diff options
Diffstat (limited to 'sci-chemistry/coot')
-rw-r--r-- | sci-chemistry/coot/ChangeLog | 10 | ||||
-rw-r--r-- | sci-chemistry/coot/coot-0.3.1.ebuild | 97 | ||||
-rw-r--r-- | sci-chemistry/coot/files/0.3.1-as-needed.patch | 449 | ||||
-rw-r--r-- | sci-chemistry/coot/files/digest-coot-0.3.1 | 3 |
4 files changed, 558 insertions, 1 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/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 |