Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13458
Modified Files:
ccp4-onlylibs-dev.info
Added Files:
ccp4-onlylibs-dev.patch
Log Message:
ccp4-onlylibs.dev 10.4 unstable patch update
--- NEW FILE: ccp4-onlylibs-dev.patch ---
diff -ruN ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h
ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h
--- ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h 2005-09-08
13:07:42.000000000 -0700
+++ ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h 2006-03-22
21:17:07.000000000 -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-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h.orig
ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h.orig
--- ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h.orig
1969-12-31 16:00:00.000000000 -0800
+++ ccp4-onlylibs-dev/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-onlylibs-dev-orig/lib/clipper/src/cphasecombine.cpp
ccp4-onlylibs-dev/lib/clipper/src/cphasecombine.cpp
--- ccp4-onlylibs-dev-orig/lib/clipper/src/cphasecombine.cpp 2005-09-09
03:50:39.000000000 -0700
+++ ccp4-onlylibs-dev/lib/clipper/src/cphasecombine.cpp 2006-03-22
21:16:33.000000000 -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-onlylibs-dev-orig/lib/clipper/src/pirancslib.cpp
ccp4-onlylibs-dev/lib/clipper/src/pirancslib.cpp
--- ccp4-onlylibs-dev-orig/lib/clipper/src/pirancslib.cpp 2005-10-14
02:37:23.000000000 -0700
+++ ccp4-onlylibs-dev/lib/clipper/src/pirancslib.cpp 2006-03-22
21:17:43.000000000 -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-onlylibs-dev-orig/lib/src/ccplib.f
ccp4-onlylibs-dev/lib/src/ccplib.f
--- ccp4-onlylibs-dev-orig/lib/src/ccplib.f 2005-09-08 08:17:41.000000000
-0700
+++ ccp4-onlylibs-dev/lib/src/ccplib.f 2006-03-22 21:16:02.000000000 -0800
@@ -16,7 +16,7 @@
C amalgamate ccppsf and fdir/fext/froot. also add tests of these
C routines to testlib.
C
-C $Id: ccplib.f,v 1.102 2005/09/08 15:17:41 mdw Exp $
+C $Id: ccplib.f,v 1.103 2006/02/27 15:26:20 ccb Exp $
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
Index: ccp4-onlylibs-dev.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- ccp4-onlylibs-dev.info 3 Mar 2006 23:53:19 -0000 1.8
+++ ccp4-onlylibs-dev.info 23 Mar 2006 06:23:07 -0000 1.9
@@ -1,7 +1,7 @@
Package: ccp4-onlylibs-dev
# Use version numbering to sync with the current CCP4 release:
Version: 6.0
-Revision: 1010
+Revision: 1011
GCC: 4.0
#Source: ftp://ftp.ccp4.ac.uk/prerelease/%n.tar.gz
#Source-MD5: cf085751833aecc7ccef9e67de7e9fcc
@@ -19,6 +19,7 @@
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
###############################################################################
+Patch: %n.patch
PatchScript: <<
#!/bin/zsh -ef
umask 0022
@@ -150,6 +151,7 @@
CCP4lib files will be installed under
%p/share/xtal/ccp4-onlylibs-dev-6.0. This is essentially
identical in content to the corresponding files in CCP4 6.0.
+Includes patches from ccp4 through March 22, 2006.
Programs requiring these libraries to build or run need to
source the appropriate
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