Bump to latest version. Now uses external, slotted sci-libs/clipper instead of the one in ccp4, because it needs newer versions than those contained in ccp4.

Package-Manager: portage-2.1.2.7

5 files changed, 574 insertions, 15 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 246c45742d97..dda1c784e249 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.9 2007/03/15 17:14:26 kugelfang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.10 2007/05/29 08:10:23 dberkholz Exp $
+
+*coot-0.3.1 (29 May 2007)
+
+  29 May 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/0.3.1-as-needed.patch, +coot-0.3.1.ebuild:
+  Bump to latest version. Now uses external, slotted sci-libs/clipper instead
+  of the one in ccp4, because it needs newer versions than those contained in
+  ccp4.
 
   15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> coot-0.1.2.ebuild:
   QA: Removed illegal use of ${ROOT}. Bug #168043
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 9339fa6db3cc..2e558b1d918e 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,15 +1,21 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
+AUX 0.3.1-as-needed.patch 18766 RMD160 00b020d46457f9e335b92c2f48088cdc950fce3a SHA1 bd2835ba0a974c8e01d6fa30f670827e6e72fc70 SHA256 cb395ba53839e16aa9e3248b2cfb16794c137730e02a41ca80927538717c4d83
+MD5 5c1b5db01f341e29a1c366002e3cc789 files/0.3.1-as-needed.patch 18766
+RMD160 00b020d46457f9e335b92c2f48088cdc950fce3a files/0.3.1-as-needed.patch 18766
+SHA256 cb395ba53839e16aa9e3248b2cfb16794c137730e02a41ca80927538717c4d83 files/0.3.1-as-needed.patch 18766
 DIST coot-0.1.2.tar.gz 2704638 RMD160 bb0ff46297fc7135b1bf31159bf41b18462b916c SHA1 66f4b13f37cab6537b454a0ad23050044eb4a95f SHA256 fcd2e5862ef57baffc19aa30b1bb48b5271baf0667cc72bf5ecd8a02911fe22a
+DIST coot-0.3.1.tar.gz 3708033 RMD160 8fefe5498171563d0ee660c87175b9af419f07ca SHA1 d612fde00e538682f64c4d204b27556fa742de5e SHA256 f13142b478a1bc9c94a242dd0bf18ac074707f7bd80bf72c8f0f906675099a34
 EBUILD coot-0.1.2.ebuild 2308 RMD160 b59de80ec0ab129eb3d739710d9f07388e6582e0 SHA1 d534ac54efd5b2a8be66b5e23e6992d49419d625 SHA256 6ce0825594abf6d21ac17cdc715cb2c9d522b809f798a7f1d70cc6cd8c392717
 MD5 d61e130fcb36e9fbc37937d6fce495c7 coot-0.1.2.ebuild 2308
 RMD160 b59de80ec0ab129eb3d739710d9f07388e6582e0 coot-0.1.2.ebuild 2308
 SHA256 6ce0825594abf6d21ac17cdc715cb2c9d522b809f798a7f1d70cc6cd8c392717 coot-0.1.2.ebuild 2308
-MISC ChangeLog 1405 RMD160 7fca95bbf66ea02495c0ffb9db08aaee88f83d43 SHA1 131c133cd6e55a5efa811b7505ab9b7f9ab643b2 SHA256 c4a8de37598c274a68ad59ece31282c752d16af24bf84bc98f184a3f9bccd554
-MD5 0dce95aa4ddb609579bb8ae90ed73f93 ChangeLog 1405
-RMD160 7fca95bbf66ea02495c0ffb9db08aaee88f83d43 ChangeLog 1405
-SHA256 c4a8de37598c274a68ad59ece31282c752d16af24bf84bc98f184a3f9bccd554 ChangeLog 1405
+EBUILD coot-0.3.1.ebuild 2508 RMD160 ede7cd9f32cee8ed8f2c8539fb3731082377db92 SHA1 db87799a1537d477fb1befb8d4f8ee643ab9c44a SHA256 e54de4b4cec064d789978266a54ec3152391fa21428a7478df1a1c830b0e2a2a
+MD5 0fa5deca240d0b4b7d6058bd7ba240d2 coot-0.3.1.ebuild 2508
+RMD160 ede7cd9f32cee8ed8f2c8539fb3731082377db92 coot-0.3.1.ebuild 2508
+SHA256 e54de4b4cec064d789978266a54ec3152391fa21428a7478df1a1c830b0e2a2a coot-0.3.1.ebuild 2508
+MISC ChangeLog 1705 RMD160 e2cec88bf42282eb4500601ec9c2bdc8c4eefb6a SHA1 6470fec30654d4898289a4656b448afca4a40dc6 SHA256 7fa461dbd49ba657cac4e7656f8f19657d6724469dae2c61dd2c0946f8bf2366
+MD5 8a64ccd25870ae8c67821fc2d9a85ef2 ChangeLog 1705
+RMD160 e2cec88bf42282eb4500601ec9c2bdc8c4eefb6a ChangeLog 1705
+SHA256 7fa461dbd49ba657cac4e7656f8f19657d6724469dae2c61dd2c0946f8bf2366 ChangeLog 1705
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -17,10 +23,6 @@ SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata
 MD5 39d53022c73d281c3d319c2c0ba3f4c6 files/digest-coot-0.1.2 235
 RMD160 dc807e2c87756c2731686576e75db488978a78e9 files/digest-coot-0.1.2 235
 SHA256 19a197b638681d05d7847a3563ef6cea23606b94a6f3056043ea775fcb88d515 files/digest-coot-0.1.2 235
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-=8LP1
------END PGP SIGNATURE-----
+MD5 563b4d4eead620811ec06a632ba3d435 files/digest-coot-0.3.1 235
+RMD160 d27b3e1c98f29bb401f14e77cb16f7e9c109d0fe files/digest-coot-0.3.1 235
+SHA256 2a6628adb6460117d951325f2e7bfc3ecaf3123ad537352b1f3d8f55df3fc1ce files/digest-coot-0.3.1 235
diff --git a/sci-chemistry/coot/coot-0.3.1.ebuild b/sci-chemistry/coot/coot-0.3.1.ebuild
new file mode 100644
index 000000000000..8c05e335cfcc
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.3.1.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.3.1.ebuild,v 1.1 2007/05/29 08:10:23 dberkholz Exp $
+
+inherit autotools eutils
+
+MY_PV=${PV/_pre/-pre-}
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+if [[ ${MY_PV} = *pre* ]]; then
+	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_P}.tar.gz"
+else
+	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
+fi
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=">=sci-libs/gsl-1.3
+	=dev-libs/glib-1.2*
+	=x11-libs/gtkglarea-1.2*
+	x11-libs/gtkglext
+	virtual/glut
+	virtual/opengl
+	sci-chemistry/ccp4
+	dev-lang/python
+	x11-libs/gtk-canvas
+	dev-lang/python
+	x11-libs/guile-gtk
+	dev-scheme/guile-gui
+	dev-scheme/net-http
+	dev-scheme/goosh
+	dev-scheme/guile-www
+	sci-libs/coot-data
+	sci-chemistry/reduce
+	sci-chemistry/probe
+	sci-libs/clipper"
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+
+	epatch "${FILESDIR}"/${PV}-as-needed.patch
+
+	# Link against single-precision fftw
+	sed -i \
+		-e "s:lfttw:lsfttw:g" \
+		-e "s:lrfttw:lsrfttw:g" \
+		"${S}"/macros/clipper.m4
+
+	# Fix where it looks for some binaries
+	sed -i \
+		-e "s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:/usr/bin/probe:g" \
+		-e "s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:/usr/bin/reduce:g" \
+		"${S}"/scheme/group-settings.scm
+
+	# Look for clipper slotted with '-2' suffix
+	sed -i \
+		-e "s~\(-lclipper[[:alnum:]-]*\)~\1-2~g" \
+		"${S}"/macros/clipper.m4 \
+		|| die "sed to find -2 slotted libraries failed"
+	grep 'include.*clipper' -rl . \
+		| xargs sed -i \
+			-e "s~\(include.*clipper\)/~\1-2/~g" \
+			|| die "sed to find -2 slotted headers failed"
+
+	cd "${S}"
+	AT_M4DIR="macros" eautoreconf
+}
+
+src_compile() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix=/usr \
+		--with-clipper-prefix=/usr \
+		--with-mmdb-prefix=/usr \
+		--with-ssmlib-prefix=/usr \
+		--with-guile=/usr \
+		--with-python=/usr \
+		|| die "econf failed"
+
+	# Parallel build's broken
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	make DESTDIR="${D}" install || die "install failed"
+
+	# Install misses this
+	insinto /usr/share/coot/python
+	doins "${S}"/src/coot.py
+}
diff --git a/sci-chemistry/coot/files/0.3.1-as-needed.patch b/sci-chemistry/coot/files/0.3.1-as-needed.patch
new file mode 100644
index 000000000000..cf334b77f2e7
--- /dev/null
+++ b/sci-chemistry/coot/files/0.3.1-as-needed.patch
@@ -0,0 +1,449 @@
+diff -urN coot-0.3.1.orig/analysis/Makefile.am coot-0.3.1/analysis/Makefile.am
+--- coot-0.3.1.orig/analysis/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/analysis/Makefile.am	2007-05-28 19:58:13.000000000 -0700
+@@ -9,6 +9,7 @@
+ 	$(MMDB_CXXFLAGS)
+ 
+ libcoot_analysis_la_SOURCES = bfkurt.cc
++libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
+ 
+ bin_PROGRAMS = bfactan
+ 
+@@ -16,7 +17,6 @@
+ 
+ bfactan_LDADD = \
+ 	libcoot-analysis.la 					\
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la 	\
+ 	$(top_builddir)/coot-utils/libcoot-utils.la 		\
+ 	$(top_builddir)/geometry/libcoot-geometry.la    	\
+ 	$(CLIPPER_LIBS) 	\
+diff -urN coot-0.3.1.orig/coords/Makefile.am coot-0.3.1/coords/Makefile.am
+--- coot-0.3.1.orig/coords/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/coords/Makefile.am	2007-05-29 00:42:28.000000000 -0700
+@@ -18,4 +18,6 @@
+ libcoot_coords_la_SOURCES =  Bond_lines.cc Cartesian.cc cos-sin.cc \
+ 		 mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \
+ 		 Bond_lines_ext.cc coot-close.cc
+-
++libcoot_coords_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-shelx.la \
++	$(top_builddir)/mini-mol/libcoot-mini-mol.la
+diff -urN coot-0.3.1.orig/coot-surface/Makefile.am coot-0.3.1/coot-surface/Makefile.am
+--- coot-0.3.1.orig/coot-surface/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/coot-surface/Makefile.am	2007-05-29 00:34:34.000000000 -0700
+@@ -6,3 +6,4 @@
+ 
+ libcoot_surface_la_SOURCES = \
+ 	 coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h
++libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la
+diff -urN coot-0.3.1.orig/coot-utils/Makefile.am coot-0.3.1/coot-utils/Makefile.am
+--- coot-0.3.1.orig/coot-utils/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/coot-utils/Makefile.am	2007-05-28 20:08:39.000000000 -0700
+@@ -20,9 +20,11 @@
+ 
+ # for pure coordinates (mmdb) things
+ libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc 
++libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
+ 
+ # shelx
+ libcoot_shelx_la_SOURCES = coot-shelx-ins.cc
++libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la
+ 
+ # for non-simple coordinates things
+ libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc
+@@ -32,21 +34,20 @@
+ 
+ # for map things that need mmdb, clipper, gsl and other things
+ libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc
++libcoot_map_heavy_la_LIBADD = $(GSL_LIBS)
+ 
+ noinst_PROGRAMS = testshelxreader testcootutils
+ 
+ testshelxreader_SOURCES = test-shelx-reader.cc
+ testshelxreader_LDADD = \
+ 	./libcoot-shelx.la \
+-	./libcoot-coord-utils.la \
+-	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	./libcoot-utils.la
+ 
+ testcootutils_SOURCES = test-utils.cc
+ testcootutils_LDADD = \
+ 	./libcoot-shelx.la \
+ 	./libcoot-coord-utils.la \
+ 	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	$(MMDB_LIBS)
+ 
+ 
+diff -urN coot-0.3.1.orig/geometry/Makefile.am coot-0.3.1/geometry/Makefile.am
+--- coot-0.3.1.orig/geometry/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/geometry/Makefile.am	2007-05-28 18:02:38.000000000 -0700
+@@ -15,6 +15,9 @@
+ libcoot_geometry_a_sources = protein-geometry.cc protein-geometry-mmdb.cc
+ 
+ libcoot_geometry_la_SOURCES = $(libcoot_geometry_a_sources)
++libcoot_geometry_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # libcoot_geometry_la_CXXFLAGS = -g -O1
+ 
+@@ -22,6 +25,4 @@
+ 
+ test_geometry_SOURCES = test-geometry.cc
+ 
+-test_geometry_LDADD = ./libcoot-geometry.la         \
+-        $(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++test_geometry_LDADD = ./libcoot-geometry.la
+diff -urN coot-0.3.1.orig/high-res/Makefile.am coot-0.3.1/high-res/Makefile.am
+--- coot-0.3.1.orig/high-res/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/high-res/Makefile.am	2007-05-28 19:52:12.000000000 -0700
+@@ -20,13 +20,16 @@
+ 
+ libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
+ 	sequence-assignment.cc
++libcoot_high_res_la_LIBADD = \
++	$(top_builddir)/ligand/libcoot-ligand.la \
++	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ noinst_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein
+ 
+ testatomgraph_SOURCES = test-atom-graph.cc
+ 
+ testatomgraph_LDADD =  libcoot-high-res.la                \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+@@ -34,90 +37,73 @@
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)			                  \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ testseqassignment_SOURCES = testseqassignment.cc
+ testseqassignment_LDADD = libcoot-high-res.la             \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ # tracehighres_LDFLAGS = -static 
+ tracehighres_SOURCES = trace-high-res.cc
+ tracehighres_LDADD = libcoot-high-res.la                  \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
+-
++	$(GSL_LIBS)
+ 
+ testseqalign_SOURCES = testseqalign.cc
+ 
+ # why do we need to link with all this (junk)?
+ testseqalign_LDADD = libcoot-high-res.la                  \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
+-
++	$(GSL_LIBS)
+ 
+ globularize_protein_SOURCES = globularize.cc
+ 
+ globularize_protein_LDADD = libcoot-high-res.la           \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
+-
++	$(GSL_LIBS)
+ 
+diff -urN coot-0.3.1.orig/ideal/Makefile.am coot-0.3.1/ideal/Makefile.am
+--- coot-0.3.1.orig/ideal/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/ideal/Makefile.am	2007-05-28 19:00:33.000000000 -0700
+@@ -24,6 +24,12 @@
+ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
+ 
+ libcoot_ideal_la_SOURCES = simple-restraint.cc  pepflip.cc regularize-minimol.cc
++libcoot_ideal_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la       \
++	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
++	$(top_builddir)/coot-utils/libcoot-shelx.la       \
++	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
++	$(GSL_LIBS)
+ 
+ noinst_PROGRAMS = test-indexing with-geometry with-map
+ # bin_PROGRAMS = 
+@@ -41,31 +47,20 @@
+ with_geometry_LDADD = \
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ with_map_LDADD =  \
+         ./libcoot-ideal.la                                 \
+ 	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+ 	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+-	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ test_indexing_LDADD = \
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+diff -urN coot-0.3.1.orig/ligand/Makefile.am coot-0.3.1/ligand/Makefile.am
+--- coot-0.3.1.orig/ligand/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/ligand/Makefile.am	2007-05-28 19:33:52.000000000 -0700
+@@ -23,6 +23,16 @@
+ libcoot_ligand_la_SOURCES = ligand.cc ligand-extras.cc  residue_by_phi_psi.cc \
+ 	wiggly-ligand.cc monomer-utils.cc dunbrack.cc chi-angles-autogen.cc   \
+ 	chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc
++libcoot_ligand_la_LIBADD = \
++	$(top_builddir)/ideal/libcoot-ideal.la       \
++	$(top_builddir)/coords/libcoot-coords.la           \
++	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
++	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
++	$(top_builddir)/db-main/libcoot-db-main.la         \
++	$(top_builddir)/coot-utils/libcoot-shelx.la        \
++	$(top_builddir)/geometry/libcoot-geometry.la       \
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
++	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
+ 
+ AM_CXXFLAGS = \
+ 	-DPKGDATADIR='"$(pkgdatadir)"' \
+@@ -40,35 +50,17 @@
+ test_random_SOURCES = test-random.cc
+ test_random_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+ 	$(top_builddir)/compat/libcoot-compat.la           \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ test_helix_placement_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+ 	$(top_builddir)/compat/libcoot-compat.la           \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -76,19 +68,10 @@
+ 
+ test_fffear_in_coot_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coords/libcoot-coords.la          \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+-	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-map-heavy.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -100,33 +83,15 @@
+ 
+ findligand_real_LDADD = \
+ 	./libcoot-ligand.la                          \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+-	$(top_builddir)/geometry/libcoot-geometry.la \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la     \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ findwaters_real_LDADD = \
+ 	./libcoot-ligand.la                               \
+-	$(top_builddir)/ideal/libcoot-ideal.la            \
+-	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -147,17 +112,8 @@
+ testdunbrack_SOURCES = testdunbrack.cc
+ 
+ testdunbrack_LDADD = ./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/geometry/libcoot-geometry.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+         $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ # lib coot-coords depends on mmdb, even though Cartesian doesn't
+diff -urN coot-0.3.1.orig/Makefile.am coot-0.3.1/Makefile.am
+--- coot-0.3.1.orig/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/Makefile.am	2007-05-29 00:46:45.000000000 -0700
+@@ -5,8 +5,8 @@
+ 
+ # see configure.in for po intl 
+ SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \
+-	skeleton ccp4mg-utils density-contour coords angles \
+-	mini-mol db-main  geometry  \
++	skeleton ccp4mg-utils density-contour mini-mol coords angles \
++	db-main  geometry  \
+ 	ideal ligand high-res build \
+ 	analysis sequence-view tw atom-utils src doc
+ 
+diff -urN coot-0.3.1.orig/mini-mol/Makefile.am coot-0.3.1/mini-mol/Makefile.am
+--- coot-0.3.1.orig/mini-mol/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/mini-mol/Makefile.am	2007-05-28 17:52:14.000000000 -0700
+@@ -13,8 +13,9 @@
+ testminimol_SOURCES = testminimol.cc
+ 
+ libcoot_mini_mol_la_SOURCES =  mini-mol.cc mini-mol-utils.cc
++libcoot_mini_mol_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
++	$(CLIPPER_LIBS)
+ 
+ testminimol_LDADD = libcoot-mini-mol.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	$(MMDB_LIBS)
+diff -urN coot-0.3.1.orig/tw/Makefile.am coot-0.3.1/tw/Makefile.am
+--- coot-0.3.1.orig/tw/Makefile.am	2007-05-28 17:08:04.000000000 -0700
++++ coot-0.3.1/tw/Makefile.am	2007-05-28 20:17:13.000000000 -0700
+@@ -20,15 +20,15 @@
+ include_HEADERS = coot-tw.hh
+ 
+ libcoot_tw_la_SOURCES = tw.cc
++libcoot_tw_la_LIBADD = \
++	$(GTKCANVAS_LIBS) \
++	@GTK_LIBS@
+ 
+ noinst_PROGRAMS = coot-tiddly
+ 
+ coot_tiddly_SOURCES = tiddly.cc
+ 
+-coot_tiddly_LDADD = libcoot-tw.la \
+-	$(GTKCANVAS_LIBS) \
+-	@GTK_LIBS@
+-
++coot_tiddly_LDADD = libcoot-tw.la
+ 
+ # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao
+ 
diff --git a/sci-chemistry/coot/files/digest-coot-0.3.1 b/sci-chemistry/coot/files/digest-coot-0.3.1
new file mode 100644
index 000000000000..524b354abf09
--- /dev/null
+++ b/sci-chemistry/coot/files/digest-coot-0.3.1
@@ -0,0 +1,3 @@
+MD5 574d14666659ab9f7be3e2d92585444a coot-0.3.1.tar.gz 3708033
+RMD160 8fefe5498171563d0ee660c87175b9af419f07ca coot-0.3.1.tar.gz 3708033
+SHA256 f13142b478a1bc9c94a242dd0bf18ac074707f7bd80bf72c8f0f906675099a34 coot-0.3.1.tar.gz 3708033