1 |
jlec 10/04/25 12:32:54 |
2 |
|
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Modified: 6.1.3-rename-superpose.patch |
4 |
6.1.3-rename-rapper.patch |
5 |
6.1.3-rename-truncate.patch |
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Log: |
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Fixes missing renames, thanks Johan Hattne for giving the patches, #314053 |
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(Portage version: 2.2_rc67/cvs/Linux x86_64) |
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|
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Revision Changes Path |
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1.2 sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch?rev=1.2&view=markup |
14 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch?rev=1.2&content-type=text/plain |
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diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch?r1=1.1&r2=1.2 |
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|
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Index: 6.1.3-rename-superpose.patch |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch,v |
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retrieving revision 1.1 |
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retrieving revision 1.2 |
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diff -u -r1.1 -r1.2 |
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--- 6.1.3-rename-superpose.patch 6 Feb 2010 00:24:32 -0000 1.1 |
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+++ 6.1.3-rename-superpose.patch 25 Apr 2010 12:32:54 -0000 1.2 |
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@@ -1,6 +1,7 @@ |
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-diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script |
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---- ccp4-6.1.1/ccp4i/scripts/superpose.script 2006-07-26 16:22:49.000000000 +0200 |
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-+++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script 2009-07-05 22:11:59.000000000 +0200 |
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+diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script |
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+index 3483c97..5027536 100755 |
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+--- a/ccp4i/scripts/superpose.script |
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++++ b/ccp4i/scripts/superpose.script |
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@@ -21,7 +21,7 @@ |
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|
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if { [regexp SSM $SUPERPOSE_MODE ] } { |
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@@ -10,3 +11,16 @@ |
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set status [Execute $cmd "" program_status report ] |
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|
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} elseif { [regexp TOP $SUPERPOSE_MODE ] } { |
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+diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl |
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+index 748bf6e..c92122a 100755 |
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+--- a/ccp4i/tasks/superpose.tcl |
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++++ b/ccp4i/tasks/superpose.tcl |
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+@@ -100,7 +100,7 @@ proc superpose_run { arrayname } { |
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+ # If user is match equivalent named residues/atoms then fit in the match fields |
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+ switch [GetValue $arrayname SUPERPOSE_MODE] \ |
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+ SSM { |
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+- if { ![file exists [FindExecutable superpose]] } { |
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++ if { ![file exists [FindExecutable superpose-ccp4]] } { |
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+ WarningMessage "The program \"superpose\" is not on your path. |
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+ Check your installation for \"superpose\" program and \"ssm\" library." |
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+ return 0 |
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|
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|
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|
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1.2 sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch?rev=1.2&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch?rev=1.2&content-type=text/plain |
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diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch?r1=1.1&r2=1.2 |
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|
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Index: 6.1.3-rename-rapper.patch |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch,v |
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retrieving revision 1.1 |
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retrieving revision 1.2 |
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diff -u -r1.1 -r1.2 |
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--- 6.1.3-rename-rapper.patch 6 Feb 2010 00:24:32 -0000 1.1 |
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+++ 6.1.3-rename-rapper.patch 25 Apr 2010 12:32:54 -0000 1.2 |
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@@ -1,5 +1,20 @@ |
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---- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100 |
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-+++ ccp4i/scripts/rapper.script.new 2009-03-12 23:34:47.000000000 +0100 |
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+diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script |
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+index def44bc..dd4bb7e 100755 |
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+--- a/ccp4i/scripts/check.script |
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++++ b/ccp4i/scripts/check.script |
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+@@ -24,7 +24,7 @@ |
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+ if $RUN_RAMPAGE { |
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+ |
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+ # Generate command line |
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+- set cmd "[BinPath rapper]" |
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++ set cmd "[BinPath rappermc]" |
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+ |
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+ set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] |
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+ set paramsfile [FileJoin $rapperdatadir params.xml] |
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+diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script |
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+index cdae1e2..faae226 100755 |
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+--- a/ccp4i/scripts/rapper.script |
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++++ b/ccp4i/scripts/rapper.script |
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@@ -17,7 +17,7 @@ |
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|
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#set up command line |
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@@ -9,4 +24,38 @@ |
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|
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set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] |
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set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] |
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- |
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+@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT" |
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+ |
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+ # Run RAPPER to join loop back to framework and out put to defined pdb file |
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+ # Also need to sort out multimodel files join - FIX ME |
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+-set cmd2 "[BinPath rapper]" |
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++set cmd2 "[BinPath rappermc]" |
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+ append cmd2 " $paramsfile joinpdb " |
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+ append cmd2 " --pdb2 \"$root\-loop.pdb\" " |
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+ append cmd2 " --pdb \"$root\-framework.pdb\" " |
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+diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl |
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+index ae88ff2..ee3307b 100755 |
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+--- a/ccp4i/tasks/check.tcl |
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++++ b/ccp4i/tasks/check.tcl |
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+@@ -46,7 +46,7 @@ proc check_run { arrayname } { |
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+ # Check for Rampage program. If it is not found, we switch off the option. |
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+ # If it was the only option, script will fail with next check. |
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+ if { $array(RUN_RAMPAGE) == 1 } { |
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+- if { [FindExecutable "rapper"] == "" } { |
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++ if { [FindExecutable "rappermc"] == "" } { |
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+ WarningMessage "Input Error: Rapper_Rampage program not found in system path." |
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+ set array(RUN_RAMPAGE) 0 |
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+ } |
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+diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl |
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+index e299057..8843a3f 100755 |
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+--- a/ccp4i/tasks/rapper.tcl |
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++++ b/ccp4i/tasks/rapper.tcl |
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+@@ -28,7 +28,7 @@ proc rapper_run { arrayname } { |
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+ # Check for RAPPER program. If it is not found, we switch off the option. |
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+ # If it was the only option, script will fail with next check. |
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+ if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} { |
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+- if { [FindExecutable "rapper"] == "" } { |
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++ if { [FindExecutable "rappermc"] == "" } { |
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+ WarningMessage "Input Error: RAPPER program not found in system path." |
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+ set build_type 0 |
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+ } |
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|
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|
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|
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1.2 sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch?rev=1.2&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch?rev=1.2&content-type=text/plain |
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diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch?r1=1.1&r2=1.2 |
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|
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Index: 6.1.3-rename-truncate.patch |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch,v |
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retrieving revision 1.1 |
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retrieving revision 1.2 |
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diff -u -r1.1 -r1.2 |
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--- 6.1.3-rename-truncate.patch 6 Feb 2010 00:24:32 -0000 1.1 |
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+++ 6.1.3-rename-truncate.patch 25 Apr 2010 12:32:54 -0000 1.2 |
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@@ -1,16 +1,85 @@ |
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---- ./ccp4i/templates/truncate.com.orig 2009-03-02 23:31:04.000000000 -0800 |
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-+++ ./ccp4i/templates/truncate.com 2009-03-02 23:31:08.000000000 -0800 |
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-@@ -11,7 +11,7 @@ |
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- $SYMMETRY symmetry $SPACE_GROUP |
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- $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6 |
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- |
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--1 truncate |
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-+1 ftruncate |
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- - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO |
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- {[IfSet $ANOMALOUS]} anomalous |
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- - $ANOMALOUS YES | NO |
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---- ./ccp4i/scripts/truncate.script.orig 2009-03-02 23:39:04.000000000 -0800 |
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-+++ ./ccp4i/scripts/truncate.script 2009-03-02 23:39:41.000000000 -0800 |
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+diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl |
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+index 7d05905..d01f1dc 100755 |
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+--- a/ccp4i/crank/plugins/prep/crank_prep.tcl |
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++++ b/ccp4i/crank/plugins/prep/crank_prep.tcl |
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+@@ -226,7 +226,7 @@ proc run_truncate { i j } { |
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+ set script "$script\n$labout" |
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+ set script "$script\nEND\n" |
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+ |
172 |
+- set run_command "truncate $command << \"$script\"" |
173 |
++ set run_command "ftruncate $command << \"$script\"" |
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+ puts $run_command |
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+ catch {eval exec $run_command } output |
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+ puts $output |
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+diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script |
178 |
+index e74aa0d..a2a1adb 100755 |
179 |
+--- a/ccp4i/scripts/dtrek2mtz.script |
180 |
++++ b/ccp4i/scripts/dtrek2mtz.script |
181 |
+@@ -36,7 +36,7 @@ |
182 |
+ set HKL_TRUNCATE [GetTmpFileName -ext mtz] |
183 |
+ |
184 |
+ CreateComScript truncate truncate_script |
185 |
+- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
186 |
++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
187 |
+ set status [Execute $cmd $truncate_script program_status report] |
188 |
+ |
189 |
+ HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate |
190 |
+diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script |
191 |
+index 90cba83..1c90c33 100755 |
192 |
+--- a/ccp4i/scripts/import.script |
193 |
++++ b/ccp4i/scripts/import.script |
194 |
+@@ -144,7 +144,7 @@ if { $FORMAT == "MTZ" } { |
195 |
+ |
196 |
+ set truncatemtz [GetTmpFileName -ext mtz ] |
197 |
+ CreateComScript truncate truncate_script |
198 |
+- set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" |
199 |
++ set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" |
200 |
+ set status [Execute $cmd $truncate_script program_status report] |
201 |
+ |
202 |
+ |
203 |
+diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script |
204 |
+index dcc619b..7250513 100755 |
205 |
+--- a/ccp4i/scripts/import_scaled.script |
206 |
++++ b/ccp4i/scripts/import_scaled.script |
207 |
+@@ -62,7 +62,7 @@ |
208 |
+ |
209 |
+ } else { |
210 |
+ CreateComScript truncate truncate_script |
211 |
+- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
212 |
++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
213 |
+ set status [Execute $cmd $truncate_script program_status report] |
214 |
+ |
215 |
+ HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate |
216 |
+diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script |
217 |
+index 6940ccd..bde10d6 100755 |
218 |
+--- a/ccp4i/scripts/scala.script |
219 |
++++ b/ccp4i/scripts/scala.script |
220 |
+@@ -275,7 +275,7 @@ END" |
221 |
+ |
222 |
+ } else { |
223 |
+ CreateComScript truncate truncate_script |
224 |
+- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
225 |
++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
226 |
+ set status [Execute $cmd $truncate_script $LOG_FILE program_status report ] |
227 |
+ } |
228 |
+ |
229 |
+diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script |
230 |
+index 986e06c..a1947a6 100755 |
231 |
+--- a/ccp4i/scripts/scalepack2mtz.script |
232 |
++++ b/ccp4i/scripts/scalepack2mtz.script |
233 |
+@@ -35,7 +35,7 @@ |
234 |
+ |
235 |
+ set HKL_TRUNCATE [GetTmpFileName -ext mtz] |
236 |
+ CreateComScript truncate truncate_script |
237 |
+- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
238 |
++ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
239 |
+ set status [Execute $cmd $truncate_script program_status report] |
240 |
+ |
241 |
+ HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate |
242 |
+diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script |
243 |
+index e0e09ce..2d448a2 100755 |
244 |
+--- a/ccp4i/scripts/truncate.script |
245 |
++++ b/ccp4i/scripts/truncate.script |
246 |
@@ -45,7 +45,7 @@ |
247 |
|
248 |
CreateComScript truncate truncate_script |