Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12923
Modified Files: ccp4.info ccp4.patch Log Message: ccp4 10.4 unstable patch update Index: ccp4.info =================================================================== RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v retrieving revision 1.7 retrieving revision 1.8 diff -u -d -r1.7 -r1.8 --- ccp4.info 3 Mar 2006 06:54:04 -0000 1.7 +++ ccp4.info 23 Mar 2006 06:22:09 -0000 1.8 @@ -1,6 +1,6 @@ Package: ccp4 Version: 6.0 -Revision: 1002 +Revision: 1003 GCC: 4 Architecture: powerpc Source: ftp://ftp.%n.ac.uk/%n/%v.0/packed/%n-%v.0-core-src.tar.gz @@ -191,20 +191,20 @@ << #lib/ccp4-6.0/libmmdb.dylib Shlibs: << - %p/lib/ccp4-6.0/libccif.dylib 0.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libccp4c.dylib 0.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libjwc_c.0.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libjwc_c.0.1.1.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libjwc_c.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libxdl_view.2.dylib 3.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libxdl_view.2.0.0.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libxdl_view.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libxdl_viewextra.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libxdl_viewextra.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libxdl_viewextra.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libssm.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libssm.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libssm.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) + %p/lib/ccp4-6.0/libccif.dylib 0.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libccp4c.dylib 0.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libjwc_c.0.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libjwc_c.0.1.1.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libjwc_c.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libxdl_view.2.dylib 3.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libxdl_view.2.0.0.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libxdl_view.dylib 2.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libxdl_viewextra.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libxdl_viewextra.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libxdl_viewextra.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libssm.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libssm.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libssm.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) << DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS academic_software_licence.pdf Description: Essential dynamic libraries for CCP4 @@ -213,7 +213,7 @@ for ccp4. It excludes the clipper dynamic libraries, which may be buggy. << << -# %p/lib/ccp4-6.0/libmmdb.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) +# %p/lib/ccp4-6.0/libmmdb.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) # ################################################################################ SplitOff2: << @@ -251,27 +251,27 @@ lib/ccp4-6.0/libclipper-phs.dylib << Shlibs: << - %p/lib/ccp4-6.0/libclipper-ccp4.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-ccp4.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-ccp4.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-cif.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-cif.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-cif.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-contrib.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-contrib.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-contrib.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-core.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-core.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-core.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-minimol.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-minimol.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-minimol.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-mmdb.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-mmdb.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-mmdb.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-phs.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-phs.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) - %p/lib/ccp4-6.0/libclipper-phs.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1002) + %p/lib/ccp4-6.0/libclipper-ccp4.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-ccp4.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-ccp4.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-cif.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-cif.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-cif.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-contrib.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-contrib.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-contrib.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-core.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-core.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-core.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-minimol.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-minimol.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-minimol.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-mmdb.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-mmdb.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-mmdb.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-phs.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-phs.0.0.0.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) + %p/lib/ccp4-6.0/libclipper-phs.dylib 1.0.0 ccp4lib-shlibs (>= 6.0-1003) << DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS academic_software_licence.pdf << @@ -341,7 +341,7 @@ 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 Feb 26, 2006. +This revision includes all available CCP4 patches as of Mar 22, 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/unstable/main/finkinfo/sci/ccp4.patch,v retrieving revision 1.4 retrieving revision 1.5 diff -u -d -r1.4 -r1.5 --- ccp4.patch 27 Feb 2006 22:54:32 -0000 1.4 +++ ccp4.patch 23 Mar 2006 06:22:09 -0000 1.5 @@ -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 @@ -1173,6 +1185,263 @@ +*** 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 @@ -1195,3 +1464,155 @@ 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 ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. 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