sci-chemistry/coot -- Version Bump

(Portage version: 2.2_rc62/git/Linux i686)
 (Signed Manifest commit)

8 files changed, 621 insertions, 15 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 117e0c9af..af4a3263e 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-chemistry/coot
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*coot-0.6.1 (30 Jan 2010)
+
+  30 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net> coot-0.6.ebuild,
+  +coot-0.6.1.ebuild, coot-9999.ebuild, +files/fix-namespace-error.patch,
+  +files/glib.m4, +files/gtk.m4:
+  Version bump
+
   14 Dec 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   -files/0.5.2-as-needed.patch, -files/0.6_pre1-gcc4.4.patch,
   -files/9999-as-needed.patch, -files/9999-test-rama.patch,
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index f2393aed6..2f1421ee4 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -2,16 +2,22 @@
 Hash: SHA1
 
 AUX 9999-rappermc.patch 477 RMD160 5d67f80be6e4bc303d7999cfa645ea36dbfc834a SHA1 4c2ff98125b6a4664f77e8b5f39f6a9a1ac72622 SHA256 83dd4ddda627baec52a0754117741d97e7b2c61e42813a314b258db93903d7c0
+AUX fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
+AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
+AUX gtk.m4 8516 RMD160 3860fe211902d5b9290f0a70e7d75ebec6b0ec67 SHA1 98b93b820423a52ebd80e3f1822a8f2bd4b3f15d SHA256 4eb6e0bb2c6863139d1fb4ca2d1d0f0ef07e3a85fdbb5ba98d03373f610f0c37
+DIST coot-0.6.1.tar.gz 12229005 RMD160 76cbf28320ff52f02b40164eea00e7ec8a6b6c2c SHA1 cdd74e394e07dc17b99f56fce7cf180a177d53d7 SHA256 7897eb62e1add5f8deddd16d24ffd9b4c763e784714cd47fa9777beb79f56066
 DIST coot-0.6.tar.gz 11929700 RMD160 6485a56f1d17b103e69b07b5fc128d266e83aa27 SHA1 ec3d486eda514e36bdbc99e8796484e584e4f851 SHA256 7700e7e758934ee5b4177c7bb8e1d7d564b838966dd3c77919fa08778627353b
-DIST greg-data.tar.gz 7853709 RMD160 8fda42be9d84cb4a6d6b8c270a15493b42b0ddf1 SHA1 2099dbc093ae9a5cefa8f4b2eee1a38d982fa1eb SHA256 33a0caf21253f9be3b3af284dbebd58ac21628d353143d8533554452e3de25c6
-EBUILD coot-0.6.ebuild 3483 RMD160 ccb7073bfe73955c85fef7d2a59f5cd2e8a9ce6f SHA1 c23507c9526ebd18353e976be4cf8090ed097733 SHA256 cf6dffd5cc517bc08de6f7235398428661ee3a993eea828c5c7dcdb178032761
-EBUILD coot-9999.ebuild 3394 RMD160 06b1b284ec65305879f75c5a8abbef898fda9d59 SHA1 a12e32ee875f85e4c5988959debc3e54207707ce SHA256 35e6ab2f67f821fccb454a5db150695d5735dd8a1f608deef2510668d4515c69
-MISC ChangeLog 7581 RMD160 8d77190a544ed26f0110666713249700b1d5afd1 SHA1 d341b51d52749896ce2d118e1fdec4daf4a17529 SHA256 0d4fdf313112b730e736b6ed6413a22a80f0f46a2a91782ebd0b62c6671f89bd
+DIST greg-data-0.6.1.tar.gz 7905778 RMD160 f4241cae9123ed6214e974e331937711029a057f SHA1 01961d1afda640c530aab59965e0fa7f865e7feb SHA256 06ea11dac94fcda590f100c64ce4aeaaab8e5ede694f3007d8a9d149a58d3019
+DIST greg-data.tar.gz 7905778 RMD160 f4241cae9123ed6214e974e331937711029a057f SHA1 01961d1afda640c530aab59965e0fa7f865e7feb SHA256 06ea11dac94fcda590f100c64ce4aeaaab8e5ede694f3007d8a9d149a58d3019
+EBUILD coot-0.6.1.ebuild 3539 RMD160 a74947e67a1ab51aa0c7693e6c4b3cf47698b5b7 SHA1 9edf8e2a0d5ec3104f2ce715faef97d623af5abf SHA256 243d49711a780aee9b7ae483717b1810d21aa71c9b6036ef0d0c6c415ceda3ea
+EBUILD coot-0.6.ebuild 3375 RMD160 761feaa33ea28492b25682a3ed5d039f3c3a2303 SHA1 2a8f7fe746b6e39642813e13a9a665ec551b68bc SHA256 a0d56b438ccbef7c3ff7384260ce9f2ac1c337530a5ff311333c60d4f76070e7
+EBUILD coot-9999.ebuild 3413 RMD160 c30fb0e5a1b3d7c08028cd363508ca82d9393d35 SHA1 a0d200ea5fe45da0b57c43c04905aa91e90a4cc3 SHA256 f4af2ac48160d092ac169f7297f48beef3966385c808503d938f36d4ec64875d
+MISC ChangeLog 7805 RMD160 71c13762b167f8db66f34350785fb7d6580df136 SHA1 42307985a94ff4a384bbda86bff2bea81b799a9a SHA256 05d8d5690349fc884f49d5fc8f6030eec793a855770fdf8bf33de1b311627880
 MISC metadata.xml 316 RMD160 845cc100ac244efa5f02595717b5da635f87d2f1 SHA1 c870d2c52c44dee3bab8623e5b6095266f400813 SHA256 64f6dbcd3bb41b26fd7897089cd60ddb93f1ea7d75f9531bca94f28b07e21b2f
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAksmqnkACgkQgAnW8HDreRZkLwCgo+uuwr8qYR7FPI4vGvOFaXvC
-DwQAnRjtv6lG0At4jbeDo71ZKHxzf4yO
-=ha3a
+iEYEARECAAYFAktkPkAACgkQgAnW8HDreRbAjQCgyecSrlax0bZc0p69W8j5FdRY
+dDYAnRdaya4lerByKYyOBGL8dib5xaB+
+=/fgo
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-0.6.1.ebuild b/sci-chemistry/coot/coot-0.6.1.ebuild
new file mode 100644
index 000000000..1c221f176
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.6.1.ebuild
@@ -0,0 +1,150 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit autotools base versionator
+
+MY_S2_PV=$(replace_version_separator 2 - ${PV})
+MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
+MY_S_P=${MY_S2_P}-${PR/r/revision-}
+MY_PV=${PV}
+MY_P=${PN}-${MY_PV}
+
+ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk"
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
+SRC_URI="
+	http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
+
+SLOT="0"
+LICENSE="GPL-3"
+#KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
+IUSE="test"
+
+SCIDEPS="
+	>=sci-libs/ccp4-libs-6.1
+	>=sci-libs/clipper-20090520
+	>=sci-libs/coot-data-2
+	>=sci-libs/gsl-1.3
+	sci-chemistry/reduce
+	sci-chemistry/refmac
+	sci-chemistry/probe"
+
+XDEPS="
+	gnome-base/libgnomecanvas
+	gnome-base/librsvg
+	media-libs/libpng
+	virtual/glut
+	>=x11-libs/gtk+-2.2
+	x11-libs/gtkglext"
+
+SCHEMEDEPS="
+	dev-scheme/net-http
+	dev-scheme/guile-gui
+	>=dev-scheme/guile-lib-0.1.6
+	dev-scheme/guile-www
+	=x11-libs/guile-gtk-2.1"
+
+RDEPEND="
+	${SCIDEPS}
+	${XDEPS}
+	${SCHEMEDEPS}
+	dev-python/pygtk
+	>=dev-libs/gmp-4.2.2-r2
+	>=net-misc/curl-7.19.6"
+DEPEND="${RDEPEND}
+	dev-lang/swig
+	test? ( dev-scheme/greg )"
+
+#S="${WORKDIR}/${MY_P}"
+#S="${WORKDIR}/${MY_S2_P}"
+
+PATCHES=(
+#	"${FILESDIR}"/link-against-guile-gtk-properly.patch
+#	"${FILESDIR}"/fix-namespace-error.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+
+	# Link against single-precision fftw
+	sed -i \
+		-e "s:lfftw:lsfftw:g" \
+		-e "s:lrfftw:lsrfftw:g" \
+		"${S}"/macros/clipper.m4
+
+	# So we don't need to depend on crazy old gtk and friends
+#	cp "${FILESDIR}"/*.m4 "${S}"/macros/
+
+	eautoreconf
+}
+
+src_configure() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix=/usr \
+		--with-clipper-prefix=/usr \
+		--with-mmdb-prefix=/usr \
+		--with-ssmlib-prefix=/usr \
+		--with-gtkgl-prefix=/usr \
+		--with-guile \
+		--with-python=/usr \
+		--with-guile-gtk \
+		--with-gtk2 \
+		--with-pygtk
+}
+
+src_compile() {
+	emake || die "emake failed"
+
+	cp "${S}"/src/coot_gtk2.py python/coot.py || die
+}
+
+src_test() {
+#	emake check || die
+
+	mkdir "${T}"/coot_test
+
+	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
+	export COOT_SCHEME_DIR="${S}/scheme/"
+	export COOT_RESOURCES_FILE="${S}/cootrc"
+	export COOT_PIXMAPS_DIR="${S}/pixmaps"
+	export COOT_DATA_DIR="${S}"
+	export COOT_PYTHON_DIR="${S}/python"
+	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
+	export PYTHONHOME=/usr
+	export CCP4_SCR="${T}"/coot_test
+
+	export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data
+
+	cat > command-line-greg.scm <<- EOF
+	(use-modules (ice-9 greg))
+		(set! greg-tools (list "greg-tests"))
+			(set! greg-debug #t)
+			(set! greg-verbose 5)
+			(let ((r (greg-test-run)))
+				(if r
+				(coot-real-exit 0)
+				(coot-real-exit 1)))
+	EOF
+
+	einfo "Running test with following paths ..."
+	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
+	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
+	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
+	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
+	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
+	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
+	einfo "PYTHONPATH $PYTHONPATH"
+	einfo "PYTHONHOME $PYTHONHOME"
+	einfo "CCP4_SCR ${CCP4_SCR}"
+
+	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+}
diff --git a/sci-chemistry/coot/coot-0.6.ebuild b/sci-chemistry/coot/coot-0.6.ebuild
index 8a6bf7bcc..37622eb34 100644
--- a/sci-chemistry/coot/coot-0.6.ebuild
+++ b/sci-chemistry/coot/coot-0.6.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: $
 
@@ -62,11 +62,6 @@ DEPEND="${RDEPEND}
 #S="${WORKDIR}/${MY_P}"
 S="${WORKDIR}/${MY_S2_P}"
 
-PATCHES=(
-	"${FILESDIR}"/link-against-guile-gtk-properly.patch
-	"${FILESDIR}"/fix-namespace-error.patch
-	)
-
 src_prepare() {
 	base_src_prepare
 
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 6e0cf03cd..6c6433833 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.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: $
 
@@ -35,6 +35,7 @@ SCIDEPS="
 XDEPS="
 	gnome-base/libgnomecanvas
 	gnome-base/librsvg
+	media-libs/libpng
 	virtual/glut
 	>=x11-libs/gtk+-2.2
 	x11-libs/gtkglext"
diff --git a/sci-chemistry/coot/files/fix-namespace-error.patch b/sci-chemistry/coot/files/fix-namespace-error.patch
new file mode 100644
index 000000000..5bf8a2d4b
--- /dev/null
+++ b/sci-chemistry/coot/files/fix-namespace-error.patch
@@ -0,0 +1,52 @@
+--- coot-utils/coot-coord-utils.cc.orig	2007-11-14 09:38:31.000000000 -0800
++++ coot-utils/coot-coord-utils.cc	2007-11-14 09:44:50.000000000 -0800
+@@ -395,28 +395,30 @@
+    return SelHnd;
+ }
+ 
+-std::ostream& coot::operator<< (std::ostream& s, const coot::atom_spec_t &spec) {
++namespace coot {
++   std::ostream& operator<< (std::ostream& s, const atom_spec_t &spec) {
+ 
+-   s << "[spec: ";
+-   s << "\"";
+-   s << spec.chain;
+-   s << "\" ";
+-   s << spec.resno;
+-   s << " ";
+-   s << "\"";
+-   s << spec.insertion_code;
+-   s << "\"";
+-   s << " ";
+-   s << "\"";
+-   s  << spec.atom_name;
+-   s << "\"";
+-   s << " ";
+-   s << "\"";
+-   s << spec.alt_conf;
+-   s << "\"]";
++      s << "[spec: ";
++      s << "\"";
++      s << spec.chain;
++      s << "\" ";
++      s << spec.resno;
++      s << " ";
++      s << "\"";
++      s << spec.insertion_code;
++      s << "\"";
++      s << " ";
++      s << "\"";
++      s  << spec.atom_name;
++      s << "\"";
++      s << " ";
++      s << "\"";
++      s << spec.alt_conf;
++      s << "\"]";
+ 
+-   return s;
++      return s;
+ 
++   }
+ }
+ 
+ 
diff --git a/sci-chemistry/coot/files/glib.m4 b/sci-chemistry/coot/files/glib.m4
new file mode 100644
index 000000000..b3c632b0e
--- /dev/null
+++ b/sci-chemistry/coot/files/glib.m4
@@ -0,0 +1,196 @@
+# Configure paths for GLIB
+# Owen Taylor     97-11-3
+
+dnl AM_PATH_GLIB([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]])
+dnl Test for GLIB, and define GLIB_CFLAGS and GLIB_LIBS, if "gmodule" or 
+dnl gthread is specified in MODULES, pass to glib-config
+dnl
+AC_DEFUN([AM_PATH_GLIB],
+[dnl 
+dnl Get the cflags and libraries from the glib-config script
+dnl
+AC_ARG_WITH(glib-prefix,[  --with-glib-prefix=PFX   Prefix where GLIB is installed (optional)],
+            glib_config_prefix="$withval", glib_config_prefix="")
+AC_ARG_WITH(glib-exec-prefix,[  --with-glib-exec-prefix=PFX Exec prefix where GLIB is installed (optional)],
+            glib_config_exec_prefix="$withval", glib_config_exec_prefix="")
+AC_ARG_ENABLE(glibtest, [  --disable-glibtest       Do not try to compile and run a test GLIB program],
+		    , enable_glibtest=yes)
+
+  if test x$glib_config_exec_prefix != x ; then
+     glib_config_args="$glib_config_args --exec-prefix=$glib_config_exec_prefix"
+     if test x${GLIB_CONFIG+set} != xset ; then
+        GLIB_CONFIG=$glib_config_exec_prefix/bin/glib-config
+     fi
+  fi
+  if test x$glib_config_prefix != x ; then
+     glib_config_args="$glib_config_args --prefix=$glib_config_prefix"
+     if test x${GLIB_CONFIG+set} != xset ; then
+        GLIB_CONFIG=$glib_config_prefix/bin/glib-config
+     fi
+  fi
+
+  for module in . $4
+  do
+      case "$module" in
+         gmodule) 
+             glib_config_args="$glib_config_args gmodule"
+         ;;
+         gthread) 
+             glib_config_args="$glib_config_args gthread"
+         ;;
+      esac
+  done
+
+  AC_PATH_PROG(GLIB_CONFIG, glib-config, no)
+  min_glib_version=ifelse([$1], ,0.99.7,$1)
+  AC_MSG_CHECKING(for GLIB - version >= $min_glib_version)
+  no_glib=""
+  if test "$GLIB_CONFIG" = "no" ; then
+    no_glib=yes
+  else
+    GLIB_CFLAGS=`$GLIB_CONFIG $glib_config_args --cflags`
+    GLIB_LIBS=`$GLIB_CONFIG $glib_config_args --libs`
+    glib_config_major_version=`$GLIB_CONFIG $glib_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
+    glib_config_minor_version=`$GLIB_CONFIG $glib_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
+    glib_config_micro_version=`$GLIB_CONFIG $glib_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
+    if test "x$enable_glibtest" = "xyes" ; then
+      ac_save_CFLAGS="$CFLAGS"
+      ac_save_LIBS="$LIBS"
+      CFLAGS="$CFLAGS $GLIB_CFLAGS"
+      LIBS="$GLIB_LIBS $LIBS"
+dnl
+dnl Now check if the installed GLIB is sufficiently new. (Also sanity
+dnl checks the results of glib-config to some extent
+dnl
+      rm -f conf.glibtest
+      AC_TRY_RUN([
+#include <glib.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+int 
+main ()
+{
+  int major, minor, micro;
+  char *tmp_version;
+
+  system ("touch conf.glibtest");
+
+  /* HP/UX 9 (%@#!) writes to sscanf strings */
+  tmp_version = g_strdup("$min_glib_version");
+  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
+     printf("%s, bad version string\n", "$min_glib_version");
+     exit(1);
+   }
+
+  if ((glib_major_version != $glib_config_major_version) ||
+      (glib_minor_version != $glib_config_minor_version) ||
+      (glib_micro_version != $glib_config_micro_version))
+    {
+      printf("\n*** 'glib-config --version' returned %d.%d.%d, but GLIB (%d.%d.%d)\n", 
+             $glib_config_major_version, $glib_config_minor_version, $glib_config_micro_version,
+             glib_major_version, glib_minor_version, glib_micro_version);
+      printf ("*** was found! If glib-config was correct, then it is best\n");
+      printf ("*** to remove the old version of GLIB. You may also be able to fix the error\n");
+      printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n");
+      printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n");
+      printf("*** required on your system.\n");
+      printf("*** If glib-config was wrong, set the environment variable GLIB_CONFIG\n");
+      printf("*** to point to the correct copy of glib-config, and remove the file config.cache\n");
+      printf("*** before re-running configure\n");
+    } 
+  else if ((glib_major_version != GLIB_MAJOR_VERSION) ||
+	   (glib_minor_version != GLIB_MINOR_VERSION) ||
+           (glib_micro_version != GLIB_MICRO_VERSION))
+    {
+      printf("*** GLIB header files (version %d.%d.%d) do not match\n",
+	     GLIB_MAJOR_VERSION, GLIB_MINOR_VERSION, GLIB_MICRO_VERSION);
+      printf("*** library (version %d.%d.%d)\n",
+	     glib_major_version, glib_minor_version, glib_micro_version);
+    }
+  else
+    {
+      if ((glib_major_version > major) ||
+        ((glib_major_version == major) && (glib_minor_version > minor)) ||
+        ((glib_major_version == major) && (glib_minor_version == minor) && (glib_micro_version >= micro)))
+      {
+        return 0;
+       }
+     else
+      {
+        printf("\n*** An old version of GLIB (%d.%d.%d) was found.\n",
+               glib_major_version, glib_minor_version, glib_micro_version);
+        printf("*** You need a version of GLIB newer than %d.%d.%d. The latest version of\n",
+	       major, minor, micro);
+        printf("*** GLIB is always available from ftp://ftp.gtk.org.\n");
+        printf("***\n");
+        printf("*** If you have already installed a sufficiently new version, this error\n");
+        printf("*** probably means that the wrong copy of the glib-config shell script is\n");
+        printf("*** being found. The easiest way to fix this is to remove the old version\n");
+        printf("*** of GLIB, but you can also set the GLIB_CONFIG environment to point to the\n");
+        printf("*** correct copy of glib-config. (In this case, you will have to\n");
+        printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n");
+        printf("*** so that the correct libraries are found at run-time))\n");
+      }
+    }
+  return 1;
+}
+],, no_glib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
+       CFLAGS="$ac_save_CFLAGS"
+       LIBS="$ac_save_LIBS"
+     fi
+  fi
+  if test "x$no_glib" = x ; then
+     AC_MSG_RESULT(yes)
+     ifelse([$2], , :, [$2])     
+  else
+     AC_MSG_RESULT(no)
+     if test "$GLIB_CONFIG" = "no" ; then
+       echo "*** The glib-config script installed by GLIB could not be found"
+       echo "*** If GLIB was installed in PREFIX, make sure PREFIX/bin is in"
+       echo "*** your path, or set the GLIB_CONFIG environment variable to the"
+       echo "*** full path to glib-config."
+     else
+       if test -f conf.glibtest ; then
+        :
+       else
+          echo "*** Could not run GLIB test program, checking why..."
+          CFLAGS="$CFLAGS $GLIB_CFLAGS"
+          LIBS="$LIBS $GLIB_LIBS"
+          AC_TRY_LINK([
+#include <glib.h>
+#include <stdio.h>
+],      [ return ((glib_major_version) || (glib_minor_version) || (glib_micro_version)); ],
+        [ echo "*** The test program compiled, but did not run. This usually means"
+          echo "*** that the run-time linker is not finding GLIB or finding the wrong"
+          echo "*** version of GLIB. If it is not finding GLIB, you'll need to set your"
+          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
+          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
+          echo "*** is required on your system"
+	  echo "***"
+          echo "*** If you have an old version installed, it is best to remove it, although"
+          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"
+          echo "***"
+          echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that"
+          echo "*** came with the system with the command"
+          echo "***"
+          echo "***    rpm --erase --nodeps gtk gtk-devel" ],
+        [ echo "*** The test program failed to compile or link. See the file config.log for the"
+          echo "*** exact error that occured. This usually means GLIB was incorrectly installed"
+          echo "*** or that you have moved GLIB since it was installed. In the latter case, you"
+          echo "*** may want to edit the glib-config script: $GLIB_CONFIG" ])
+          CFLAGS="$ac_save_CFLAGS"
+          LIBS="$ac_save_LIBS"
+       fi
+     fi
+     GLIB_CFLAGS=""
+     GLIB_LIBS=""
+     ifelse([$3], , :, [$3])
+  fi
+  AC_SUBST(GLIB_CFLAGS)
+  AC_SUBST(GLIB_LIBS)
+  rm -f conf.glibtest
+])
diff --git a/sci-chemistry/coot/files/gtk.m4 b/sci-chemistry/coot/files/gtk.m4
new file mode 100644
index 000000000..beb1859e3
--- /dev/null
+++ b/sci-chemistry/coot/files/gtk.m4
@@ -0,0 +1,199 @@
+# Configure paths for GTK+
+# Owen Taylor     97-11-3
+AC_DEFUN([GTK_AC_DIVERT_BEFORE_HELP],
+[ifdef([m4_divert_text], [m4_divert_text([NOTICE],[$1])],
+       [ifdef([AC_DIVERT], [AC_DIVERT([NOTICE],[$1])],
+              [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)dnl
+$1
+AC_DIVERT_POP()])])])
+dnl AM_PATH_GTK([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]])
+dnl Test for GTK, and define GTK_CFLAGS and GTK_LIBS
+dnl
+AC_DEFUN([AM_PATH_GTK],
+[dnl 
+dnl Get the cflags and libraries from the gtk-config script
+dnl
+AC_ARG_WITH(gtk-prefix,[  --with-gtk-prefix=PFX   Prefix where GTK is installed (optional)],
+            gtk_config_prefix="$withval", gtk_config_prefix="")
+AC_ARG_WITH(gtk-exec-prefix,[  --with-gtk-exec-prefix=PFX Exec prefix where GTK is installed (optional)],
+            gtk_config_exec_prefix="$withval", gtk_config_exec_prefix="")
+AC_ARG_ENABLE(gtktest, [  --disable-gtktest       Do not try to compile and run a test GTK program],
+		    , enable_gtktest=yes)
+
+  for module in . $4
+  do
+      case "$module" in
+         gthread) 
+             gtk_config_args="$gtk_config_args gthread"
+         ;;
+      esac
+  done
+
+  if test x$gtk_config_exec_prefix != x ; then
+     gtk_config_args="$gtk_config_args --exec-prefix=$gtk_config_exec_prefix"
+     if test x${GTK_CONFIG+set} != xset ; then
+        GTK_CONFIG=$gtk_config_exec_prefix/bin/gtk-config
+     fi
+  fi
+  if test x$gtk_config_prefix != x ; then
+     gtk_config_args="$gtk_config_args --prefix=$gtk_config_prefix"
+     if test x${GTK_CONFIG+set} != xset ; then
+        GTK_CONFIG=$gtk_config_prefix/bin/gtk-config
+     fi
+  fi
+
+  AC_PATH_PROG(GTK_CONFIG, gtk-config, no)
+  min_gtk_version=ifelse([$1], ,0.99.7,$1)
+  AC_MSG_CHECKING(for GTK - version >= $min_gtk_version)
+  no_gtk=""
+  if test "$GTK_CONFIG" = "no" ; then
+    no_gtk=yes
+  else
+    GTK_CFLAGS=`$GTK_CONFIG $gtk_config_args --cflags`
+    GTK_LIBS=`$GTK_CONFIG $gtk_config_args --libs`
+    gtk_config_major_version=`$GTK_CONFIG $gtk_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
+    gtk_config_minor_version=`$GTK_CONFIG $gtk_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
+    gtk_config_micro_version=`$GTK_CONFIG $gtk_config_args --version | \
+           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
+    if test "x$enable_gtktest" = "xyes" ; then
+      ac_save_CFLAGS="$CFLAGS"
+      ac_save_LIBS="$LIBS"
+      CFLAGS="$CFLAGS $GTK_CFLAGS"
+      LIBS="$GTK_LIBS $LIBS"
+dnl
+dnl Now check if the installed GTK is sufficiently new. (Also sanity
+dnl checks the results of gtk-config to some extent
+dnl
+      rm -f conf.gtktest
+      AC_TRY_RUN([
+#include <gtk/gtk.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+int 
+main ()
+{
+  int major, minor, micro;
+  char *tmp_version;
+
+  system ("touch conf.gtktest");
+
+  /* HP/UX 9 (%@#!) writes to sscanf strings */
+  tmp_version = g_strdup("$min_gtk_version");
+  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
+     printf("%s, bad version string\n", "$min_gtk_version");
+     exit(1);
+   }
+
+  if ((gtk_major_version != $gtk_config_major_version) ||
+      (gtk_minor_version != $gtk_config_minor_version) ||
+      (gtk_micro_version != $gtk_config_micro_version))
+    {
+      printf("\n*** 'gtk-config --version' returned %d.%d.%d, but GTK+ (%d.%d.%d)\n", 
+             $gtk_config_major_version, $gtk_config_minor_version, $gtk_config_micro_version,
+             gtk_major_version, gtk_minor_version, gtk_micro_version);
+      printf ("*** was found! If gtk-config was correct, then it is best\n");
+      printf ("*** to remove the old version of GTK+. You may also be able to fix the error\n");
+      printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n");
+      printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n");
+      printf("*** required on your system.\n");
+      printf("*** If gtk-config was wrong, set the environment variable GTK_CONFIG\n");
+      printf("*** to point to the correct copy of gtk-config, and remove the file config.cache\n");
+      printf("*** before re-running configure\n");
+    } 
+#if defined (GTK_MAJOR_VERSION) && defined (GTK_MINOR_VERSION) && defined (GTK_MICRO_VERSION)
+  else if ((gtk_major_version != GTK_MAJOR_VERSION) ||
+	   (gtk_minor_version != GTK_MINOR_VERSION) ||
+           (gtk_micro_version != GTK_MICRO_VERSION))
+    {
+      printf("*** GTK+ header files (version %d.%d.%d) do not match\n",
+	     GTK_MAJOR_VERSION, GTK_MINOR_VERSION, GTK_MICRO_VERSION);
+      printf("*** library (version %d.%d.%d)\n",
+	     gtk_major_version, gtk_minor_version, gtk_micro_version);
+    }
+#endif /* defined (GTK_MAJOR_VERSION) ... */
+  else
+    {
+      if ((gtk_major_version > major) ||
+        ((gtk_major_version == major) && (gtk_minor_version > minor)) ||
+        ((gtk_major_version == major) && (gtk_minor_version == minor) && (gtk_micro_version >= micro)))
+      {
+        return 0;
+       }
+     else
+      {
+        printf("\n*** An old version of GTK+ (%d.%d.%d) was found.\n",
+               gtk_major_version, gtk_minor_version, gtk_micro_version);
+        printf("*** You need a version of GTK+ newer than %d.%d.%d. The latest version of\n",
+	       major, minor, micro);
+        printf("*** GTK+ is always available from ftp://ftp.gtk.org.\n");
+        printf("***\n");
+        printf("*** If you have already installed a sufficiently new version, this error\n");
+        printf("*** probably means that the wrong copy of the gtk-config shell script is\n");
+        printf("*** being found. The easiest way to fix this is to remove the old version\n");
+        printf("*** of GTK+, but you can also set the GTK_CONFIG environment to point to the\n");
+        printf("*** correct copy of gtk-config. (In this case, you will have to\n");
+        printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n");
+        printf("*** so that the correct libraries are found at run-time))\n");
+      }
+    }
+  return 1;
+}
+],, no_gtk=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
+       CFLAGS="$ac_save_CFLAGS"
+       LIBS="$ac_save_LIBS"
+     fi
+  fi
+  if test "x$no_gtk" = x ; then
+     AC_MSG_RESULT(yes)
+     ifelse([$2], , :, [$2])     
+  else
+     AC_MSG_RESULT(no)
+     if test "$GTK_CONFIG" = "no" ; then
+       echo "*** The gtk-config script installed by GTK could not be found"
+       echo "*** If GTK was installed in PREFIX, make sure PREFIX/bin is in"
+       echo "*** your path, or set the GTK_CONFIG environment variable to the"
+       echo "*** full path to gtk-config."
+     else
+       if test -f conf.gtktest ; then
+        :
+       else
+          echo "*** Could not run GTK test program, checking why..."
+          CFLAGS="$CFLAGS $GTK_CFLAGS"
+          LIBS="$LIBS $GTK_LIBS"
+          AC_TRY_LINK([
+#include <gtk/gtk.h>
+#include <stdio.h>
+],      [ return ((gtk_major_version) || (gtk_minor_version) || (gtk_micro_version)); ],
+        [ echo "*** The test program compiled, but did not run. This usually means"
+          echo "*** that the run-time linker is not finding GTK or finding the wrong"
+          echo "*** version of GTK. If it is not finding GTK, you'll need to set your"
+          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
+          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
+          echo "*** is required on your system"
+	  echo "***"
+          echo "*** If you have an old version installed, it is best to remove it, although"
+          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"
+          echo "***"
+          echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that"
+          echo "*** came with the system with the command"
+          echo "***"
+          echo "***    rpm --erase --nodeps gtk gtk-devel" ],
+        [ echo "*** The test program failed to compile or link. See the file config.log for the"
+          echo "*** exact error that occured. This usually means GTK was incorrectly installed"
+          echo "*** or that you have moved GTK since it was installed. In the latter case, you"
+          echo "*** may want to edit the gtk-config script: $GTK_CONFIG" ])
+          CFLAGS="$ac_save_CFLAGS"
+          LIBS="$ac_save_LIBS"
+       fi
+     fi
+     GTK_CFLAGS=""
+     GTK_LIBS=""
+     ifelse([$3], , :, [$3])
+  fi
+  AC_SUBST(GTK_CFLAGS)
+  AC_SUBST(GTK_LIBS)
+  rm -f conf.gtktest
+])