Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4482
Added Files:
refmac.info refmac.patch
Log Message:
reintroduce stand-alone refmac package to augment coot
--- NEW FILE: refmac.patch ---
diff -ruN refmac-orig/covmat.h refmac/covmat.h
--- refmac-orig/covmat.h 2011-11-30 17:03:44.000000000 -0800
+++ refmac/covmat.h 2013-08-14 15:13:23.000000000 -0700
@@ -44,7 +44,7 @@
~covar_matrix();
void Make_matrix(); //
computes re and im from sigmas and D's
void Print();
- void SetZeroRows(int,int,int,int,int,int); // specifies the order
numbers of rows(=columns) for which the covariances should be 0.
+ void SetZeroRows(int = -1,int = -1,int = -1,int = -1,int = -1,int =
-1); // specifies the order numbers of rows(=columns) for which the
covariances should be 0.
int CheckZeroRow(int row); // returns 1 if
row has been set to be covariance zeroed, 0 otherwise
int GetNumZeroRows(); // returns the
number of rows with covariaces zeroed
@@ -2106,7 +2106,7 @@
// defines zero rows. If the first argument is negative, resets all no
non-zero.
template <typename realnum>
-void covar_matrix<realnum>::SetZeroRows( int r1=-1, int r2=-1, int r3=-1, int
r4=-1, int r5=-1, int r6=-1 )
+void covar_matrix<realnum>::SetZeroRows( int r1, int r2, int r3, int r4, int
r5, int r6 )
{
int r[6] = {r1,r2,r3,r4,r5,r6};
int i=0;
diff -ruN refmac-orig/makefile refmac/makefile
--- refmac-orig/makefile 2011-07-19 03:41:56.000000000 -0700
+++ refmac/makefile 2013-08-14 15:15:22.000000000 -0700
@@ -1,19 +1,29 @@
-VERSION = gfortran
-FC = gfortran
-CC = gcc
-CPP = g++
-FOPTIM = -O2
-COPTIM = -O2
-XFFLAGS = -fno-second-underscore -static
-
-XCFLAGS = -DGFORTRAN -DPROTOTYPE
-FFLAGS = $(FOPTIM) $(XFFLAGS)
-CFLAGS = $(COPTIM) $(XCFLAGS)
+VERSION = 5
+FC = ${PREFIX_SW}/lib/gcc4.8/bin/gfortran
+CC = llvm-gcc-4.2
+CXX = llvm-g++-4.2
+FOPTIM = -O3
+COPTIM = -O
+XFFLAGS = -m64 -fno-second-underscore
+
+
+XCFLAGS = -DGFORTRAN -DPROTOTYPE
+FFLAGS = $(FOPTIM) $(XFFLAGS)
+
+
+CFLAGS = $(COPTIM) $(XCFLAGS)
CPPFLAGS = $(CFLAGS)
+CLIB = ${PREFIX_SW}/lib
+
LLIBCIF =
-LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a
-LLIBLAPACK = $(CLIB)/liblapack.a $(CLIB)/libblas.a
-LLIBOTHERS = -lgfortran -lgfortranbegin -lstdc++
+BLAS_DIR =
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A
+
+LLIBCCP = /usr/lib/libSystem.B.dylib ${BLAS_DIR}/libBLAS.dylib
${BLAS_DIR}/libLAPACK.dylib
+
+LLIBLAPACK =
+
+LLIBOTHERS = -L/usr/lib -L${CLIB} -L${PREFIX_SW}/lib/gcc4.8/lib -lgfortran
${CLIB}/libccp4c.dylib ${CLIB}/libccp4f.dylib -lstdc++
/usr/lib/libSystem.B.dylib -lSystem -lm
include makefile_refmac.inc1
+
--- NEW FILE: refmac.info ---
Package: refmac
Version: 5.7.0032
Revision: 1
Source:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/SourceEtal/%n5.7_source_v%v.tar.gz
Source-MD5: 6bde74d6fc1c7f32026ced6fd8741c99
Source2:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/Dictionary/%n_dictionary_v5.41.tar.gz
Source2-MD5: e7acb760fcbbe663147f5245b6c523c4
NoSourceDirectory: yes
Depends: gcc48-shlibs (>= 4.8.1-1000), libccp4-shlibs (>= 6.3.1-2),
libccp4-lib (>= 6.3.1-2)
BuildDepends: gcc48 (>= 4.8.1-1000), gcc48-compiler (>= 4.8.1-1000),
libccp4-dev (>= 6.3.1-2)
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchFile: refmac.patch
PatchFile-MD5: e15a5cbe31c50217a5c907c6e2c1cc80
CompileScript: <<
#!/bin/bash -efv
export PREFIX_SW=%p
make -j 1 refmac
<<
InstallScript: <<
#!/bin/bash -efv
mkdir -p %i/bin
mkdir -p %i/share/%n
mkdir -p %i/etc/profile.d
cp refmac5 %i/bin/.
cp refmac5 %i/bin/%n
touch %i/share/%n/environ.def %i/share/%n/default.def
cp -R monomers %i/share/%n/.
#
echo 'if [[ ! -f ${CINCL}/environ.def ]];then' >
%i/etc/profile.d/refmac.sh
echo ' export CINCL=%p/share/%n' >>
%i/etc/profile.d/refmac.sh
echo ' export CCP4_SCR="/tmp/$USER"; mkdir -p "$CCP4_SCR"' >>
%i/etc/profile.d/refmac.sh
echo 'fi' >>
%i/etc/profile.d/refmac.sh
#
echo 'if ( ! -d ${CINCL} ) then' >
%i/etc/profile.d/refmac.csh
echo ' setenv CINCL %p/share/%n' >>
%i/etc/profile.d/refmac.csh
echo ' setenv CCP4_SCR "/tmp/$USER"; mkdir -p "$CCP4_SCR"' >>
%i/etc/profile.d/refmac.csh
echo 'endif' >>
%i/etc/profile.d/refmac.csh
<<
RunTimeVars: <<
CLIBD_MON: %p/share/%n/monomers/
SYMINFO: %p/share/ccp4/syminfo.lib
ATOMSF: %p/share/ccp4/atomsf.lib
<<
Description: CCP4 refmac5 standalone update
DescDetail: <<
This is a drop-in update replacement for refmac5. As long as you have
sourced %p/bin/init.(c)sh and %p is at the head of your path, no further
configuration is required.
<<
License: LGPL
Homepage: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
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