Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv12910
Modified Files:
coot.info
Added Files:
coot.patch
Log Message:
a reasonably stable coot for sci-stable
--- NEW FILE: coot.patch ---
diff -ruN coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc
coot-0.4-pre-1/coot-utils/coot-fffear.cc
--- coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc 2007-04-16
15:42:06.000000000 -0700
+++ coot-0.4-pre-1/coot-utils/coot-fffear.cc 2007-10-31 10:28:44.000000000
-0700
@@ -160,30 +160,7 @@
}
- for (unsigned int iop=0; iop<ops.size(); iop++) {
-
- clipper::Xmap<float> r1;
- r1.init(clipper::Spacegroup::p1(), xmap.cell(), xmap.grid_sampling());
// fixed to be consistent with above results init.
- clipper::FFFear_fft<float> search(xmap);
- clipper::NX_operator nxop( xmap, nxmap, ops[iop]);
- search(r1, nxmap, nxmap_mask, nxop); // fill r1 with fffear search
values at this orientation
-
- clipper::Xmap<float>::Map_reference_index ix;
- for ( ix = r1.first(); !ix.last(); ix.next() )
- if ( r1[ix] < results[ix].first) {
- results[ix].first = r1[ix];
- results[ix].second = iop;
- }
-
- icount++;
- // std::cout << ops.size() - iop << " ";
- std::cout.flush();
- if (icount == 50) {
- std::cout << " " <<100*(float(iop)/float(ops.size())) << "%";
- std::cout.flush();
- icount = 0;
- }
- }
+
std::cout << "\n";
}
}
diff -ruN coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp
coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp
--- coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp 2007-07-01
07:12:02.000000000 -0700
+++ coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp 2007-10-31 11:08:12.000000000
-0700
@@ -193,46 +193,7 @@
\param resulttrn The best translations.
\param xmap The map to search.
\param rtops The oprientations to search. */
-void LLK_map_target::search( clipper::Xmap<float>& resultscr,
clipper::Xmap<int>& resultrot, clipper::Xmap<int>& resulttrn, const
clipper::Xmap<float>& xmap, const std::vector<clipper::RTop_orth>& rtops ) const
-{
- // set up results
- const clipper::Spacegroup& spgr = xmap.spacegroup();
- const clipper::Cell& cell = xmap.cell();
- const clipper::Grid_sampling& grid = xmap.grid_sampling();
- resultscr.init( spgr, cell, grid );
- resultrot.init( spgr, cell, grid );
- resulttrn.init( spgr, cell, grid );
- resultscr = 1.0e20;
-
- // now search for ML target in each orientation in turn
- clipper::Xmap<float> resultp1( clipper::Spacegroup::p1(), cell, grid );
- clipper::Xmap<float>::Map_reference_index i1(resultp1);
- clipper::Xmap<float>::Map_reference_coord ix(resultscr);
-
- // set up z scoring
- clipper::FFFear_fft<float> srch( xmap );
- clipper::NX_operator nxop( xmap, target, rtops[0] );
- srch( resultp1, target, weight, nxop );
- clipper::Map_stats zstats( resultp1 );
-
- // loop over orientations
- for ( int op = 0; op < rtops.size(); op++ ) {
- // do the fffear search
- clipper::NX_operator nxop( xmap, target, rtops[op].inverse() );
- srch( resultp1, target, weight, nxop );
-
- // store best scores
- for ( i1 = resultp1.first(); !i1.last(); i1.next() ) {
- ix.set_coord( i1.coord() );
- float score = ( resultp1[i1] - zstats.mean() ) / zstats.std_dev();
- if ( score < resultscr[ix] ) {
- resultscr[ix] = score;
- resultrot[ix] = op;
- resulttrn[ix] = grid.index( i1.coord() );
- }
- }
- }
-}
+
clipper::String LLK_map_target::format() const
Index: coot.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- coot.info 12 Sep 2007 18:53:40 -0000 1.9
+++ coot.info 29 Dec 2007 19:57:20 -0000 1.10
@@ -1,14 +1,14 @@
Package:coot
-Version: 0.4-pre-1-revision-375
+Version: 0.4.0-pre-1
Revision: 1
GCC: 4.0
#Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz
-Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz
-Source-MD5: a43cc7d3f4e32b85d55d5748359c18aa
+Source:
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-0.4-pre-1.tar.gz
+Source-MD5: 0efaa27595a7b1d15fe53ad2ddd612f5
#SourceDirectory: %n-%v
SourceDirectory: %n-0.4-pre-1
-Source2:
http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz
-Source2-MD5: 88cdbabf47914740f2d13e6960eea3c6
+Source2:
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac5.3_dictionary.tar.gz
+Source2-MD5: 53faccfdb396125c1f885cdba4a5bd5b
Source3:
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
Source3-MD5: c09bb6b5524901cb0fde14589546224e
#
@@ -27,16 +27,19 @@
echo "include \"/sw/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 \"/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\"
+.
+Install povray and raster3d fink packages to use the F8 key for producing
+ray-traced images.
<<
###############################################################################
-Recommends: povray, ccp4
+Recommends: povray, ccp4, raster3d
BuildDepends: <<
- atk1 ,
- ccp4-onlylibs-dev (>= 6.0.2-1) ,
+ ccp4-onlylibs-dev (>= 6.0.2-9),
+ atk1 ,
freeglut ,
giflib ,
glib2-dev ,
- gmp ,
+ gmp ,
gnome-libs-dev ,
gsl ,
gtk+2 ,
@@ -55,11 +58,12 @@
libjpeg ,
libpng3 ,
librsvg2-gtk ,
- libtool14 ,
- pango1-xft2-dev ,
+ libtool14 ,
+ pango1-xft2-dev ,
+ python25 ,
swig
<<
-# Note: gtkglext1 required at runtime for stereo functionality
+# Note: gtkglext1 IS required at runtime for stereo functionality
Depends: <<
atk1-shlibs ,
coot-shlibs (= %v-%r) ,
@@ -93,7 +97,7 @@
libtool14-shlibs ,
librsvg2-gtk ,
pango1-xft2-shlibs ,
- raster3d
+ python25
<<
#
###############################################################################
@@ -102,6 +106,11 @@
# Patch: %n.patch
PatchScript: <<
#!/bin/zsh -exf
+if [[ $(sw_vers -productVersion) < 10.5 ]]; then
+ :
+else
+ patch -p1 < %a/%n.patch
+fi
perl -pi.bak -e 's|use-modules \(goosh\)|use-modules \(goosh goosh\)|g'
scheme/coot-utils.scm
#perl -pi.bak -e 's/include <malloc.h>//g' **/*.c
# Use the correct povray directory
@@ -110,47 +119,51 @@
perl -pi.bak -e 's|coot-png-display-program
\"display\"|coot-png-display-program \"open\"|g' scheme/raster3d.scm
# This is required to get the map displayed on both sides of side-by-side
stereo
echo "(set-display-lists-for-maps 0)" >>| scheme/group-settings.scm
+# Fix configure to work with gpp4 library instead of ccp4c
+# perl -pi -e 's|ccp4c|gpp4|g' configure
<<
###############################################################################
ConfigureParams: <<
---with-mmdb-prefix=$CCP4 --with-clipper-prefix=$CCP4 --with-fftw=$CCP4 \
+--with-mmdb-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.2
--with-clipper-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.2
--with-fftw=%p/share/xtal/ccp4-onlylibs-dev-6.0.2 \
--with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 --with-gtk2 \
---with-gnomecanvas-prefix=%p --with-ssmlib-prefix=$CCP4 \
+--with-gnomecanvas-prefix=%p
--with-ssmlib-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.2 \
--with-imlib-prefix=%p --with-gtkgl-prefix=%p --with-glib-prefix=%p \
--with-guile-gtk --with-guile-gtk-prefix=%p \
---with-gsl-prefix=%p --with-guile --with-python
- <<
+--with-gsl-prefix=%p --with-guile --with-python
+<<
###############################################################################
CompileScript: <<
-#!/bin/zsh -efv
-alias
python="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3"
-source %p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup-zsh
-export
PATH=/System/Library/Frameworks/Python.framework/Versions/Current/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
+#!/bin/zsh -efx
+export PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
export SED=/usr/bin/sed
-export
PYTHONPATH="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3"
-FLIBS="-L/System/Library/Frameworks/Python.framework/Versions/Current/lib
-L%p/lib" \
-CPPFLAGS="-I$CCP4/lib/clipper/clipper/mmdbold
-I/System/Library/Frameworks/Python.framework/Versions/Current/include/python2.3"
\
-LDFLAGS="-L$CLIB -L/usr/lib -lSystemStubs -flat_namespace
-L/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3/config"
\
-CXX="g++" \
-CC="gcc" \
-py_path=/System/Library/Frameworks/Python.framework/Versions/Current/bin/python2.3
\
+export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
+export
PYTHONPATH=%p/share/coot/python:%p/lib/python2.5:%p/lib/python2.5/site-packages:%p/lib/python2.5/site-packages/gtk-2.0:%p/lib/python2.5/site-packages/gtk-2.0
+FLIBS="-L%p/lib" \
+CPPFLAGS="-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include
-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib
-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib/ssm -I%p/include" \
+LDFLAGS="-L%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -L%p/lib -L/usr/lib
-lSystemStubs -flat_namespace -L%p/lib/python2.5/config
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \
+CXX="/usr/bin/g++" \
+CC="/usr/bin/gcc" \
./configure %c
+# py_path="%p/bin/python2.5" \
+#
#remake the src/coot_wrap_python.cc and src/coot_wrap_guile.cc files
-/bin/rm -f **/coot_wrap_*.cc
-cd src
-make coot_wrap_guile.cc
-make coot_wrap_python.cc
-cp coot_wrap_guile_pre.cc coot_wrap_guile.cc
-cd ..
-make
+ /bin/rm -f **/coot_wrap_**.cc
+ cd src
+ touch c-interface-database.hh
+ make coot_wrap_guile.cc
+ make coot_wrap_python.cc
+ cp coot_wrap_guile_pre.cc coot_wrap_guile.cc
+ cd ..
+ make
<<
###############################################################################
InstallScript: <<
-#!/bin/zsh -exf
-source %p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup-zsh
+#!/bin/zsh -efv
export PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
export PYTHONPATH=""
+export
PYTHONPATH=%p/share/coot/python:%p/lib/python2.5:%p/lib/python2.5/site-packages:%p/lib/python2.5/site-packages/gtk-2.0:%p/lib/python2.5/site-packages/gtk-2.0
export SED=/usr/bin/sed
+export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
cp src/coot.py python/coot.py
make install prefix=%i
#
@@ -170,7 +183,9 @@
mkdir -p %i/share/coot/python
cp src/coot.py %i/share/coot/python/coot.py
cp -R setup %i/share/coot/.
-cp -R ../lib %i/share/coot/.
+# This installs the refmac monomer library
+mkdir -p %i/share/coot/lib/data
+cp -R ../dic %i/share/coot/lib/data/monomers
# cp %i/share/coot/etc/python/coot.py %i/share/coot/python/.
# Reference structures should be in %i/share/coot/reference-structures
cp -R ../reference-structures %i/share/coot/.
@@ -185,6 +200,7 @@
/bin/rm -rf %i/include
/bin/rm -rf %i/**/.libs
<<
+RuntimeVars: COOT_REFMAC_LIB_DIR: %p/share/coot/lib
###############################################################################
DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
License: GPL
@@ -197,6 +213,7 @@
Files: <<
lib/libccp4mg-*.dylib
lib/libcoot-*.dylib
+lib/libcootaneer*.dylib
<<
Shlibs: <<
%p/lib/libccp4mg-surface.0.0.0.dylib 1.0.0
%n (>= 0.3-1)
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