Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14733
Added Files:
coot-pre.info coot-pre.patch
Log Message:
coot variant to placate those demanding access to the latest features
--- NEW FILE: coot-pre.patch ---
diff -ruN coot-0.6.2-pre-1-orig/scheme/group-settings.scm
coot-0.6.2-pre-1/scheme/group-settings.scm
--- coot-0.6.2-pre-1-orig/scheme/group-settings.scm 2009-07-04
05:57:36.000000000 -0700
+++ coot-0.6.2-pre-1/scheme/group-settings.scm 2010-03-31 09:52:42.000000000
-0700
@@ -28,6 +28,7 @@
(set-browser-interface "firefox"))
(if (string=? os-type "Darwin")
+ (set-display-lists-for-maps 0)
(set-browser-interface "open")))
;; York setting for molprobity.
diff -ruN coot-0.6.2-pre-1-orig/scheme/povray.scm
coot-0.6.2-pre-1/scheme/povray.scm
--- coot-0.6.2-pre-1-orig/scheme/povray.scm 2009-07-04 05:57:34.000000000
-0700
+++ coot-0.6.2-pre-1/scheme/povray.scm 2010-03-31 09:54:43.000000000 -0700
@@ -14,7 +14,7 @@
(lambda ()
; this is directory that contains colors.inc
- (list (string-append "+L/sw/share/povray-" povray-version "/include")
+ (list (string-append "+L@PREFIX@/share/povray-" povray-version "/include")
"+FN16")))
;; Run provray using current displayed image and write .pov file to
diff -ruN coot-0.6.2-pre-1-orig/scheme/raster3d.scm
coot-0.6.2-pre-1/scheme/raster3d.scm
--- coot-0.6.2-pre-1-orig/scheme/raster3d.scm 2009-07-04 05:57:34.000000000
-0700
+++ coot-0.6.2-pre-1/scheme/raster3d.scm 2010-03-31 09:55:54.000000000
-0700
@@ -1,7 +1,7 @@
(define coot-r3d-file-name "coot.r3d")
(define coot-png-file-name "coot.png")
-(define coot-png-display-program "display")
+(define coot-png-display-program "open")
;; run raster3d
(define render-image
--- NEW FILE: coot-pre.info ---
Package: coot-pre
Version: 0.8-pre
Revision: 4747
SourceDirectory: coot-%v
Distribution: 10.6, 10.7, 10.8
GCC: 4.0
Source:
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/coot-%v-revision-%r.tar.gz
Source-MD5: 049a0af2bbeda5d4a9761c682f74c8a0
Source2:
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
Source2-MD5: 257ab90d44f1c877ada96720dbb87c13
###############################################################################
Description: Crystallographic molecular graphics
DescDetail: <<
This version contains "pre-release" features and will be updated upon request.
.
Coot stands for Crystallograhic Object Oriented Toolkit. It is a toolkit and
interactive molecular graphical display and manipulation program designed for
macromolecular crystallography. 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 (modelling) operations. The
mmdb, clipper, ssm and mccp4 libraries are provided in individual fink packages
that replace the now obsolete ccp4-onlylibs-dev fink package. On-line
documentation is available from the coot website accessed via the help menu,
or manually, via the web-site, (see below) and is updated regularly.
.
To have an Aqua-like Coot gtk+2 environment, issue the following command:
echo "include \"%p/share/themes/Glossy_P/gtk-2.0/gtkrc\"">~/.gtkrc-2.0
or simply create a file called ~/.gtkrc-2.0 and put this line in it:
include \"%p/share/themes/Glossy_P/gtk-2.0/gtkrc\"
.
Install povray and raster3d fink packages to use the F8 key for producing
ray-traced images. You may have to re-map the Spaces.app keybinding.
.
Coot now works with Zalman LCD hardware stereo and old-fashioned CRT hardware
stereo on OS X.
<<
###############################################################################
Recommends: povray, ccp4, raster3d
Conflicts: coot
Replaces: coot
BuildDepends: <<
fink (>= 0.24.12) ,
boost1.53.python27 (>= 1.53.0-1),
clipper-dev (>= 1:2.1.20130601-1),
libccp4-dev (>= 6.3.1-3) ,
mmdb-dev (>= 1.25.3-1) ,
ssm-dev (>= 1.3-1) ,
atk1 (>= 1.28.0-1) ,
cairo (>= 1.8.8-3) ,
expat1 ,
fftw | fftw-mpi ,
fontconfig2-dev (>= 2.8.0-4) ,
freetype219 (>= 2.3.12-1) ,
freeglut ,
giflib ,
glib2-dev (>= 2.22.0-1) ,
glitz ,
goocanvas (>= 0.15-2) ,
gmp5 ,
gsl ,
gtk+2 (>= 2.18.0-1) ,
gtk+2-dev (>= 2.18.0-1) ,
gtkglext1 ,
guile18 ,
guile18-dev ,
guile18-lib ,
guile18-gtk-dev (>= 2.0-10) ,
libart2 (>= 2.3.16-2) ,
libcurl4 ,
libgettext8-dev ,
libglade2 (>= 2.6.2-1) ,
libgnomecanvas2-dev (>= 2.20.0) ,
libjpeg8 ,
libpng15 ,
libtool2 ,
libxml2 ,
openldap24-dev ,
pango1-xft2-ft219-dev (>= 1.24.5-4) ,
pixman (>= 0.16.0-1) ,
pkgconfig (>= 0.23) ,
pygtk2-gtk-py27-dev ,
pygobject2-py27-dev ,
python27 ,
rdkit-dev (>= 2013.03.2-4) ,
rdkit (>= 2013.03.2-4) ,
swig ,
x11-dev
<<
#
Depends: <<
%N-shlibs (= %v-%r) ,
boost1.53.python27-shlibs (>= 1.53.0-1),
clipper-shlibs (>= 1:2.1.20130601-1),
libccp4-shlibs (>= 6.3.1-3) ,
libccp4-lib (>= 6.3.1-3) ,
mmdb-shlibs (>= 1.25.3-1) ,
ssm-shlibs (>= 1.3-1) ,
atk1-shlibs (>= 1.28.0-1) ,
fftw-shlibs | fftw-mpi-shlibs ,
freeglut-shlibs ,
gcc48-shlibs (>= 4.7.1-1000) ,
giflib-shlibs ,
glib2-shlibs (>= 2.22.0-1) ,
goocanvas-shlibs (>= 0.15-2) ,
gmp5-shlibs ,
gnome-themes-glossy-p ,
gsl-shlibs ,
gtk+2-shlibs (>= 2.18.0-1) ,
gtkglext1-shlibs ,
guile18 ,
guile18-gtk (>= 2.0-9) ,
guile18-gtk-shlibs (>= 2.0-9) ,
guile18-gui ,
guile18-lib ,
guile18-shlibs ,
libart2-shlibs ,
libcurl4-shlibs ,
libgettext8-shlibs ,
libgnomecanvas2-shlibs (>= 2.20.0),
libjpeg8-shlibs ,
libpng15-shlibs ,
librsvg2-gtk (>= 2.20.0-1) ,
libtiff-shlibs ,
libtool2-shlibs ,
librsvg2-gtk (>= 2.20.0-1) ,
libxml2-shlibs ,
openldap24-shlibs ,
pango1-xft2-ft219-shlibs (>= 1.24.5-4) ,
pygtk2-gtk-py27 ,
python27 ,
raster3d (>= 3.0-2-3) ,
rdkit-shlibs (>= 2013.03.2-4) ,
rdkit (>= 2013.03.2-4) ,
refmac (>=5.7.0032-1) ,
x11
<<
#
###############################################################################
BuildDependsOnly: false
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchFile: %n.patch
PatchFile-MD5: 847c69ea1ded1d4238b66ab4840a8141
PatchScript: <<
sed 's|@PREFIX@|%p|g' <%{PatchFile} | patch -p1
perl -pi -e 's|CXX\=\"libtool --mode\=link \$CXX\"|#CXX|g' configure
<<
###############################################################################
ConfigureParams: <<
--disable-openmp --with-ccp4=%p --with-mmdb=%p --with-ssmlib-prefix=%p
--with-clipper-prefix=%p \
--with-fftw=%p --with-gnomecanvas-prefix=%p --with-gtk2 --with-glut-prefix=%p
\
--with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
\
--with-gtkgl-prefix=%p --with-glib-prefix=%p --with-goocanvas-prefix=%p
\
--with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p
--with-enterprise-tools
<<
###############################################################################
CompileScript: <<
#!/bin/bash -efv
alias python=%p/bin/python2.7
export PYTHON=%p/bin/python2.7
export python=%p/bin/python2.7
export GUILE=%p/bin/guile-1.8
if [[ $(sw_vers -productVersion) < 10.6 ]]; then
export PATH=%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH
else
export
PATH=%p/var/lib/fink/path-prefix-10.6:%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH
fi
export SED=/usr/bin/sed
export GDK_USE_XFT='1'
export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
export
PKG_CONFIG_PATH=%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:${PKG_CONFIG_PATH}
rdkit_libs='-lMolChemicalFeatures -lDescriptors -lSubgraphs -lPartialCharges
-lForceFieldHelpers -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers
-lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lFileParsers
-lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral
-lboost_python ' \
rdkit_prefix=%p \
FLIBS="-L%p/lib -L%p/lib/rdkit" \
CPPFLAGS="-I%b/ccp4mg-utils -I%p/include/rdkit -I%b/lidia-core
-I%p/include/libglade-2.0/glade -I%p/include/libglade-2.0
-I%p/include/python2.7 -I%p/include/mmdb -I%p/include/ssm -I%p/include/ccp4
-I%p/include/clipper -I%p/include -I/usr/X11R6/include" \
LDFLAGS="-Wl,-dylib_file,%p/lib/libboost_python.dylib:%p/lib/python2.7/site-packages/libboost_python-1_53.dylib:%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
-L%p/lib -L/usr/lib -flat_namespace
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \
DYLD_LIBRARY_PATH="" \
RDKIT_CXXFLAGS=-I$rdkit_prefix/include/rdkit \
RDKIT_LIBS="\"-L%p/lib/rdkit $rdkit_libs\"" \
PYTHON=%p/bin/python2.7 ./configure %c
#
# Force coot to link to single-precision fftw libraries. The double-precision
libraries
# cause coot to crash.
find . -name "Makefile" -exec perl -pi -e 's|lrfftw |lsrfftw |g' '{}' \;
find . -name "Makefile" -exec perl -pi -e 's|lfftw |lsfftw |g' '{}' \;
perl -pi -e 's|include <rfftw.h>|include <srfftw.h>|g'
surface/CXXFFTSolventMap.h
#
if [[ $(sw_vers -productVersion) < 10.5 ]]; then
# Fix libtool compatibility issues
sed -e '/verstring=/s/\${wl}//g' < libtool > libtool.fixed
mv libtool.fixed libtool
fi
perl -pi -e 's|lidia_LDFLAGS = -Wl,--export-dynamic||g' lbg/Makefile
#
NUMPROC="$(sysctl -n hw.ncpu)"
# NUMPROC="1"
PYTHON=%p/bin/python2.7 make -j $NUMPROC
<<
###############################################################################
InstallScript: <<
#!/bin/zsh -efv
alias python=%p/bin/python2.7
export PYTHON=%p/bin/python2.7
export python=%p/bin/python2.7
export GUILE=%p/bin/guile-1.8
export PATH=$PWD/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
export SED=/usr/bin/sed
export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
#
NUMPROC="$(sysctl -n hw.ncpu)"
#NUMPROC="1"
make -j $NUMPROC install prefix=%i
#
# Clean up the 120 MB mess, which zsh makes so much fun:
/bin/rm -f **/*.o
# Add ancillary files to %i/share/coot:
#
mkdir -p %i/share/coot/etc
mkdir -p %i/share/coot/python
mkdir -p %i/bin
#
# Fix a bug with system python linking
if [[ -f
/System/Library/Frameworks/Python.framework/Versions/2.7/Python ]];then
install_name_tool -change
/System/Library/Frameworks/Python.framework/Versions/2.7/Python
%p/lib/python2.7/config/libpython2.7.dylib %i/bin/coot-real
elif [[ -f /System/Library/Frameworks/Python.framework/Versions/2.6/Python
]];then
install_name_tool -change
/System/Library/Frameworks/Python.framework/Versions/2.6/Python
%p/lib/python2.6/config/libpython2.6.dylib %i/bin/coot-real
fi
# This consolidates the refmac monomer library
mkdir -p %i/share/coot/lib/data
ln -s %p/share/refmac/monomers/ener_lib.cif %i/share/coot/lib/.
ln -s %p/share/refmac/monomers %i/share/coot/lib/data/.
# Reference structures should be in %i/share/coot/reference-structures
cp -R ../reference-structures %i/share/coot/.
cp -R * %i/share/coot/etc/.
# The original wrapper creates problems. Get rid of it.
# Replace with a new wrapper to set the required PYTHONPATH variable
# and a few others as follows:
/bin/rm -f %i/bin/coot
echo '#!/bin/sh -f ' > %i/bin/coot
echo 'export GUILE_WARN_DEPRECATED="no"' >> %i/bin/coot
echo "export LC_NUMERIC=C" >> %i/bin/coot
echo "export COOT_REFMAC_LIB_DIR=%p/share/coot/lib" >> %i/bin/coot
echo "export COOT_PYTHON_DIR=%p/share/coot/python" >> %i/bin/coot
echo 'export COOT_SBASE_DIR="%p/share/ccp4"' >> %i/bin/coot
echo 'export CLIBD="%p/share/ccp4"' >> %i/bin/coot
echo "export
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python"
>> %i/bin/coot
echo "%p/bin/coot-real \"\$@\" " >> %i/bin/coot
chmod a+x %i/bin/coot
# Clean up the rest of the mess.
/bin/rm -rf %i/include %i/**/.libs %i/lib/*.la %i/share/coot/etc/**/*.la
<<
###############################################################################
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
License: GPL
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
Homepage: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
###############################################################################
#
SplitOff: <<
Package: %N-shlibs
Conflicts: coot-shlibs
Replaces: coot-shlibs
Files: <<
lib/libccp4mg-*.0*.dylib
lib/libcoot-*.0*.dylib
lib/libcootaneer.0*.dylib
lib/libcootilus.0*.dylib
<<
Shlibs: <<
%p/lib/libccp4mg-surface.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libccp4mg-utils.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-AngleInfo.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-cabuild.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-compat.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-coord-utils.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-coords.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-db-main.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-goograph.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-gtkgraph.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-ideal.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-isosurface.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-lidia-core.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-lidia.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-ligand.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-map-heavy.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-map-utils.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-protein-db.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-shelx.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-surface.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-tw.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcoot-utils.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcootaneer.0.dylib 1.0.0 %n (>= 0.8-1)
%p/lib/libcootilus.0.dylib 1.0.0 %n (>= 0.8-1)
<<
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
<<
#
###############################################################################
#
SplitOff2: <<
Package: %N-dev
Depends: %N (= %v-%r)
Conflicts: coot-dev
Replaces: coot-dev
BuildDependsOnly: True
Files: <<
lib/*.a
<<
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
<<
###############################################################################
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