[gentoo-science] [PATCH] sci-chemistry/ghemical: Added ghemical package

[Reinis Danne]

Added patches from #212689, #232292 and #246414 to ebuilds for ghemical-2.95 and 2.98.
---
 sci-chemistry/ghemical/ChangeLog                   |   18 +++++
 sci-chemistry/ghemical/Manifest                    |   12 +++
 .../files/ghemical-2.95-g_threads-246414.patch     |   26 +++++++
 .../files/ghemical-2.95-import_export-212689.patch |   54 ++++++++++++++
 .../ghemical-2.95-libf2c_config_test-232292.patch  |   13 ++++
 .../files/ghemical-2.98-import_export-212689.patch |   54 ++++++++++++++
 .../ghemical-2.98-libf2c_config_test-232292.patch  |   13 ++++
 sci-chemistry/ghemical/files/ghemical-gcc43.patch  |   14 ++++
 sci-chemistry/ghemical/ghemical-2.95.ebuild        |   74 ++++++++++++++++++++
 sci-chemistry/ghemical/ghemical-2.98.ebuild        |   74 ++++++++++++++++++++
 sci-chemistry/ghemical/metadata.xml                |   21 ++++++
 11 files changed, 373 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/ghemical/ChangeLog
 create mode 100644 sci-chemistry/ghemical/Manifest
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-gcc43.patch
 create mode 100644 sci-chemistry/ghemical/ghemical-2.95.ebuild
 create mode 100644 sci-chemistry/ghemical/ghemical-2.98.ebuild
 create mode 100644 sci-chemistry/ghemical/metadata.xml

diff --git a/sci-chemistry/ghemical/ChangeLog b/sci-chemistry/ghemical/ChangeLog
new file mode 100644
index 0000000..012896a
--- /dev/null
+++ b/sci-chemistry/ghemical/ChangeLog
@@ -0,0 +1,18 @@
+# ChangeLog for sci-chemistry/ghemical
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ghemical-2.98 (06 Feb 2009)
+*ghemical-2.95 (06 Feb 2009)
+
+  06 Feb 2009; Reinis Danne <rei4dan@×××××.com>
+  +files/ghemical-2.95-g_threads-246414.patch,
+  +files/ghemical-2.95-import_export-212689.patch,
+  +files/ghemical-2.95-libf2c_config_test-232292.patch,
+  +files/ghemical-2.98-import_export-212689.patch,
+  +files/ghemical-2.98-libf2c_config_test-232292.patch,
+  +files/ghemical-gcc43.patch, +metadata.xml, +ghemical-2.95.ebuild,
+  +ghemical-2.98.ebuild:
+  Added patches from #212689, #232292 and #246414 to ebuilds for
+  ghemical-2.95 and 2.98.
+
diff --git a/sci-chemistry/ghemical/Manifest b/sci-chemistry/ghemical/Manifest
new file mode 100644
index 0000000..a281a40
--- /dev/null
+++ b/sci-chemistry/ghemical/Manifest
@@ -0,0 +1,12 @@
+AUX ghemical-2.95-g_threads-246414.patch 553 RMD160 d06e847c0c2f4c445b3e73b624cd81ccec4589b2 SHA1 d523d4e092aaa79581bffeb11283c685065117f0 SHA256 e5bf7ceed065218397b9611c24a390f0ed96ce485a29e945095092dbe38ef188
+AUX ghemical-2.95-import_export-212689.patch 1288 RMD160 abbbce698c8f2eff1e4c35224ccccd8e7411d20b SHA1 5edb4c1f951d0dc6724f78bf5b6a9a544f8c7be7 SHA256 fc487c38e8ac30c2936781aa194b57a2d7f5621ea9af484b7ab734b5dbd819bd
+AUX ghemical-2.95-libf2c_config_test-232292.patch 321 RMD160 366614a65c978602af23d7d8ed3c4135bc226ef5 SHA1 cca2e3cc88ec4d38c4e55a5c3a368e0a62a5cd25 SHA256 3497cdf758fac1aa207f1bb7fca9621e2145402ca346bc5406fff49b6d570a33
+AUX ghemical-2.98-import_export-212689.patch 1288 RMD160 abbbce698c8f2eff1e4c35224ccccd8e7411d20b SHA1 5edb4c1f951d0dc6724f78bf5b6a9a544f8c7be7 SHA256 fc487c38e8ac30c2936781aa194b57a2d7f5621ea9af484b7ab734b5dbd819bd
+AUX ghemical-2.98-libf2c_config_test-232292.patch 321 RMD160 366614a65c978602af23d7d8ed3c4135bc226ef5 SHA1 cca2e3cc88ec4d38c4e55a5c3a368e0a62a5cd25 SHA256 3497cdf758fac1aa207f1bb7fca9621e2145402ca346bc5406fff49b6d570a33
+AUX ghemical-gcc43.patch 403 RMD160 7ed2b8633e0ec98024e97417cd1751cea2a33a96 SHA1 bcb7336fddf379c202abc61a8423d5c9f9be8d91 SHA256 de2ed1a0190a5fb450c88217fa88c62b99c6243c3547776e0f806c1acd0b0630
+DIST ghemical-2.95.tar.gz 2062097 RMD160 866cb26b7980d9cdfc1f73ddc03240df583ded20 SHA1 ac9419292554103f2b9bc7be8dfc921906134351 SHA256 1083bd02aba1a73fe7008a2f23d1b974147ac95f34f7ef2f90d8d2f9a823e8cc
+DIST ghemical-2.98.tar.gz 2065429 RMD160 836e1ec7a45615b58aa4a369d2fc21f5d599fbf4 SHA1 d4212aefe12b4d1f98ce6859e0f0d0a658c64a5d SHA256 2163b321df97698487017d32df77fdf4a9afb385b60f93145fd161a277c7ae82
+EBUILD ghemical-2.95.ebuild 1916 RMD160 c7a1581f426a168184f921b2eec056c3d0bb40f5 SHA1 e8d04b780e343e1415124e30a77d5f54db7e0bee SHA256 48f3967160544ba1cc7a3482d231799e87ef22c5791d0da8101f196878c496c0
+EBUILD ghemical-2.98.ebuild 1903 RMD160 c07a4268703e34f60a0a44d9349840c2e45afa79 SHA1 4094546e55523b25b27c0f916e6f468bf75b3659 SHA256 a34a7731d61fa9a2c66d4d73ec92a59780ccd04cac5ae9d26b591d80e7d760bc
+MISC ChangeLog 677 RMD160 d2aa468f0f2e0661a23fcd9b15d220d08ef4f98d SHA1 857d6eeb3649eeaac8bb82c860d931449f56ff9f SHA256 c6abeb4834485ac321c5a32c6fe4c80785b45434ad8478dbc6727d0c7781a0ea
+MISC metadata.xml 917 RMD160 5ada96e4b3d836e6525a5613076ea6da69e5daec SHA1 bcaf353e9ba29dfa292785049d643f798e46f24a SHA256 3400c4d52b6b7864856cca423c808bbec063fe565bf570411283d66af3771a70
diff --git a/sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch b/sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch
new file mode 100644
index 0000000..7e2c594
--- /dev/null
+++ b/sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch
@@ -0,0 +1,26 @@
+--- src/gtk_main.cpp.orig	2007-05-23 14:21:19.000000000 +0300
++++ src/gtk_main.cpp	2008-11-11 17:53:02.000000000 +0200
+@@ -33,6 +33,13 @@
+ 
+ int main(int argc, char ** argv)
+ {
++#ifdef ENABLE_THREADS
++
++    g_thread_init(NULL);
++	gdk_threads_init();
++
++#endif	// ENABLE_THREADS
++
+ 	GError * error = NULL;
+ 	
+ 	GOptionContext * option_context = g_option_context_new("- a GTK2 molecular modelling program");
+@@ -46,9 +53,6 @@
+ 	
+ #ifdef ENABLE_THREADS
+ 	
+-	g_thread_init(NULL);
+-	gdk_threads_init();
+-	
+ 	gdk_threads_enter();
+ 	
+ #endif	// ENABLE_THREADS
diff --git a/sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch b/sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch
new file mode 100644
index 0000000..b643eb6
--- /dev/null
+++ b/sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch
@@ -0,0 +1,54 @@
+--- src/project.cpp	2007-08-16 11:20:00.000000000 +0200
++++ src/project.cpp	2008-11-10 21:39:15.000000000 +0200
+@@ -307,6 +307,12 @@
+ 	ifstream ifile;
+ 	ostringstream intermed;
+ 	file_trans translator;
++
++	// Store the current locale and switch to "C"
++	
++	static char my_num_locale[32] = "C";
++	strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL));
++	setlocale(LC_NUMERIC, "C");
+ 	
+ 	if (index == 0)		// Automatic detection
+ 	{
+@@ -328,7 +334,13 @@
+ 	}
+ 	
+ 	istringstream interInput(intermed.str());
+-	return ReadGPR((* this), interInput, false);
++	bool retval = ReadGPR((* this), interInput, false);
++
++	// Change back to the original locale
++	
++	setlocale(LC_NUMERIC, my_num_locale);
++
++	return retval;
+ }
+ 
+ bool project::ExportFile(const char * filename, int index)
+@@ -337,6 +349,12 @@
+ 	stringstream intermed;
+ 	file_trans translator;
+ 	
++	// Store the current locale and switch to "C"
++	
++	static char my_num_locale[32] = "C";
++	strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL));
++	setlocale(LC_NUMERIC, "C");
++
+ 	WriteGPR_v100((* this), intermed);		// this is for openbabel-1.100.2
+ 	istringstream interInput(intermed.str());
+ 	
+@@ -359,6 +377,10 @@
+ 		ofile.close();
+ 	}
+ 	
++	// Change back to the original locale
++	
++	setlocale(LC_NUMERIC, my_num_locale);
++
+ 	return true;
+ }
+ 
diff --git a/sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch b/sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch
new file mode 100644
index 0000000..c847e9e
--- /dev/null
+++ b/sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch
@@ -0,0 +1,13 @@
+--- configure.ac.orig	2008-07-17 22:34:51.000000000 -0400
++++ configure.ac	2008-07-17 22:35:56.000000000 -0400
+@@ -83,6 +83,9 @@
+ 
+ AC_CHECK_LIB(X11,XOpenDisplay,,[AC_MSG_ERROR([X11 library missing])])
+ 
++## Need libf2c for MOPAC
++AC_CHECK_LIB(f2c,i_len)
++
+ ## are the rest necessary???
+ 
+ AC_CHECK_LIB(Xmu,XmuDrawLogo)
+
diff --git a/sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch b/sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch
new file mode 100644
index 0000000..b643eb6
--- /dev/null
+++ b/sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch
@@ -0,0 +1,54 @@
+--- src/project.cpp	2007-08-16 11:20:00.000000000 +0200
++++ src/project.cpp	2008-11-10 21:39:15.000000000 +0200
+@@ -307,6 +307,12 @@
+ 	ifstream ifile;
+ 	ostringstream intermed;
+ 	file_trans translator;
++
++	// Store the current locale and switch to "C"
++	
++	static char my_num_locale[32] = "C";
++	strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL));
++	setlocale(LC_NUMERIC, "C");
+ 	
+ 	if (index == 0)		// Automatic detection
+ 	{
+@@ -328,7 +334,13 @@
+ 	}
+ 	
+ 	istringstream interInput(intermed.str());
+-	return ReadGPR((* this), interInput, false);
++	bool retval = ReadGPR((* this), interInput, false);
++
++	// Change back to the original locale
++	
++	setlocale(LC_NUMERIC, my_num_locale);
++
++	return retval;
+ }
+ 
+ bool project::ExportFile(const char * filename, int index)
+@@ -337,6 +349,12 @@
+ 	stringstream intermed;
+ 	file_trans translator;
+ 	
++	// Store the current locale and switch to "C"
++	
++	static char my_num_locale[32] = "C";
++	strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL));
++	setlocale(LC_NUMERIC, "C");
++
+ 	WriteGPR_v100((* this), intermed);		// this is for openbabel-1.100.2
+ 	istringstream interInput(intermed.str());
+ 	
+@@ -359,6 +377,10 @@
+ 		ofile.close();
+ 	}
+ 	
++	// Change back to the original locale
++	
++	setlocale(LC_NUMERIC, my_num_locale);
++
+ 	return true;
+ }
+ 
diff --git a/sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch b/sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch
new file mode 100644
index 0000000..c847e9e
--- /dev/null
+++ b/sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch
@@ -0,0 +1,13 @@
+--- configure.ac.orig	2008-07-17 22:34:51.000000000 -0400
++++ configure.ac	2008-07-17 22:35:56.000000000 -0400
+@@ -83,6 +83,9 @@
+ 
+ AC_CHECK_LIB(X11,XOpenDisplay,,[AC_MSG_ERROR([X11 library missing])])
+ 
++## Need libf2c for MOPAC
++AC_CHECK_LIB(f2c,i_len)
++
+ ## are the rest necessary???
+ 
+ AC_CHECK_LIB(Xmu,XmuDrawLogo)
+
diff --git a/sci-chemistry/ghemical/files/ghemical-gcc43.patch b/sci-chemistry/ghemical/files/ghemical-gcc43.patch
new file mode 100644
index 0000000..93557d4
--- /dev/null
+++ b/sci-chemistry/ghemical/files/ghemical-gcc43.patch
@@ -0,0 +1,14 @@
+--- src-orig/pangofont_wcl.cpp  2008-11-30 16:15:23.932475487 -0600
++++ src/pangofont_wcl.cpp       2008-11-30 16:16:09.620396370 -0600
+@@ -22,6 +22,10 @@
+ 
+ #include <gtk/gtkgl.h>
+ 
++#include <string.h>
++
++#include <cstdlib>
++using namespace std;
+ /*################################################################################################*/
+ 
+ pangofont_wcl::pangofont_wcl(ogl_camera * cam) :
+
diff --git a/sci-chemistry/ghemical/ghemical-2.95.ebuild b/sci-chemistry/ghemical/ghemical-2.95.ebuild
new file mode 100644
index 0000000..63b6fbd
--- /dev/null
+++ b/sci-chemistry/ghemical/ghemical-2.95.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils flag-o-matic autotools
+
+DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
+HOMEPAGE="http://bioinformatics.org/ghemical/"
+
+SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86"
+IUSE="threads openbabel seamonkey"
+RDEPEND="virtual/glut
+	virtual/glu
+	virtual/opengl
+	sci-chemistry/mpqc
+	x11-libs/libICE
+	x11-libs/libSM
+	x11-libs/libX11
+	x11-libs/libXext
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXt
+	x11-libs/pango
+	>=x11-libs/gtk+-2.6
+	>=x11-libs/gtkglext-1.0.5
+	>=gnome-base/libglade-2.4
+	>=sci-libs/libghemical-2.96
+	>=x11-libs/liboglappth-0.96
+	openbabel? ( >=sci-chemistry/openbabel-2 )
+	threads? ( >=dev-libs/glib-2.4 )"
+
+DEPEND="${RDEPEND}
+	>=dev-util/pkgconfig-0.15"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}/${P}-import_export-212689.patch" || die "Faild to apply ${P}-import_export-212689.patch"
+	epatch "${FILESDIR}/${P}-libf2c_config_test-232292.patch" || die "Failed to apply ${P}-libf2c_config_test-232292.patch"
+	epatch "${FILESDIR}/${P}-g_threads-246414.patch" || die "Failed to apply ${P}-g_threads-246414.patch"
+
+	eautoreconf
+}
+
+src_compile() {
+
+# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now.
+
+# Change the built-in help browser.
+	if use seamonkey ; then
+		sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!"
+	else
+		sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for seamonkey!"
+	fi
+
+	# For libf2c
+	append-ldflags -Xlinker -defsym -Xlinker MAIN__=main
+
+	econf \
+		$(use_enable openbabel) \
+		$(use_enable threads) \
+		|| die "configure failed"
+	emake || die "make failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-chemistry/ghemical/ghemical-2.98.ebuild b/sci-chemistry/ghemical/ghemical-2.98.ebuild
new file mode 100644
index 0000000..c07d72c
--- /dev/null
+++ b/sci-chemistry/ghemical/ghemical-2.98.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils flag-o-matic autotools
+
+DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
+HOMEPAGE="http://bioinformatics.org/ghemical/"
+
+SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86"
+IUSE="threads openbabel seamonkey"
+RDEPEND="virtual/glut
+	virtual/glu
+	virtual/opengl
+	sci-chemistry/mpqc
+	x11-libs/libICE
+	x11-libs/libSM
+	x11-libs/libX11
+	x11-libs/libXext
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXt
+	x11-libs/pango
+	>=x11-libs/gtk+-2.6
+	>=x11-libs/gtkglext-1.0.5
+	>=gnome-base/libglade-2.4
+	>=sci-libs/libghemical-2.96
+	>=x11-libs/liboglappth-0.96
+	openbabel? ( >=sci-chemistry/openbabel-2 )
+	threads? ( >=dev-libs/glib-2.4 )"
+
+DEPEND="${RDEPEND}
+	>=dev-util/pkgconfig-0.15"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}/ghemical-gcc43.patch" || die "Failed to apply ghemical-gcc43.patch"
+	epatch "${FILESDIR}/${P}-import_export-212689.patch" || die "Failed to apply ${P}-import_export-212689.patch"
+	epatch "${FILESDIR}/${P}-libf2c_config_test-232292.patch" || die "Failed to apply ${P}-libf2c_config_test-232292.patch"
+
+	eautoreconf
+}
+
+src_compile() {
+
+# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now.
+
+# Change the built-in help browser.
+	if use seamonkey ; then
+		sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!"
+	else
+		sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for seamonkey!"
+	fi
+
+	# For libf2c
+	append-ldflags -Xlinker -defsym -Xlinker MAIN__=main
+
+	econf \
+		$(use_enable openbabel) \
+		$(use_enable threads) \
+		|| die "configure failed"
+	emake || die "make failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-chemistry/ghemical/metadata.xml b/sci-chemistry/ghemical/metadata.xml
new file mode 100644
index 0000000..9627988
--- /dev/null
+++ b/sci-chemistry/ghemical/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<longdescription>
+Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models 
+and molecular mechanics models (there is an experimental Tripos 5.2-like force 
+field for organic molecules). Also a tool for reduced protein models is 
+included. Geometry optimization, molecular dynamics and a large set of 
+visualization tools are currently available.
+</longdescription>
+<use>
+  <flag name='gamess'>Add GAMESS interface for QM/MM
+    (<pkg>sci-chemistry/gamess</pkg>)</flag>
+  <flag name='mopac7'>Apply compilation fix for
+    <pkg>sci-chemistry/mopac7</pkg> support</flag>
+  <flag name='openbabel'>Use <pkg>sci-chemistry/openbabel</pkg> for file
+    conversions</flag>
+  <flag name='toolbar'>Build the shortcuts toolbar</flag>
+</use>
+</pkgmetadata>
-- 
1.6.0.6