Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16011
Modified Files:
ccp4.info ccp4.patch
Log Message:
ccp4 patch upgrade
Index: ccp4.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- ccp4.info 23 Feb 2006 19:38:06 -0000 1.10
+++ ccp4.info 30 Mar 2006 03:36:27 -0000 1.11
@@ -1,6 +1,6 @@
Package: ccp4
Version: 6.0
-Revision: 1
+Revision: 3
GCC: 3.3
Source: ftp://ftp.%n.ac.uk/%n/%v.0/packed/%n-%v.0-core-src.tar.gz
Source2: ftp://ftp.%n.ac.uk/%n/%v.0/packed/phaser-1.3.2-cctbx-src.tar.gz
@@ -279,7 +279,7 @@
License agreement is part of configure file -- print out form and mail in,
additional comments at http://chemistry.ucsc.edu/~wgscott/xtal/ccp4.html
CCP4 files will be installed under /sw/share/xtal/ccp4-6.0
-This revision includes all available CCP4 patches as of December 1, 2005.
+This revision includes all available CCP4 patches as of March 27, 2006.
and new bash and zsh command completions specific to ccp4.
<<
DocFiles: README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps
ccp4i_installation.html academic_software_licence.pdf
academic_software_licence.ps.gz academic_software_licence.rtf
Index: ccp4.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4.patch,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- ccp4.patch 23 Feb 2006 19:38:06 -0000 1.7
+++ ccp4.patch 30 Mar 2006 03:36:28 -0000 1.8
@@ -192,6 +192,18 @@
}
#d_index_title Interaction with Netscape
+diff -ruN ccp4-6.0-orig/ccp4i/templates/molrep.com
ccp4-6.0/ccp4i/templates/molrep.com
+--- ccp4-6.0-orig/ccp4i/templates/molrep.com 2005-11-07 08:52:31.000000000
-0800
++++ ccp4-6.0/ccp4i/templates/molrep.com 2006-03-22 14:25:46.000000000
-0800
+@@ -136,7 +136,7 @@
+ {[IfSet $FUNCTION] && ![StringSame $FUNCTION A]} FUN $FUNCTION
+ ENDIF
+
+-{[IfSet $MODEL_CORRECTION] && ![StringSame $MODEL_CORRECTION N] } SURF
$MODEL_CORRECTION
++1 SURF $MODEL_CORRECTION
+
+ IF { $NMONOMERS > 0 }
+ { [IfSet $NMONOMERS] } NMON $NMONOMERS
diff -ruN ccp4-6.0-orig/configure ccp4-6.0/configure
--- ccp4-6.0-orig/configure 2006-02-08 08:28:03.000000000 -0800
+++ ccp4-6.0/configure 2006-02-21 07:54:22.000000000 -0800
@@ -700,13 +712,907 @@
+
diff -ruN ccp4-6.0-orig/lib/cctbx/cctbx_install_script.csh
ccp4-6.0/lib/cctbx/cctbx_install_script.csh
--- ccp4-6.0-orig/lib/cctbx/cctbx_install_script.csh 2005-11-08
09:06:57.000000000 -0800
-+++ ccp4-6.0/lib/cctbx/cctbx_install_script.csh 2006-02-21
08:13:32.000000000 -0800
-@@ -29,7 +29,7 @@
- set build_mode=release
++++ ccp4-6.0/lib/cctbx/cctbx_install_script.csh 2006-02-26
08:36:24.000000000 -0800
+@@ -1,232 +1,5 @@
+-#! /bin/csh -f
++#! /bin/sh -ef
- if ("`uname`" == "Darwin") then
+-set install_root="$cwd"
+-set bundle="cctbx"
+-set sources="$cwd/${bundle}_sources"
+-set build="$cwd/${bundle}_build"
+-set prefer_usr_bin_python=0
++echo "Skipping final build of cctbx"
++echo "Install fink's cctbx package if you need this"
+
+-unalias cat
+-unalias cd
+-unalias grep
+-unalias ls
+-unalias mkdir
+-
+-unsetenv PYTHONHOME
+-
+-if (-f "$sources/TAG") then
+- echo "Build tag:"
+- cat "$sources/TAG"
+-endif
+-
+-if (-d "$sources/boost") then
+- set have_sources=1
+-else
+- set have_sources=0
+-endif
+-
+-set python_exe=None
+-set build_mode=release
+-
+-if ("`uname`" == "Darwin") then
- set
python_exe="/Library/Frameworks/Python.framework/Versions/2.3/bin/python"
+- if (! -x "$python_exe") then
+- set python_exe="/System$python_exe"
+- endif
+- "$python_exe" -V
+- if ($status != 0) then
+- echo "Under Mac OS 10 Python 2.3 must be pre-installed."
+- echo "Please refer to the following web page for more information:"
+- echo "http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html";
+- exit 1
+- endif
+-endif
+-
+-if ($have_sources == 0) then
+-
+- if (-d "$build/python") then
+- set python_exe="$build/python/bin/python"
+- endif
+- if ($prefer_usr_bin_python) then
+- if ("$python_exe" == None && -x /usr/bin/python) then
+- /usr/bin/python -V |& head -1
+- if ($status == 0) then
+- set python_exe=/usr/bin/python
+- endif
+- endif
+- endif
+- if ("$python_exe" == None) then
+- python -V |& head -1
+- if ($status == 0) then
+- set python_exe=python
+- endif
+- endif
+- if (! $prefer_usr_bin_python) then
+- if ("$python_exe" == None && -x /usr/bin/python) then
+- /usr/bin/python -V |& head -1
+- if ($status == 0) then
+- set python_exe=/usr/bin/python
+- endif
+- endif
+- endif
+-
+-else
+-
+- if ($#argv == 0) then
+- echo -n "Please enter the number of available CPU's [1]: "
+- set n_cpu_s=(`echo "$<"`)
+- if ($#n_cpu_s > 1) then
+- echo "Not a number! Please try again."
+- exit 1
+- else if ($#n_cpu_s == 0) then
+- set n_cpu_s=1
+- else
+- set n_cpu_s="$n_cpu_s[1]"
+- endif
+- else if ($#argv == 1) then
+- set n_cpu_s="$1"
+- else
+- echo "usage: $0 number_of_cpu_s"
+- exit 1
+- endif
+- echo "Number of available CPU's: $n_cpu_s"
+- if ("$n_cpu_s" == "0") exit 0
+-
+- if ("$python_exe" == None) then
+-
+- set python_sources=(`ls | grep Python-`)
+- if ($#python_sources == 0) then
+- set python_sources=None
+- else if ($#python_sources == 1) then
+- set python_sources="$python_sources[1]"
+- else
+- echo "ERROR: Multiple Python source code directories."
+- echo " Move or remove all but one directory."
+- exit 1
+- endif
+-
+- if ("$python_sources" == None) then
+-
+- echo "Trying to find a pre-installed Python:"
+- set python_exe=None
+- if (-x "$build/python/bin/python") then
+- "$build/python/bin/python" -V |& head -1
+- if ($status == 0) then
+- set python_exe="$build/python/bin/python"
+- endif
+- endif
+- if ("$python_exe" == None) then
+- python -V |& head -1
+- if ($status == 0) then
+- set python_exe=python
+- endif
+- endif
+- if ("$python_exe" == None) then
+- python2 -V |& head -1
+- if ($status == 0) then
+- set python_exe=python2
+- endif
+- endif
+- if ("$python_exe" == None && -x /usr/bin/python) then
+- /usr/bin/python -V |& head -1
+- if ($status == 0) then
+- set python_exe=/usr/bin/python
+- endif
+- endif
+- if ("$python_exe" != None) then
+- set python_version=(`"$python_exe" -V |& tr "." " "`)
+- if ("$python_version[2]") then
+- set minor=`echo "$python_version[3]" | cut -c-1`
+- if ($minor < 2 || ($minor == 2 && $#python_version == 3)) then
+- echo "A more recent Python version is required (2.2.1 or higher)."
+- set python_exe=None
+- endif
+- endif
+- endif
+- if ("$python_exe" == None) then
+- echo ""
+- echo "Cannot find a Python interpreter."
+- echo ""
+- echo "Please download an installer with Python included"
+- echo "or add a matching Python to the PATH environment variable."
+- echo ""
+- echo "Installation aborted."
+- exit 1
+- endif
+-
+- else
+-
+- echo "Installing $python_sources from sources"
+- mkdir -p "$build"
+- cd "$build"
+- cd ..
+- cd "$python_sources"
+- set py_install_log="../py_install_log"
+- echo "Configuring Python"
+- ./configure --prefix="$build/python" >& "$py_install_log"
+- echo "Compiling Python. This may take a while."
+- make >>& "$py_install_log"
+- echo "Installing Python"
+- make install >>& "$py_install_log"
+- echo "Done installing Python."
+- cd "$install_root"
+- set python_exe="$build/python/bin/python"
+- "$python_exe" -V
+- if ($status != 0) then
+- echo "ERROR: Python installation failed."
+- echo "Please check the log file for errors:"
+- echo " $py_install_log"
+- exit 1
+- endif
+-
+- endif
+-
+- endif
+-
+- mkdir -p "$build"
+-
+-endif
+-
+-echo ""
+-echo "Precompiling all .py files. This may take a minute or two."
+-"$python_exe" "$sources/libtbx/libtbx/command_line/py_compile_all.py"
+-
+-echo ""
+-cd "$build"
+-echo "Configuring $bundle build directory"
+-"$python_exe" "$sources/libtbx/configure.py" --build="$build_mode" mmtbx
clipper
+-source setpaths_all.csh
+-
+-if ($have_sources != 0) then
+- echo ""
+- echo "Installing $bundle modules. This may take a while."
+- libtbx.scons -j "$n_cpu_s" .
+-endif
+-
+-set test_py="$BOOST_ADAPTBX_DIST/tst_rational.py"
+-if (-f "$test_py") then
+- echo ""
+- echo "Running a selected test"
+- set cmd='libtbx.python "'"$test_py"'"'
+- echo "$cmd"
+- eval $cmd
+-endif
+-
+-cat << EOT
+-
+-***
+-*** csh and tcsh users:
+-*** To use this installation in a new shell or process run the command:
+-***
+-*** source "$LIBTBX_BUILD/setpaths.csh"
+-***
+-*** You may want to add this line to your .cshrc file.
+-***
+-*** sh and bash users:
+-*** To use this installation in a new shell or process run the command:
+-***
+-*** . "$LIBTBX_BUILD/setpaths.sh"
+-***
+-*** You may want to add this line to your .profile or .bashrc file.
+-***
+-EOT
+diff -ruN ccp4-6.0-orig/lib/cctbx/cctbx_install_script.csh-original
ccp4-6.0/lib/cctbx/cctbx_install_script.csh-original
+--- ccp4-6.0-orig/lib/cctbx/cctbx_install_script.csh-original 1969-12-31
16:00:00.000000000 -0800
++++ ccp4-6.0/lib/cctbx/cctbx_install_script.csh-original 2006-02-21
08:13:32.000000000 -0800
+@@ -0,0 +1,232 @@
++#! /bin/csh -f
++
++set install_root="$cwd"
++set bundle="cctbx"
++set sources="$cwd/${bundle}_sources"
++set build="$cwd/${bundle}_build"
++set prefer_usr_bin_python=0
++
++unalias cat
++unalias cd
++unalias grep
++unalias ls
++unalias mkdir
++
++unsetenv PYTHONHOME
++
++if (-f "$sources/TAG") then
++ echo "Build tag:"
++ cat "$sources/TAG"
++endif
++
++if (-d "$sources/boost") then
++ set have_sources=1
++else
++ set have_sources=0
++endif
++
++set python_exe=None
++set build_mode=release
++
++if ("`uname`" == "Darwin") then
+ set
python_exe="/System/Library/Frameworks/Python.framework/Versions/Current/bin/python"
- if (! -x "$python_exe") then
- set python_exe="/System$python_exe"
- endif
++ if (! -x "$python_exe") then
++ set python_exe="/System$python_exe"
++ endif
++ "$python_exe" -V
++ if ($status != 0) then
++ echo "Under Mac OS 10 Python 2.3 must be pre-installed."
++ echo "Please refer to the following web page for more information:"
++ echo "http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html";
++ exit 1
++ endif
++endif
++
++if ($have_sources == 0) then
++
++ if (-d "$build/python") then
++ set python_exe="$build/python/bin/python"
++ endif
++ if ($prefer_usr_bin_python) then
++ if ("$python_exe" == None && -x /usr/bin/python) then
++ /usr/bin/python -V |& head -1
++ if ($status == 0) then
++ set python_exe=/usr/bin/python
++ endif
++ endif
++ endif
++ if ("$python_exe" == None) then
++ python -V |& head -1
++ if ($status == 0) then
++ set python_exe=python
++ endif
++ endif
++ if (! $prefer_usr_bin_python) then
++ if ("$python_exe" == None && -x /usr/bin/python) then
++ /usr/bin/python -V |& head -1
++ if ($status == 0) then
++ set python_exe=/usr/bin/python
++ endif
++ endif
++ endif
++
++else
++
++ if ($#argv == 0) then
++ echo -n "Please enter the number of available CPU's [1]: "
++ set n_cpu_s=(`echo "$<"`)
++ if ($#n_cpu_s > 1) then
++ echo "Not a number! Please try again."
++ exit 1
++ else if ($#n_cpu_s == 0) then
++ set n_cpu_s=1
++ else
++ set n_cpu_s="$n_cpu_s[1]"
++ endif
++ else if ($#argv == 1) then
++ set n_cpu_s="$1"
++ else
++ echo "usage: $0 number_of_cpu_s"
++ exit 1
++ endif
++ echo "Number of available CPU's: $n_cpu_s"
++ if ("$n_cpu_s" == "0") exit 0
++
++ if ("$python_exe" == None) then
++
++ set python_sources=(`ls | grep Python-`)
++ if ($#python_sources == 0) then
++ set python_sources=None
++ else if ($#python_sources == 1) then
++ set python_sources="$python_sources[1]"
++ else
++ echo "ERROR: Multiple Python source code directories."
++ echo " Move or remove all but one directory."
++ exit 1
++ endif
++
++ if ("$python_sources" == None) then
++
++ echo "Trying to find a pre-installed Python:"
++ set python_exe=None
++ if (-x "$build/python/bin/python") then
++ "$build/python/bin/python" -V |& head -1
++ if ($status == 0) then
++ set python_exe="$build/python/bin/python"
++ endif
++ endif
++ if ("$python_exe" == None) then
++ python -V |& head -1
++ if ($status == 0) then
++ set python_exe=python
++ endif
++ endif
++ if ("$python_exe" == None) then
++ python2 -V |& head -1
++ if ($status == 0) then
++ set python_exe=python2
++ endif
++ endif
++ if ("$python_exe" == None && -x /usr/bin/python) then
++ /usr/bin/python -V |& head -1
++ if ($status == 0) then
++ set python_exe=/usr/bin/python
++ endif
++ endif
++ if ("$python_exe" != None) then
++ set python_version=(`"$python_exe" -V |& tr "." " "`)
++ if ("$python_version[2]") then
++ set minor=`echo "$python_version[3]" | cut -c-1`
++ if ($minor < 2 || ($minor == 2 && $#python_version == 3)) then
++ echo "A more recent Python version is required (2.2.1 or higher)."
++ set python_exe=None
++ endif
++ endif
++ endif
++ if ("$python_exe" == None) then
++ echo ""
++ echo "Cannot find a Python interpreter."
++ echo ""
++ echo "Please download an installer with Python included"
++ echo "or add a matching Python to the PATH environment variable."
++ echo ""
++ echo "Installation aborted."
++ exit 1
++ endif
++
++ else
++
++ echo "Installing $python_sources from sources"
++ mkdir -p "$build"
++ cd "$build"
++ cd ..
++ cd "$python_sources"
++ set py_install_log="../py_install_log"
++ echo "Configuring Python"
++ ./configure --prefix="$build/python" >& "$py_install_log"
++ echo "Compiling Python. This may take a while."
++ make >>& "$py_install_log"
++ echo "Installing Python"
++ make install >>& "$py_install_log"
++ echo "Done installing Python."
++ cd "$install_root"
++ set python_exe="$build/python/bin/python"
++ "$python_exe" -V
++ if ($status != 0) then
++ echo "ERROR: Python installation failed."
++ echo "Please check the log file for errors:"
++ echo " $py_install_log"
++ exit 1
++ endif
++
++ endif
++
++ endif
++
++ mkdir -p "$build"
++
++endif
++
++echo ""
++echo "Precompiling all .py files. This may take a minute or two."
++"$python_exe" "$sources/libtbx/libtbx/command_line/py_compile_all.py"
++
++echo ""
++cd "$build"
++echo "Configuring $bundle build directory"
++"$python_exe" "$sources/libtbx/configure.py" --build="$build_mode" mmtbx
clipper
++source setpaths_all.csh
++
++if ($have_sources != 0) then
++ echo ""
++ echo "Installing $bundle modules. This may take a while."
++ libtbx.scons -j "$n_cpu_s" .
++endif
++
++set test_py="$BOOST_ADAPTBX_DIST/tst_rational.py"
++if (-f "$test_py") then
++ echo ""
++ echo "Running a selected test"
++ set cmd='libtbx.python "'"$test_py"'"'
++ echo "$cmd"
++ eval $cmd
++endif
++
++cat << EOT
++
++***
++*** csh and tcsh users:
++*** To use this installation in a new shell or process run the command:
++***
++*** source "$LIBTBX_BUILD/setpaths.csh"
++***
++*** You may want to add this line to your .cshrc file.
++***
++*** sh and bash users:
++*** To use this installation in a new shell or process run the command:
++***
++*** . "$LIBTBX_BUILD/setpaths.sh"
++***
++*** You may want to add this line to your .profile or .bashrc file.
++***
++EOT
+diff -ruN ccp4-6.0-orig/lib/clipper/clipper/core/derivs.h
ccp4-6.0/lib/clipper/clipper/core/derivs.h
+--- ccp4-6.0-orig/lib/clipper/clipper/core/derivs.h 2005-09-08
13:07:42.000000000 -0700
++++ ccp4-6.0/lib/clipper/clipper/core/derivs.h 2006-03-22 14:23:46.000000000
-0800
+@@ -169,7 +169,7 @@
+ template<class T> Curv_orth<T> Curv_frac<T>::curv_orth( const Cell& cell )
const
+ {
+ Mat33<T> m( cell.matrix_frac() );
+- return Curv_frac<T>( m.transpose() * (*this) * m );
++ return Curv_orth<T>( m.transpose() * (*this) * m );
+ }
+
+ /*! \param g The grid concerned \return The transformed derivative. */
+diff -ruN ccp4-6.0-orig/lib/clipper/clipper/core/derivs.h.orig
ccp4-6.0/lib/clipper/clipper/core/derivs.h.orig
+--- ccp4-6.0-orig/lib/clipper/clipper/core/derivs.h.orig 1969-12-31
16:00:00.000000000 -0800
++++ ccp4-6.0/lib/clipper/clipper/core/derivs.h.orig 2005-09-08
13:07:42.000000000 -0700
+@@ -0,0 +1,211 @@
++/*! \file lib/derivs.h
++ Fundamental types for the clipper libraries
++*/
++//C Copyright (C) 2000-2004 Kevin Cowtan and University of York
++//C Copyright (C) 2000-2005 Kevin Cowtan and University of York
++
++//L This code is distributed under the terms and conditions of the
++//L CCP4 Program Suite Licence Agreement as a CCP4 Library.
++//L A copy of the CCP4 licence can be obtained by writing to the
++//L CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
++
++#ifndef CLIPPER_DERIVS
++#define CLIPPER_DERIVS
++
++
++#include "coords.h"
++
++
++namespace clipper
++{
++ template<class T> class Grad_orth;
++ template<class T> class Grad_frac;
++ template<class T> class Grad_map;
++ template<class T> class Curv_orth;
++ template<class T> class Curv_frac;
++ template<class T> class Curv_map;
++
++
++ //! orthogonal (Angstom) gradient, with respect to orthogonal x,y,z
++ template<class T> class Grad_orth : public Vec3<T>
++ {
++ public:
++ Grad_orth() {} //!< null constructor
++ explicit Grad_orth( const Vec3<T>& v ) :
++ Vec3<T>( v ) {} //!< constructor: copy/convert
++ Grad_orth( const T& dx, const T& dy, const T& dz ) :
++ Vec3<T>( dx, dy, dz ) {} //!< constructor: from d/dx,d/dy,d/dz
++ const T& dx() const { return (*this)[0]; } //!< get d/dx
++ const T& dy() const { return (*this)[1]; } //!< get d/dy
++ const T& dz() const { return (*this)[2]; } //!< get d/dz
++ //! orthogonal-fractional derivative conversion
++ Grad_frac<T> grad_frac( const Cell& cell ) const;
++ String format() const; //!< return formatted String representation
++ };
++
++
++ //! fractional (cell) gradient, with respect to fractional u,v,w
++ template<class T> class Grad_frac : public Vec3<T>
++ {
++ public:
++ Grad_frac() {} //!< null constructor
++ explicit Grad_frac( const Vec3<T>& v ) :
++ Vec3<T>( v ) {} //!< constructor: copy/convert
++ Grad_frac( const T& du, const T& dv, const T& dw ) :
++ Vec3<T>( du, dv, dw ) {} //!< constructor: from d/du,d/dv,d/dw
++ const T& du() const { return (*this)[0]; } //!< get d/du
++ const T& dv() const { return (*this)[1]; } //!< get d/dv
++ const T& dw() const { return (*this)[2]; } //!< get d/dw
++ //! fractional-orthogonal derivative conversion
++ Grad_orth<T> grad_orth( const Cell& cell ) const;
++ //! fractional-grid derivative conversion
++ Grad_map<T> grad_map( const Grid& g ) const;
++ String format() const; //!< return formatted String representation
++ };
++
++
++ //! map coordinate gradient, with respect to grid u,v,w
++ template<class T> class Grad_map : public Vec3<T>
++ {
++ public:
++ Grad_map() {} //!< null constructor
++ explicit Grad_map( const Vec3<T>& v ) :
++ Vec3<T>( v ) {} //!< constructor: copy/convert
++ Grad_map( const T& du, const T& dv, const T& dw ) :
++ Vec3<T>( du, dv, dw ) {} //!< constructor: from d/du,d/dv,d/dw
++ const T& du() const { return (*this)[0]; } //!< get d/du
++ const T& dv() const { return (*this)[1]; } //!< get d/dv
++ const T& dw() const { return (*this)[2]; } //!< get d/dw
++ //! grid-fractional derivative conversion
++ Grad_frac<T> grad_frac( const Grid& g ) const;
++ String format() const; //!< return formatted String representation
++ };
++
++
++ //! orthogonal (Angstom) curvatures, with respect to orthogonal x,y,z
++ template<class T> class Curv_orth : public Mat33<T>
++ {
++ public:
++ Curv_orth() {} //!< null constructor
++ explicit Curv_orth( const Mat33<T>& m ) :
++ Mat33<T>( m ) {} //!< constructor: copy/convert
++ //! orthogonal-fractional derivative conversion
++ Curv_frac<T> curv_frac( const Cell& cell ) const;
++ };
++
++
++ //! fractional (cell) curvatures, with respect to fractional u,v,w
++ template<class T> class Curv_frac : public Mat33<T>
++ {
++ public:
++ Curv_frac() {} //!< null constructor
++ explicit Curv_frac( const Mat33<T>& m ) :
++ Mat33<T>( m ) {} //!< constructor: copy/convert
++ //! fractional-orthogonal derivative conversion
++ Curv_orth<T> curv_orth( const Cell& cell ) const;
++ //! fractional-grid derivative conversion
++ Curv_map<T> curv_map( const Grid& g ) const;
++ };
++
++
++ //! map coordinate curvatures, with respect to grid u,v,w
++ template<class T> class Curv_map : public Mat33<T>
++ {
++ public:
++ Curv_map() {} //!< null constructor
++ explicit Curv_map( const Mat33<T>& m ) :
++ Mat33<T>( m ) {} //!< constructor: copy/convert
++ //! grid-fractional derivative conversion
++ Curv_frac<T> curv_frac( const Grid& g ) const;
++ };
++
++
++
++ // template implementations
++
++ /*! The result is an RT operator. This is a redudent representation,
++ but is handy for assembling compound operators.
++ \return The operator */
++ /*! \return The formatted text string */
++ template<class T> String Grad_orth<T>::format() const
++ { return "d/dx,d/dy,d/dz =
("+String(dx())+","+String(dy())+","+String(dz())+")"; }
++
++ /*! \param cell The cell concerned \return The transformed derivative. */
++ template<class T> inline Grad_frac<T> Grad_orth<T>::grad_frac( const Cell&
cell ) const
++ { return Grad_frac<T>( (*this) * Mat33<T>( cell.matrix_orth() ) ); }
++
++
++ /*! \return The formatted text string */
++ template<class T> String Grad_frac<T>::format() const
++ { return "d/du,d/dv,d/dw =
("+String(du())+","+String(dv())+","+String(dw())+")"; }
++
++ /*! \param cell The cell concerned \return The transformed derivative. */
++ template<class T> inline Grad_orth<T> Grad_frac<T>::grad_orth( const Cell&
cell ) const
++ { return Grad_orth<T>( (*this) * Mat33<T>( cell.matrix_frac() ) ); }
++
++ /*! \param g The grid concerned \return The transformed derivative. */
++ template<class T> inline Grad_map<T> Grad_frac<T>::grad_map( const Grid& g
) const
++ { return Grad_map<T>( du()/g.nu(), dv()/g.nv(), dw()/g.nw() ); }
++
++
++ /*! \return The formatted text string */
++ template<class T> String Grad_map<T>::format() const
++ { return "d/du,d/dv,d/dw =
("+String(du())+","+String(dv())+","+String(dw())+")"; }
++
++ /*! \param g The grid concerned \return The transformed derivative. */
++ template<class T> inline Grad_frac<T> Grad_map<T>::grad_frac( const Grid& g
) const
++ { return Grad_frac<T>( du()*g.nu(), dv()*g.nv(), dw()*g.nw() ); }
++
++
++ /*! \param cell The cell concerned \return The transformed derivative. */
++ template<class T> Curv_frac<T> Curv_orth<T>::curv_frac( const Cell& cell )
const
++ {
++ Mat33<T> m( cell.matrix_orth() );
++ return Curv_frac<T>( m.transpose() * (*this) * m );
++ }
++
++
++ /*! \param cell The cell concerned \return The transformed derivative. */
++ template<class T> Curv_orth<T> Curv_frac<T>::curv_orth( const Cell& cell )
const
++ {
++ Mat33<T> m( cell.matrix_frac() );
++ return Curv_frac<T>( m.transpose() * (*this) * m );
++ }
++
++ /*! \param g The grid concerned \return The transformed derivative. */
++ template<class T> Curv_map<T> Curv_frac<T>::curv_map( const Grid& g ) const
++ {
++ Curv_map<T> c;
++ c(0,0) = (*this)(0,0) / T(g.nu()*g.nu());
++ c(0,1) = (*this)(0,1) / T(g.nu()*g.nv());
++ c(0,2) = (*this)(0,2) / T(g.nu()*g.nw());
++ c(1,0) = (*this)(1,0) / T(g.nv()*g.nu());
++ c(1,1) = (*this)(1,1) / T(g.nv()*g.nv());
++ c(1,2) = (*this)(1,2) / T(g.nv()*g.nw());
++ c(2,0) = (*this)(2,0) / T(g.nw()*g.nu());
++ c(2,1) = (*this)(2,1) / T(g.nw()*g.nv());
++ c(2,2) = (*this)(2,2) / T(g.nw()*g.nw());
++ return c;
++ }
++
++
++ /*! \param g The grid concerned \return The transformed derivative. */
++ template<class T> Curv_frac<T> Curv_map<T>::curv_frac( const Grid& g ) const
++ {
++ Curv_frac<T> c;
++ c(0,0) = (*this)(0,0) * T(g.nu()*g.nu());
++ c(0,1) = (*this)(0,1) * T(g.nu()*g.nv());
++ c(0,2) = (*this)(0,2) * T(g.nu()*g.nw());
++ c(1,0) = (*this)(1,0) * T(g.nv()*g.nu());
++ c(1,1) = (*this)(1,1) * T(g.nv()*g.nv());
++ c(1,2) = (*this)(1,2) * T(g.nv()*g.nw());
++ c(2,0) = (*this)(2,0) * T(g.nw()*g.nu());
++ c(2,1) = (*this)(2,1) * T(g.nw()*g.nv());
++ c(2,2) = (*this)(2,2) * T(g.nw()*g.nw());
++ return c;
++ }
++
++
++} // namespace clipper
++
++#endif
+diff -ruN ccp4-6.0-orig/lib/clipper/src/cphasecombine.cpp
ccp4-6.0/lib/clipper/src/cphasecombine.cpp
+--- ccp4-6.0-orig/lib/clipper/src/cphasecombine.cpp 2005-09-09
03:50:39.000000000 -0700
++++ ccp4-6.0/lib/clipper/src/cphasecombine.cpp 2006-03-22 14:23:16.000000000
-0800
+@@ -37,9 +37,9 @@
+ } else if ( args[arg] == "-colin-hl-2" ) {
+ if ( ++arg < args.size() ) ipcolh2 = args[arg];
+ } else if ( args[arg] == "-weight-hl-1" ) {
+- if ( ++arg < args.size() ) hlwt1 = clipper::String(args[arg]).i();
++ if ( ++arg < args.size() ) hlwt1 = clipper::String(args[arg]).f();
+ } else if ( args[arg] == "-weight-hl-2" ) {
+- if ( ++arg < args.size() ) hlwt2 = clipper::String(args[arg]).i();
++ if ( ++arg < args.size() ) hlwt2 = clipper::String(args[arg]).f();
+ } else if ( args[arg] == "-colout" ) {
+ if ( ++arg < args.size() ) opcol = args[arg];
+ } else {
+diff -ruN ccp4-6.0-orig/lib/clipper/src/pirancslib.cpp
ccp4-6.0/lib/clipper/src/pirancslib.cpp
+--- ccp4-6.0-orig/lib/clipper/src/pirancslib.cpp 2005-10-14
02:37:23.000000000 -0700
++++ ccp4-6.0/lib/clipper/src/pirancslib.cpp 2006-03-22 14:26:18.000000000
-0800
+@@ -1083,9 +1083,9 @@
+ Local_rtop rtinv = ncsops[i].inverse();
+ int j;
+ for ( j = 0; j < ncsopsi.size(); j++ )
+- if ( rtinv.symm_match( ncsops[j], spgr, cell, tol_dst_, tol_ang_ ).first
++ if ( rtinv.symm_match( ncsopsi[j], spgr, cell, tol_dst_, tol_ang_
).first
+ < 2.0 ) break;
+- if ( j == ncsopsi.size() ) ncsopsi.push_back( ncsops[j] );
++ if ( j == ncsopsi.size() ) ncsopsi.push_back( ncsops[i] );
+ }
+ return ncsopsi;
+ }
+diff -ruN ccp4-6.0-orig/lib/fftw/configure ccp4-6.0/lib/fftw/configure
+--- ccp4-6.0-orig/lib/fftw/configure 2006-01-11 04:52:05.000000000 -0800
++++ ccp4-6.0/lib/fftw/configure 2006-02-26 08:24:31.000000000 -0800
+@@ -1907,7 +1907,8 @@
+ enableval="$enable_shared"
+ p=${PACKAGE-default}
+ case $enableval in
+- yes) enable_shared=yes ;;
++ # brute force it not to build shared fftw libs
++ yes) enable_shared=no ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+@@ -1916,7 +1917,7 @@
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+- enable_shared=yes
++ enable_shared=no
+ fi
+ done
+ IFS="$lt_save_ifs"
+diff -ruN ccp4-6.0-orig/lib/src/ccplib.f ccp4-6.0/lib/src/ccplib.f
+--- ccp4-6.0-orig/lib/src/ccplib.f 2005-09-08 08:17:41.000000000 -0700
++++ ccp4-6.0/lib/src/ccplib.f 2006-03-22 14:21:46.000000000 -0800
+@@ -16,7 +16,7 @@
+ C amalgamate ccppsf and fdir/fext/froot. also add tests of these
+ C routines to testlib.
+ C
+-C $Id$
++C $Id$
+ C
+ C CCFILL Set specified number of elements of byte array
+ C CCPALC Call subroutine with allocated memory
+@@ -1307,7 +1307,7 @@
+ INTEGER GETPID,LENSTR
+ LOGICAL VAXVMS, WINMVS
+ CHARACTER FDIR* (ISTRLN),FEXTN* (ISTRLN),FROOT* (ISTRLN), RTNBKS
+- EXTERNAL GETPID,LENSTR,VAXVMS,FDIR,FEXTN,FROOT
++ EXTERNAL LENSTR,VAXVMS,FDIR,FEXTN,FROOT
+ C ..
+ C .. External Subroutines ..
+ EXTERNAL CCPERR,UGTARG,QPRINT,UGTENV,USTENV
+diff -ruN ccp4-6.0-orig/src/geomcalc.f ccp4-6.0/src/geomcalc.f
+--- ccp4-6.0-orig/src/geomcalc.f 2005-09-06 04:25:14.000000000 -0700
++++ ccp4-6.0/src/geomcalc.f 2006-03-22 14:25:22.000000000 -0800
+@@ -157,7 +157,7 @@
+ c=============================================================
+ c
+ call ccpfyp
+- call ccprcs (6, 'GEOMCALC', '$Date$')
++ call ccprcs (6, 'GEOMCALC', '$Date$')
+ call XYZINIT
+ lunout = 6
+ c
+@@ -336,7 +336,7 @@
+ write (6,'(/,a,i6,a,/)')
+ $ ' Plane fitted to ', natpln(iplane),' atoms'
+ write (6, '(a,/,a,/)')
+- $ ' "Thickness" is RMS deviation along principle axis, ',
++ $ ' "Thickness" is RMS deviation along principal axis, ',
+ $ ' Radii are in plane perpendicular to axis'
+ write (6, '(a)')
+ $ ' Axis Axes Centre Thickness Radii'
+@@ -405,7 +405,7 @@
+ c
+ c TRANSFORM
+ c Apply transformation to put whole molecule into frame of plane
+-c (principle axes along x,y,z, normal along z)
++c (principal axes along x,y,z, normal along z)
+ c
+ 300 if (natpln(iplane) .le. 0) then
+ call ccperr(2,' *** No plane fitted ***')
+@@ -827,8 +827,11 @@
+ common /cmolec/ atname_mol(maxat), restyp_mol(maxat),
+ $ chain_mol(maxat)
+ character atname_mol*4, restyp_mol*4, chain_mol*4
++
++ common /dmolec/ segid_mol(maxat), id_mol(maxat)
++ character segid_mol*4, id_mol*4
+ c
+- save /molec/, /cmolec/
++ save /molec/, /cmolec/, /dmolec/
+ c
+ c=========================================================================
+
+@@ -903,6 +906,8 @@
+ do 30 i=1,6
+ b_mol(i,nat) = b(i)
+ 30 continue
++ segid_mol(nat) = segid
++ id_mol(nat) = id
+ c
+ c
+ c Store chain as left-justified *4
+@@ -951,7 +956,10 @@
+ $ chain_mol(maxat)
+ character atname_mol*4, restyp_mol*4, chain_mol*4
+ c
+- save /molec/, /cmolec/
++ common /dmolec/ segid_mol(maxat), id_mol(maxat)
++ character segid_mol*4, id_mol*4
++c
++ save /molec/, /cmolec/, /dmolec/
+ c
+ c=========================================================================
+
+@@ -959,6 +967,8 @@
+ c
+ integer i, ixyzin, ixyzout, k
+ real xx, yy, zz, occ, b(6)
++ character resno*4, inscod*1, altcod*1
++ integer iz
+ c
+ istat = +1
+
+@@ -987,6 +997,9 @@
+ b(i) = b_mol(i,k)
+ 20 continue
+
++ call XYZATOM(IXYZOUT,k,atname_mol(k),restyp_mol(k),
++ $ chain_mol(k),numres_mol(k),resno,inscod,altcod,segid_mol(k),
++ $ iz,id_mol(k))
+ call XYZCOORD(IXYZOUT,'O','B',xx,yy,zz,occ,biso,b)
+ call XYZADVANCE(IXYZOUT,0,0,*30,*30)
+ 10 continue
+@@ -1236,7 +1249,7 @@
+ c spec*(*) atom specification
+ c
+ c On exit:
+-c chain chain ID, left-justfied, unchanged if absent
++c chain chain ID, left-justified, unchanged if absent
+ c iresidue residue number, , unchanged if absent
+ c atname atom name, left-justified
+ c istat = 0 OK, = -1 illegal format
+@@ -1291,7 +1304,7 @@
+ $ plane_normal, cofg, rmat, thickness, radii, radius, istat)
+ c =============================================================
+ c
+-c Fit atoms to plane, from principle axes of inertia matrix
++c Fit atoms to plane, from principal axes of inertia matrix
+ c
+ c On entry:
+ c xyz(3,nat) atom coordinates
+@@ -1306,9 +1319,9 @@
+ c cofg(3) centre of gravity of plane
+ c rmat(3,3) rotation matrix to rotate into plane coordinates
+ c (plane normal along z)
+-c thickness(3) "thickness" = weighted rms deviation along principle axes
++c thickness(3) "thickness" = weighted rms deviation along principal axes
+ c radii(3) "radii" = weighted rms deviation in plane perpendicular
+-c to principle axes
++c to principal axes
+ c radius rms radius
+ c istat = 0 OK, = -1 failure (too few atoms)
+ c
+@@ -1365,7 +1378,7 @@
+ c
+ call eign3(a, vmat, resid)
+ c resid eigenvalues of residual matrix, in descending order
+-c = sums of weighted squared residuals along principle directions
++c = sums of weighted squared residuals along principal directions
+ c vmat(i,j) eigenvector matrix
+ c column vmat(.,3) is the plane normal
+ c
+@@ -1699,7 +1712,7 @@
+ C (Leading spaces ignored; further space terminates
+ C the number string interpreted)
+ C FP (W) Returns the value as a floating point value (0.0 if
+-C synatx error)
++C syntax error)
+ C IV (W) Returns the value as an integer (the nearest integer
+ C if value contained a decimal point) (0 if syntax
error)
+ C
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