908b26d824a1d19dd932bdb6c5d9e887e059924 size 3615
+DIST vmd-1.8.3.src.tar.gz 8590337 RMD160 4ad1b58721005ef85f580f437c032c28f6d786f1 SHA256 36fb014004a765e54bbcd6608ef8738c808355268fd05dce618bc498d1f29c3e
+DIST vmd-1.8.4.src.tar.gz 12042149 RMD160 f49a68ae63a607cd37a58d894df2f22d7df55b85 SHA1 0a19265074bf8c2fa688485018204f452c8daf92 SHA256 29b046767f1efe90d5f3e3dbbdcd4988d5335d1db226405f5ddb9f171c811cac
+EBUILD vmd-1.8.3.ebuild 3615 RMD160 2bbeaf3e7ebb73ce89aa4c8d56269790f9900071 SHA1 52d65b2e66a0e0c5aa5fa5dfe3a68ced725f350d SHA256 afb3dc12dfbaab4cd9bcf14e3908b26d824a1d19dd932bdb6c5d9e887e059924
 MD5 7b4f1380ec72e3ec6ab436d3c557e33b vmd-1.8.3.ebuild 3615
 RMD160 2bbeaf3e7ebb73ce89aa4c8d56269790f9900071 vmd-1.8.3.ebuild 3615
 SHA256 afb3dc12dfbaab4cd9bcf14e3908b26d824a1d19dd932bdb6c5d9e887e059924 vmd-1.8.3.ebuild 3615
-EBUILD vmd-1.8.4.ebuild 3744 RMD160 feaaa172c06211db51b474f60cc8abfc97aef4ea SHA1 124718556e8d5aabb6fc0479994095bfbdef1a70 SHA256 bcf706a28add41d94d5ac2120d448c8210203f67fada754161f116955bc24d8b size 3744
+EBUILD vmd-1.8.4-r1.ebuild 4003 RMD160 64ef2882391b5b051e1fea41ee4fd6e9e7607d4c SHA1 77dcb634ec0bcd6b82a1cd9c22b4e4a6624c0aa0 SHA256 4914216543216e69c2bffc4dca6539ed83119cf14e353dbfa1922923163dd728
+MD5 36562b0ecc187afe09e61581d116f694 vmd-1.8.4-r1.ebuild 4003
+RMD160 64ef2882391b5b051e1fea41ee4fd6e9e7607d4c vmd-1.8.4-r1.ebuild 4003
+SHA256 4914216543216e69c2bffc4dca6539ed83119cf14e353dbfa1922923163dd728 vmd-1.8.4-r1.ebuild 4003
+EBUILD vmd-1.8.4.ebuild 3744 RMD160 feaaa172c06211db51b474f60cc8abfc97aef4ea SHA1 124718556e8d5aabb6fc0479994095bfbdef1a70 SHA256 bcf706a28add41d94d5ac2120d448c8210203f67fada754161f116955bc24d8b
 MD5 e494359bcb14b7fe3f295f118c7c5f7b vmd-1.8.4.ebuild 3744
 RMD160 feaaa172c06211db51b474f60cc8abfc97aef4ea vmd-1.8.4.ebuild 3744
 SHA256 bcf706a28add41d94d5ac2120d448c8210203f67fada754161f116955bc24d8b vmd-1.8.4.ebuild 3744
-MISC ChangeLog 939 RMD160 b5719bf4b4bb3962e688df57c28fa27c3bd493cc SHA1 c4792eede8148ca5043b7c074ee50dac15eafe5e SHA256 4066a3bb2b4d5b20de47823571dd182a5ba73dc6090681d2a016c7414dbeba77 size 939
-MD5 64c65ecfa7cd9c04af88da4d5cd3fa66 ChangeLog 939
-RMD160 b5719bf4b4bb3962e688df57c28fa27c3bd493cc ChangeLog 939
-SHA256 4066a3bb2b4d5b20de47823571dd182a5ba73dc6090681d2a016c7414dbeba77 ChangeLog 939
-MISC metadata.xml 272 RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 SHA1 960809f50e770bf2df44dda2557cf62ab9190c13 SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 size 272
+MISC ChangeLog 1229 RMD160 fa7f1f1acc169a70f18f1faf87d5a6f7ed17646a SHA1 d2844ac4d7f7e45a2789173630d82ba181d2efda SHA256 182f9841c7a11736c557e2dfcd13eb0e8379af462909710cf3433833abba270e
+MD5 49d306f9953121ef0e397b9ac10a070e ChangeLog 1229
+RMD160 fa7f1f1acc169a70f18f1faf87d5a6f7ed17646a ChangeLog 1229
+SHA256 182f9841c7a11736c557e2dfcd13eb0e8379af462909710cf3433833abba270e ChangeLog 1229
+MISC metadata.xml 272 RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 SHA1 960809f50e770bf2df44dda2557cf62ab9190c13 SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77
 MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272
 RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272
 SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272
@@ -37,10 +42,6 @@ SHA256 afb2b7701f35aeaedd2191351e44ba399d7c2b449edfd8b3d9adac47fd266734 files/di
 MD5 6938330c3067d798a3014e5b9808d45d files/digest-vmd-1.8.4 247
 RMD160 64861c785c0dc69121006bec5a4ee50b2680c15d files/digest-vmd-1.8.4 247
 SHA256 778a381e0c4131689eb531ef9eb3e2658318510fd68ee09d5f014c33159fd466 files/digest-vmd-1.8.4 247
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.4.3 (GNU/Linux)
-
-iD8DBQFEUrWyW78445TWHXcRAkpaAJ93zCVtiCwReIX0QKcrRnyhJBxdawCfddcl
-yWfsJSKW1Yg0a4AkGehtlrA=
-=xH9B
------END PGP SIGNATURE-----
+MD5 6938330c3067d798a3014e5b9808d45d files/digest-vmd-1.8.4-r1 247
+RMD160 64861c785c0dc69121006bec5a4ee50b2680c15d files/digest-vmd-1.8.4-r1 247
+SHA256 778a381e0c4131689eb531ef9eb3e2658318510fd68ee09d5f014c33159fd466 files/digest-vmd-1.8.4-r1 247
diff --git a/sci-chemistry/vmd/files/digest-vmd-1.8.4-r1 b/sci-chemistry/vmd/files/digest-vmd-1.8.4-r1
new file mode 100644
index 000000000000..9ea1e6202b57
--- /dev/null
+++ b/sci-chemistry/vmd/files/digest-vmd-1.8.4-r1
@@ -0,0 +1,3 @@
+MD5 3cf6f2e23898ace4ffe022115470ec28 vmd-1.8.4.src.tar.gz 12042149
+RMD160 f49a68ae63a607cd37a58d894df2f22d7df55b85 vmd-1.8.4.src.tar.gz 12042149
+SHA256 29b046767f1efe90d5f3e3dbbdcd4988d5335d1db226405f5ddb9f171c811cac vmd-1.8.4.src.tar.gz 12042149
diff --git a/sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch b/sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch
new file mode 100644
index 000000000000..d0d5e63bcf5b
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch
@@ -0,0 +1,28 @@
+diff -Naur plugins/paratool/paratool_readwrite.tcl plugins-new/paratool/paratool_readwrite.tcl
+--- plugins/paratool/paratool_readwrite.tcl	2006-04-05 18:53:03.000000000 -0400
++++ plugins-new/paratool/paratool_readwrite.tcl	2006-08-01 22:05:50.000000000 -0400
+@@ -651,12 +651,8 @@
+ ##########################################################
+ 
+ proc ::Paratool::load_basemolecule { file {file2 {}}} {
+-<<<<<<< paratool_readwrite.tcl
+-    puts "Files $file $file2"
+-=======
+    puts "Loading base molecule $file"
+ 
+->>>>>>> 1.20
+    save_viewpoint_orig
+    set newmolid [mol new $file]
+    if {[llength $file2]} {
+diff -Naur plugins/resptool/resptool.tcl plugins-new/resptool/resptool.tcl
+--- plugins/resptool/resptool.tcl	2005-12-20 11:08:16.000000000 -0500
++++ plugins-new/resptool/resptool.tcl	2006-08-01 22:06:00.000000000 -0400
+@@ -14,7 +14,7 @@
+ # * Clear selection button
+ 
+ package provide resptool 1.0
+-package require paratool
++#package require paratool
+ 
+ namespace eval ::RESPTool:: {
+   variable w
diff --git a/sci-chemistry/vmd/vmd-1.8.4-r1.ebuild b/sci-chemistry/vmd/vmd-1.8.4-r1.ebuild
new file mode 100644
index 000000000000..fcc3ccbbc917
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.4-r1.ebuild
@@ -0,0 +1,152 @@
+# 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-1.8.4-r1.ebuild,v 1.1 2006/08/13 17:48:01 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="~ppc ~x86"
+IUSE="hardened"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	|| ( x11-libs/libXft virtual/x11 )
+	virtual/opengl
+	x11-libs/fltk
+	sci-libs/netcdf
+	=dev-lang/tcl-8.4*
+	=dev-lang/tk-8.4*
+	>=dev-lang/python-2.3
+	sci-biology/stride
+	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 ${A}
+
+	# apply LINUX-arch patches to vmd configure
+	epatch "${FILESDIR}"/${P}-config-gentoo.patch
+	epatch "${FILESDIR}"/${P}-plugin-autopsf.patch
+	epatch "${FILESDIR}"/${P}-paratool.patch
+
+	# prepare the plugins 
+
+	cd "${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"
+
+	sed -e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-i ${S}/bin/vmd || die "failed setting up vmd wrapper script"
+
+	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 TCLINC="-I/usr/include" \
+		TCLLIB="-L/usr/$(get_libdir)/tcl8.4" || \
+		die "failed to build plugins"
+
+	# build vmd
+	cd "${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"
+
+	# export STRIDE_BIN so VMD find stride
+	echo "STRIDE_BIN=/usr/bin/stride" > ${T}/99${PN} || \
+		die "Failed to create vmd env file"
+	doenvd ${T}/99${PN} || die "Failed to install vmd env file"
+
+	# 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
+}
+