initial commit

.gitignore

@@ -0,0 +1,2 @@
+coot-0.6.1-20100127svn2740.tar.gz
+coot-reference-structures.tar.gz

__init__.py

@@ -0,0 +1 @@
+# File to allow this directory to be treated as a python package.

coot-configure.in.patch

@@ -0,0 +1,41 @@
+--- configure.in_orig	2010-01-27 16:15:51.387782244 -0800
++++ configure.in	2010-01-27 16:44:53.586783325 -0800
+@@ -132,13 +132,26 @@
+ AM_PATH_GLUT(, [echo You need the GLUT utility library; exit 1], AC_MSG_ERROR([Cannot find proper GLUT version]))
+ 
+ dnl Check for MMDB.
+-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
++# AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
+ 
+-AM_WITH_MMDBSSM
++# AM_WITH_MMDBSSM
++PKG_CHECK_MODULES(MMDB, mmdb >= 1.12)
++MMDB_CXXFLAGS="-DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP $MMDB_CFLAGS"
++AC_SUBST(MMDB_CXXFLAGS)
++AC_SUBST(MMDB_LIBS)
++
++PKG_CHECK_MODULES(MMDBSSM, ssm >= 0.1)
++MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB $MMDBSSM_CFLAGS"
++AC_SUBST(MMDBSSM_CXXFLAGS)
++AC_SUBST(MMDBSSM_LIBS)
+ 
+ dnl Check for Clipper.  we exit if clipper is not found.
+ #
+-AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
++# AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
++PKG_CHECK_MODULES(CLIPPER, clipper >= 2.0)
++CLIPPER_CXXFLAGS=$CLIPPER_CFLAGS
++AC_SUBST(CLIPPER_CXXFLAGS)
++AC_SUBST(CLIPPER_LIBS)
+ 
+ # we set default coot_guile to true
+ coot_guile=true
+@@ -146,7 +159,7 @@
+ if test x$coot_guile = xtrue ; then
+    GUILE_FLAGS
+    AM_GUILE_LIB
+-   AM_GUILE_GUI
++#   AM_GUILE_GUI
+    GUILE_VERSION=$($ac_cv_path_GUILE_CONFIG --version  2>&1 | awk '{split($NF, arr, "[[.]]");  print arr[[1]] "." arr[[2]]}')
+    echo checking GUILE_VERSION: $GUILE_VERSION
+    AC_SUBST(GUILE_VERSION)

coot-user-manual.texi.patch

@@ -0,0 +1,24 @@
+--- doc/user-manual.texi_orig	2010-01-27 16:23:57.630783062 -0800
++++ doc/user-manual.texi	2010-01-27 16:50:48.507782342 -0800
+@@ -4470,10 +4470,10 @@
+ @c note that texi2html (and makeinfo) requires that this c-interface texi file be in the 
+ @c same directory as this file (user-manual.texi) NOT the directory that 
+ @c texi2html is run in.
+-@include c-interface.h.texi
++@include c-interface_8h.texi
+ @node    More Scripting Functions
+ @chapter More Scripting Functions
+-@include cc-interface.hh.texi
++@c @include cc-interface.hh.texi
+ 
+ 
+ 
+@@ -4491,7 +4491,7 @@
+ @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node
+ @c
+ 
+-@include ../../coot/scheme/coot-scheme-functions.texi
++@c @include ../../coot/scheme/coot-scheme-functions.texi
+ 
+ 
+ 

coot.desktop

@@ -0,0 +1,10 @@
+[Desktop Entry]
+Encoding=UTF-8
+Name=coot
+GenericName=coot
+Comment=macromolecular model builder
+Exec=coot
+Icon=coot
+Terminal=false
+Type=Application
+Categories=Graphics;Science

coot.in

@@ -0,0 +1,62 @@
+#!/bin/sh
+# -*-shell-script-*-
+# coot wrapper script 
+# Copyright 2004, 2005, 2006, 2007 University of York
+# written by Paul Emsley
+
+COOT_PREFIX="@prefix@"
+current_exe_dir="@bindir@"
+
+coot_real=$current_exe_dir/coot-real
+# echo coot-real is at $coot_real
+
+# ----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
+# If the COOT_PREFIX is correct, then these should not need modification
+# i.e.  nothing below here need be changed.
+# ----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
+# 
+prefix=$COOT_PREFIX
+
+SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib
+COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme
+COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb
+COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps
+COOT_DATA_DIR=$COOT_PREFIX/share/coot
+COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc
+COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures
+COOT_PYTHON_DIR=
+COOT_REFMAC_LIB_DIR=
+
+PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR
+
+GUILE_WARN_DEPRECATED=no
+
+if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then 
+    GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH
+    export GUILE_LOAD_PATH
+fi
+
+# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH
+
+export SYMINFO
+export COOT_PREFIX
+export COOT_STANDARD_RESIDUES
+export COOT_REFMAC_LIB_DIR
+export COOT_PYTHON_DIR
+export PYTHONPATH
+export COOT_SCHEME_DIR
+export COOT_REF_STRUCTS
+export COOT_RESOURCES_FILE
+export COOT_PIXMAPS_DIR
+export COOT_DATA_DIR
+
+echo $coot_real $*
+$coot_real $*
+status=$?
+
+if [ $status != 0 ] ; then
+    @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real
+fi 
+

coot.spec

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+%{!?python_sitelib: %define python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
+%define refmac_dictionary %(rpm -q --queryformat '%%{name}-%%{version}' refmac-dictionary)
+
+Name: coot
+Summary: The crystallographic object-oriented toolkit
+URL: http://www.biop.ox.ac.uk/coot/
+Version: 0.6.1
+Release: 3.20100127svn2740%{?dist}
+# source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown)
+License: GPLv3+ and LGPLv2+
+Group: Applications/Engineering
+# The source for this package was pulled from upstream's vcs.  Use the
+# following commands to generate the tarball:
+#  svn co -r 2740 http://coot.googlecode.com/svn/trunk/ coot-0.6.1
+#  tar cvzf coot-0.6.1-20100127svn2740.tar.gz coot-0.6.1
+Source0: coot-0.6.1-20100127svn2740.tar.gz
+Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz
+Source2: svn-revision.cc
+Source3: coot.in
+Source4: %{name}.png
+Source5: %{name}.desktop
+Source6: __init__.py
+Patch0: coot-configure.in.patch
+Patch1: coot-user-manual.texi.patch
+BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+BuildRequires: autoconf
+BuildRequires: automake
+BuildRequires: clipper-devel >= 2.1-7
+BuildRequires: desktop-file-utils
+BuildRequires: freeglut-devel
+BuildRequires: gsl-devel
+BuildRequires: gtk2-devel
+BuildRequires: gtkglext-devel
+BuildRequires: guile-devel
+BuildRequires: guile-lib
+BuildRequires: imlib-devel
+BuildRequires: libcurl-devel
+BuildRequires: libgnomecanvas-devel
+BuildRequires: libtool
+BuildRequires: mmdb-devel >= 1.19
+BuildRequires: python-devel
+BuildRequires: pygtk2-devel
+BuildRequires: refmac-dictionary
+BuildRequires: ssm-devel
+BuildRequires: swig
+%if 0%{?rhel}
+BuildRequires: tetex-latex
+%else
+BuildRequires: tex(latex)
+%endif
+BuildRequires: texinfo-tex
+Requires: refmac-dictionary
+
+%description
+
+Coot is a toolkit for Macromolecular Crystallography and
+model-building.  Coot uses professional (and free) widgets (with the
+GUI builder glade), mmdb, clipper, and OpenGL, together with a new
+approach to map contouring and importing/creation and other modeling
+and building operations.
+
+%package devel
+Summary: Header files and library for developing programs with coot
+Requires: %{name} = %{version}-%{release}
+Group: Development/Libraries
+
+%description devel
+
+This package contains libraries and header files needed for program
+development using the coot macromolecular model building package.
+
+%package doc
+Summary: documentation PDF files for coot
+Requires: %{name} = %{version}-%{release}
+Group: Applications/Engineering
+
+%description doc
+
+the coot-doc package contains information concerning the use and
+button/key shortcuts for the coot macromolecular model building
+package.
+
+%prep
+%setup -q -a 1
+%patch0 -p0
+%patch1 -p0
+
+cp %{SOURCE2} ./src/
+cp %{SOURCE3} ./src/
+
+# various cleanups
+rm src/coot_wrap_guile_pre.cc
+rm src/coot_wrap_python_pre.cc
+iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README
+find . -executable \( -name "*.cc" -o -name "*.cpp" -o -name "*.h" -o -name "*.hh" \) -exec chmod 644 {} \;
+
+aclocal -I macros
+libtoolize --automake --copy
+autoconf
+automake --copy --add-missing --gnu
+
+%build
+%configure --with-gtk2 --with-guile --with-python --with-pygtk --with-gtkcanvas-prefix=/usr --disable-static CPPFLAGS="-I/usr/include/mmdb -I/usr/include/ssm" CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing"
+
+sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
+sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
+
+make %{?_smp_mflags}
+pushd doc
+texi2pdf user-manual.texi
+make coot-keys-and-buttons.pdf
+popd
+
+%install
+rm -rf %{buildroot}
+make install DESTDIR=%{buildroot} INSTALL='install -p'
+
+mv reference-structures %{buildroot}%{_datadir}/coot/
+sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=%{python_sitelib}/coot|' src/coot
+sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=%{_datadir}/%{refmac_dictionary}|' src/coot
+install -p -m 755 src/coot %{buildroot}%{_bindir}/
+
+# remove unpackaged files from the buildroot
+rm -f %{buildroot}%{_libdir}/*.la
+
+# headers
+mkdir %{buildroot}%{_includedir}/coot
+mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/
+mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/
+
+# python stuff
+mkdir -p %{buildroot}%{python_sitelib}/coot
+mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/
+cp %{SOURCE6} %{buildroot}%{python_sitelib}/coot/
+chmod 644 %{buildroot}%{python_sitelib}/coot/coot.py
+
+# desktop file
+desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications %{SOURCE5}
+mkdir -p %{buildroot}%{_datadir}/pixmaps
+install -p -m 644 %{SOURCE4} %{buildroot}%{_datadir}/pixmaps/
+
+%clean
+rm -rf %{buildroot}
+
+%check
+# this fails - need to fix upstream
+# make check
+
+%post -p /sbin/ldconfig
+
+%postun -p /sbin/ldconfig
+
+%files
+%defattr(-,root,root,-)
+%doc AUTHORS README COPYING
+%{_bindir}/*
+# libccp4mg-utils.so* is LGPLv2+
+# libcoot-surface.so* is a mix of LGPLv2+ and GPLv3+
+# all others are GPLv3+ 
+%{_libdir}/*.so.*
+%{_datadir}/coot/
+%{_datadir}/applications/%{name}.desktop
+%{_datadir}/pixmaps/%{name}.png
+%{python_sitelib}/coot/
+
+%files devel
+%defattr(-,root,root,-)
+%{_libdir}/*.so
+%{_includedir}/coot/
+
+%files doc
+%defattr(-,root,root,-)
+%doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf
+
+%changelog
+* Thu Aug 05 2010 Tim Fenn <fenn@stanford.edu> - 0.6.1-3.20100127svn2740
+- fix file attr
+- add comment to make check error
+
+* Tue Jul 20 2010 Tim Fenn <fenn@stanford.edu> - 0.6.1-2.20100127svn2740
+- move some documentation to subpackage
+- add check section
+
+* Wed Jan 27 2010 Tim Fenn <fenn@stanford.edu> - 0.6.1-1.20100127svn2740
+- update to SVN 2740, 0.6.1 release
+- add curl buildrequires
+
+* Thu Dec 03 2009 Tim Fenn <fenn@stanford.edu> - 0.6-6.20091203svn2545
+- update to SVN 2545, 0.6 release
+
+* Mon Nov 30 2009 Tim Fenn <fenn@stanford.edu> - 0.6-5.20091130svn2528
+- fix texi, include user-manual
+- update to SVN 2528
+- remove net-http, guile-goosh and guile-gui
+
+* Wed Oct 07 2009 Tim Fenn <fenn@stanford.edu> - 0.6-4.20091007svn2404
+- update buildrequires
+- use tetex-latex on EL builds
+- update to SVN 2404 (fixes some licensing issues)
+
+* Mon Oct 05 2009 Tim Fenn <fenn@stanford.edu> - 0.6-3.20091005svn2400
+- update to SVN 2400
+
+* Wed Sep 23 2009 Tim Fenn <fenn@stanford.edu> - 0.6-2.20090920svn2334
+- edit summary
+- update upstream URL
+- make create_server.py non-executable
+- chmod src to 644
+
+* Sun Sep 20 2009 Tim Fenn <fenn@stanford.edu> - 0.6-1.20090920svn2334
+- update to 0.6
+- get source from VCS system
+
+* Wed Mar 25 2009 Tim Fenn <fenn@stanford.edu> - 0.5.2-3
+- fix summary
+- add additional licensing information
+- split guile-extras into original tarballs
+
+* Sat Mar 14 2009 Tim Fenn <fenn@stanford.edu> - 0.5.2-2
+- fix for desktop-file-install
+- gcc 4.4 patch
+
+* Mon Dec 15 2008 Tim Fenn <fenn@stanford.edu> - 0.5.2-1
+- update to 0.5.2
+
+* Thu Nov 27 2008 Tim Fenn <fenn@stanford.edu> - 0.5-3
+- use consistent buildroot
+- include gtkglext-devel, guile-lib, desktop-file-utils in buildrequires
+- remove pyobject2 in buildrequires
+
+* Tue Nov 18 2008 Tim Fenn <fenn@stanford.edu> - 0.5-2
+- enable guile
+- include extra guile modules
+
+* Mon Nov 17 2008 Tim Fenn <fenn@stanford.edu> - 0.5-1
+- initial build

sources

@@ -0,0 +1,2 @@
+ecf43a60294f660946f5a14b8bf98769  coot-0.6.1-20100127svn2740.tar.gz
+59df05751b1ab445a6517757a1ace302  coot-reference-structures.tar.gz

svn-revision.cc

@@ -0,0 +1,6 @@
+extern "C" {
+int svn_revision() { 
+   return  2740;
+}
+}
+