Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11916
Modified Files:
clipper.info
Added Files:
clipper.patch
Log Message:
clipper bug fix for cif file i/o bug causing coot to seg fault
--- NEW FILE: clipper.patch ---
--- clipper-2.1.20130601/clipper/cif/cif_data_io.cpp 2012-03-07
03:59:51.000000000 -0800
+++ clipper-2.1-fixup/clipper/cif/cif_data_io.cpp 2012-07-16
07:18:48.000000000 -0700
@@ -66,8 +66,7 @@
{
mode = NONE;
- // Argh, bug. It's things like this that make me dislike object
- // oriented programming - "Magic happens behind your back". The
+ // The
// problem was that we were trying to import into f_phi_i in
// close_read() when f_phi_i had not been initialised by calling
// import_hkl_data for it (because it comes from a function that
@@ -80,7 +79,11 @@
f_sigf_i = NULL;
f_phi_i = NULL;
rfree_i = NULL;
-
+ d_sigd_i = NULL;
+ ABCD_i = NULL;
+ I_sigI_i = NULL;
+ f_sigf_ano_i = NULL;
+
// set these when we find them....
clipper_cell_set_flag = 0;
clipper_reso_set_flag = 0;
@@ -184,9 +187,13 @@
Message::message( Message_fatal( "CIFfile: no file open for read" ) );
// make sure the data list is sized
- if ( f_sigf_i != NULL ) f_sigf_i->update();
- if ( f_phi_i != NULL ) f_phi_i->update();
- if ( rfree_i != NULL ) rfree_i->update();
+ if ( f_sigf_i != NULL ) f_sigf_i->update();
+ if ( f_phi_i != NULL ) f_phi_i->update();
+ if ( rfree_i != NULL ) rfree_i->update();
+ if ( d_sigd_i != NULL ) d_sigd_i->update();
+ if ( ABCD_i != NULL ) ABCD_i->update();
+ if ( I_sigI_i != NULL ) I_sigI_i->update();
+ if ( f_sigf_ano_i != NULL ) f_sigf_ano_i->update();
int ret_val = 0;
int n_calc_data = 0;
@@ -288,29 +295,32 @@
}
// RFree flag
- char *s = mmCIFLoop->GetString("status", j, ierr_rfree_flag);
- if (! ierr_rfree_flag) {
- x1[0] = -1;
- if (s) {
- // std::cout << "read status :" << s << ":" << std::endl;
- if (strncmp(s, "o", 1)) {
- x1[0] = 1;
- } else {
- if (strncmp(s, "f", 1)) {
- x1[0] = 0;
+ if (rfree_i) {
+ char *s = mmCIFLoop->GetString("status", j, ierr_rfree_flag);
+ if (! ierr_rfree_flag) {
+ x1[0] = -1;
+ if (s) {
+ // std::cout << "read status :" << s << ":" <<
std::endl;
+ // could be also "x"; not observed, just listed
+ if (! strncmp(s, "o", 1)) {
+ x1[0] = 1;
+ } else {
+ if (! strncmp(s, "f", 1)) {
+ x1[0] = 0;
+ }
}
}
+ //
+ // Every output reflection gets one of these, even if
+ // it is set to -1. Is that the correct thing to do?
+ // I have looked at over 200 recent sf mmCIFs and if
+ // the contain conventional data then they all have
+ // the status flag.
+ //
+ // However, SFS from EM data do not
+ //
+ rfree_i->data_import( HKL(h,k,l), x1);
}
- //
- // Every output reflection gets one of these, even if
- // it is set to -1. Is that the correct thing to do?
- // I have looked at over 200 recent sf mmCIFs and if
- // the contain conventional data then they all have
- // the status flag.
- //
- // However, SFS from EM data do not
- //
- rfree_i->data_import( HKL(h,k,l), x1);
}
Index: clipper.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- clipper.info 9 Aug 2013 04:09:02 -0000 1.6
+++ clipper.info 28 Aug 2013 16:10:17 -0000 1.7
@@ -1,7 +1,7 @@
Package: clipper
Epoch: 1
Version: 2.1.20130601
-Revision: 1
+Revision: 2
GCC:4.0
BuildDepends: <<
fftw (>= 2.1.5-1010) | fftw-mpi (>= 2.1.5-1010),
@@ -19,6 +19,8 @@
Source: ftp://ftp.ccp4.ac.uk/opensource/%n-%v.tar.gz
Source-MD5: 2e0d3faec7cc5a1eb377392122e6e254
SourceDirectory: %n-%v
+PatchFile: %n.patch
+Patchfile-MD5: 986698b06772d70cfd2fe06f296f8210
DocFiles: README AUTHORS COPYING ChangeLog
Description: Object-oriented crystallographic libraries
DescDetail: <<
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