Author: bugman
Date: Fri Aug 12 10:52:37 2011
New Revision: 14369
URL: http://svn.gna.org/viewcvs/relax?rev=14369&view=rev
Log:
Merged revisions
13961,13983-13984,14008-14009,14011,14013,14071,14103,14107-14110,14146,14157,14179,14181,14185,14249,14262,14285,14292,14324,14329,14331,14333,14335-14336,14338,14341-14343,14347-14352,14354-14355,14361-14366
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
................
r13961 | bugman | 2011-07-28 16:53:26 +0200 (Thu, 28 Jul 2011) | 3 lines
Fix for the overriding of the command line specified mode - the args must
be processed anyway.
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r13983 | bugman | 2011-07-29 09:59:57 +0200 (Fri, 29 Jul 2011) | 3 lines
Created a basic system test checking the reading of a non-PDB file by
structure.read_pdb.
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r13984 | bugman | 2011-07-29 10:06:14 +0200 (Fri, 29 Jul 2011) | 5 lines
Fix for structure.read_pdb for when the file contains no PDB data.
This is now caught, and a warning is given and the function exists cleanly.
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r14008 | bugman | 2011-07-29 18:36:30 +0200 (Fri, 29 Jul 2011) | 3 lines
Shifted the pedantic flag into the status object.
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r14009 | bugman | 2011-07-29 18:37:15 +0200 (Fri, 29 Jul 2011) | 3 lines
RelaxWarnings now only show a traceback when the pedantic flag is True.
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r14011 | bugman | 2011-07-29 19:01:35 +0200 (Fri, 29 Jul 2011) | 5 lines
The relax state is now saved on a RelaxError when the pedantic rather than
debugging flag is turned on.
As both flags can be given, this allows for this state saving to be
activated or deactivated.
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r14013 | bugman | 2011-07-29 19:08:13 +0200 (Fri, 29 Jul 2011) | 3 lines
The relax_io.read_spin_data() function no longer skips short lines so that
a warning is given for it.
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r14071 | bugman | 2011-08-02 16:54:53 +0200 (Tue, 02 Aug 2011) | 5 lines
generic_fns.sequence.validate_sequence() now also checks for the spin ID,
data and error columns.
This is now used by relax_io.read_spin_data().
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r14103 | bugman | 2011-08-04 11:08:58 +0200 (Thu, 04 Aug 2011) | 6 lines
Fix for the RelaxWarning system on Mac OS X, the base class __str__ method
now returns a simple string.
On a Mac, the warning message text was in unicode whereas the __str__()
method must return a standard
string. So now __str__() is using the str() method to convert.
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r14107 | bugman | 2011-08-04 11:37:57 +0200 (Thu, 04 Aug 2011) | 6 lines
Files created by the grace.write user function are now put into a new list
cdp.results_files.
This is a list of lists, with the sublist composed of two elements. The
first is an identifier
string such as 'grace'. The second is the file name.
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r14108 | bugman | 2011-08-04 11:39:43 +0200 (Thu, 04 Aug 2011) | 3 lines
Fix for the addition of grace files to cdp.result_files - the file path is
now used.
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r14109 | bugman | 2011-08-04 11:41:13 +0200 (Thu, 04 Aug 2011) | 5 lines
Another fix for the grace.write user function addition to the
cdp.result_files list.
The proper variable name is now used.
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r14110 | bugman | 2011-08-04 11:41:31 +0200 (Thu, 04 Aug 2011) | 3 lines
The value.write user function now also adds to the cdp.result_files
structure.
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r14146 | bugman | 2011-08-04 18:08:13 +0200 (Thu, 04 Aug 2011) | 5 lines
Fix for the structure.vectors user function.
It no longer complains about a PDB already loaded when no PDB has been
loaded.
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r14157 | bugman | 2011-08-04 20:24:02 +0200 (Thu, 04 Aug 2011) | 6 lines
Modified the execution lock to have a mode.
This allows for greater control and avoid string comparison of names to
determine if a script or
auto-analysis acquired the lock.
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r14179 | bugman | 2011-08-05 15:01:19 +0200 (Fri, 05 Aug 2011) | 5 lines
The dauvergne_protocol is now more robust if the program is interrupted and
restarted later.
The opt/results.bz2 file is now searched for, and if not the round is
assumed incomplete.
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r14181 | bugman | 2011-08-05 15:40:08 +0200 (Fri, 05 Aug 2011) | 5 lines
Fix for the resetting of the global optimisation round in the
dauvergne_protocol auto-analysis.
The value was being reset to None at every round.
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r14185 | bugman | 2011-08-05 15:50:37 +0200 (Fri, 05 Aug 2011) | 5 lines
Fix for the round determination in the dauvergne_protocol auto-analysis.
The 'opt' directory was missing in the path.
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r14249 | bugman | 2011-08-08 11:12:46 +0200 (Mon, 08 Aug 2011) | 6 lines
Bug fix for the saving/loading of a results file in GUI mode.
The save files were containing the ds.relax_gui object and restoring it on
loading. This caused
the data storage of the GUI to change underneath the GUI resulting in a
crash or race conditions.
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r14262 | bugman | 2011-08-08 17:10:15 +0200 (Mon, 08 Aug 2011) | 6 lines
Bug fix for the resetting of the relax data store - the cdp structure is
now set to None.
Previously the data store would be cleared, but the __builtin__.cdp
structure would point to the old
current data pipe, keeping it in existence.
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r14285 | bugman | 2011-08-09 12:07:39 +0200 (Tue, 09 Aug 2011) | 3 lines
The pymol.tensor_pdb() user function now shows the diffusion tensor using
PyMOL sticks.
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r14292 | bugman | 2011-08-09 14:42:06 +0200 (Tue, 09 Aug 2011) | 3 lines
Bug fix for the xydxdy type Grace graphs - the dx data was not being placed
in the file.
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r14324 | bugman | 2011-08-10 22:05:58 +0200 (Wed, 10 Aug 2011) | 6 lines
Bug fix for the structure.create_diff_tensor_pdb user function for when no
element info is available.
These atoms where the element is not in the PDB file or cannot be
determined should have been
skipped.
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r14329 | bugman | 2011-08-11 08:45:10 +0200 (Thu, 11 Aug 2011) | 3 lines
Bug fix for the molmol macro user functions - one of the args 'param'
should have been 'data_type'.
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r14331 | bugman | 2011-08-11 08:49:24 +0200 (Thu, 11 Aug 2011) | 5 lines
Bug fix for the spin_loop() calls when generating Molmol macros.
The full_info argument should have been set to True.
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r14333 | bugman | 2011-08-11 10:08:26 +0200 (Thu, 11 Aug 2011) | 3 lines
Fix for the molmol.write macro creation user function - the file arg can be
None!
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r14335 | bugman | 2011-08-11 10:13:18 +0200 (Thu, 11 Aug 2011) | 6 lines
Bug fix for the molmol.write user function for model-free parameters.
Some of the parameters were using the ancient self.relax code path which
was eliminated with the
redesign of relax 1.2 to 1.3.
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r14336 | bugman | 2011-08-11 10:16:24 +0200 (Thu, 11 Aug 2011) | 5 lines
Fixes for the old scripts/optimisation_testing.py script.
This was also using the ancient self.relax code path.
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r14338 | bugman | 2011-08-11 10:20:12 +0200 (Thu, 11 Aug 2011) | 3 lines
Fix for the molmol macro of the ts parameter, the spin container variable
was spelt incorrectly.
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r14341 | bugman | 2011-08-11 10:57:24 +0200 (Thu, 11 Aug 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12831" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/xyz
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r14342 | bugman | 2011-08-11 11:05:46 +0200 (Thu, 11 Aug 2011) | 967 lines
Merged revisions
12942,12946,12953,12958,12968,13061,13082,13089-13091,13106,13109-13110,13121-13122,13162-13165,13167,13169,13179-13180,13211,13214-13215,13227,13234-13235,13239,13245-13246,13249,13414-13417,13891,13894,13900,13924,13931,13933-13934,13944,13947,14038
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/xyz
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r12942 | bugman | 2011-06-09 18:49:18 +0200 (Thu, 09 Jun 2011) | 10 lines
Creation of a new system test test_read_xyz_internal1().
This is Han's patch http://gna.org/task/download.php?file_id=13143
attached to the task
http://gna.org/task/?7404.
In order to create a system test for reading the xyz file, a new function
'test_read_xyz_internal1()' has been generated in the
xyz/test_suite/system_tests/structure.py. It
is based on the function 'test_read_pdb_internal1()'.
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r12946 | bugman | 2011-06-09 20:02:09 +0200 (Thu, 09 Jun 2011) | 9 lines
Modifying the function test 'test_read_xyz_internal1()'.
This is Han's patch https://gna.org/task/download.php?file_id=13144
attached to the task
http://gna.org/task/?7404.
The function 'test_read_xyz_internal1()' was modified so that it is more
specific to the XYZ file
added to relax and for the new XYZ reader.
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r12953 | bugman | 2011-06-10 11:14:46 +0200 (Fri, 10 Jun 2011) | 8 lines
Modifying the function test 'test_read_xyz_internal1()'.
This is Han's patch https://gna.org/task/download.php?file_id=13147
attached to the task
http://gna.org/task/?7404.
In the 'test_read_xyz_internal1()' option parser='internal' has been
removed.
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r12958 | bugman | 2011-06-10 12:13:16 +0200 (Fri, 10 Jun 2011) | 9 lines
Generating new user function 'read_xyz()'.
This is Han's patch https://gna.org/task/download.php?file_id=13148
attached to the task
http://gna.org/task/?7404.
The user function 'read_xyz()' was generated in the prompt/structure.py
by duplication of
'read_pdb()' and modified accordingly.
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r12968 | bugman | 2011-06-10 15:08:46 +0200 (Fri, 10 Jun 2011) | 9 lines
Generating new user function 'read_xyz()'.
This is Han's patch https://gna.org/task/download.php?file_id=13153
attached to the task
http://gna.org/task/?7404.
The user function 'read_xyz()' was generated and modified in the
generic_fns/structure/main.py based
on the function 'read_pdb()'.
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r13061 | bugman | 2011-06-16 11:37:42 +0200 (Thu, 16 Jun 2011) | 11 lines
Adding a new test xyz file.
This is Han's patch https://gna.org/task/download.php?file_id=13224
attached to the task
http://gna.org/task/?7404.
This is a new xyz file, which contains several different models. This
file should be put in the
directory: test_suite/shared_data/structures.
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r13082 | bugman | 2011-06-17 10:38:40 +0200 (Fri, 17 Jun 2011) | 8 lines
Modifying the user function 'read_xyz()'.
This is Han's patch https://gna.org/task/download.php?file_id=13243
attached to the task
http://gna.org/task/?7404.
In the user function generic_fns/structure/main.py a single blank line
was removed.
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r13089 | bugman | 2011-06-17 11:17:27 +0200 (Fri, 17 Jun 2011) | 9 lines
Modifying test_suite/shared_data/structures/Indol_test.xyz
This is Han's patch https://gna.org/task/download.php?file_id=13245
attached to the task
http://gna.org/task/?7404.
In the test_suite/shared_data/structures/Indol_test.xyz 0.00000 after the
molecule name was removed.
The reason for that is because in a typical xyz file the second line is
just the molecule name.
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r13090 | bugman | 2011-06-17 11:39:57 +0200 (Fri, 17 Jun 2011) | 9 lines
Generating new system test 'test_read_xyz_internal2()'.
This is Han's patch https://gna.org/task/download.php?file_id=13246
attached
to the task http://gna.org/task/?7404.
The new system test was generated in test_suite/system_tests/structure.py
for
reading a xyz file 'SSS-cluster4-new-test.xyz' with multiple models.
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r13091 | bugman | 2011-06-17 12:05:06 +0200 (Fri, 17 Jun 2011) | 9 lines
Generating new user functions load_xyz() and __parse_models_xyz().
This is Han's patch https://gna.org/task/download.php?file_id=13247
attached to the task
http://gna.org/task/?7404.
New user functions load_xyz() and __parse_models_xyz() were generated in
generic_fns/structures/internal.py based on the functions load_pdb() and
__parse_models().
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r13106 | bugman | 2011-06-17 14:50:41 +0200 (Fri, 17 Jun 2011) | 9 lines
Changing the name of the user function __parse_models() to
__parse_models_pdb()
This is Han's patch https://gna.org/task/download.php?file_id=13250
attached to the task
http://gna.org/task/?7404.
The name of the user function __parse_models() in
'generic_fns/structure/internal.py' has been
changed to __parse_models_pdb(). This function is specific for reading
the pdb files.
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r13109 | bugman | 2011-06-17 15:57:30 +0200 (Fri, 17 Jun 2011) | 9 lines
Debugging and cleaning up the user functions load_xyz() and
__parse_models_xyz().
This is Han's patch https://gna.org/task/download.php?file_id=13251
attached to the task
http://gna.org/task/?7404.
Debugging and several print outs in the user functions load_xyz() and
__parse_models_xyz() in
generic_fns/structures/internal.py have been removed.
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r13110 | bugman | 2011-06-17 16:10:19 +0200 (Fri, 17 Jun 2011) | 9 lines
Generating two new functions '__parse_xyz_record()' and
'fill_object_from_xyz()'.
This is Han's patchhttps://gna.org/task/download.php?file_id=13252
attached to the task
http://gna.org/task/?7404.
Two new functions '__parse_xyz_record()' and 'fill_object_from_xyz()'
were generated in the class
'MolContainer()' in the file 'generic_fns/structure/internal.py'.
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r13121 | han87 | 2011-06-20 10:07:35 +0200 (Mon, 20 Jun 2011) | 4 lines
Debugging the user functions load_xyz() and test_read_xyz_internal2().
The user functions load_xyz() in 'generic_fns/structure/internal.py' and
test_read_xyz_internal2() in 'test_suite/system_tests/structure.py' have been
changed so that the molecule name can be read properly.
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r13122 | han87 | 2011-06-20 15:52:58 +0200 (Mon, 20 Jun 2011) | 5 lines
changing the description in the user functions load_spins() and
read_xyz().
An example for loading the spins for xyz file format was added in the
description of the user function load_spins() and the description of the user
function read_xyz() was changed. Both user functions are located in
'prompt/structure.py'.
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r13162 | han87 | 2011-06-22 16:11:25 +0200 (Wed, 22 Jun 2011) | 4 lines
Debugging in the system_test test_read_xyz_internal2().
In the function to load a single spin, the sign for recognizing the
molecule "#" was added and the second atom was loaded instead of loading all
C atoms.
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r13163 | han87 | 2011-06-22 16:15:11 +0200 (Wed, 22 Jun 2011) | 4 lines
Debugging the user function fill_object_from_xyz()..
In the user function fill_object_from_xyz() in
generic_fns/structure/internal.py the initialisation of the atom number was
changed from 0 to 1.
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r13164 | han87 | 2011-06-22 16:17:25 +0200 (Wed, 22 Jun 2011) | 5 lines
Debugging in the system_test test_read_xyz_internal2().
In the function to load a single spin, the sign for recognizing the
molecule "#" was added and the second atom was loaded instead of loading all
C atoms.
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r13165 | han87 | 2011-06-22 17:11:05 +0200 (Wed, 22 Jun 2011) | 4 lines
Debugging the user function load_spins() and add_item().
In the function load_spins() in generic_fns/structure/main.py a parameter
'res_num_exist' was added to check whether in the structural data the residue
number exists or not. Normally in the pdb file there is a residue number and
in the xyz file not. And then this parameter was used as a flag in the
add_item() to avoid the Error message 'RelaxError("The residue number '" +
repr(res_num) + "' already exists in the sequence.")' in case for xyz file
when residue number does not exist.
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r13167 | han87 | 2011-06-22 17:16:17 +0200 (Wed, 22 Jun 2011) | 4 lines
Changing the description in the user function load_spins().
In description of the funtion load_spins() in prompt/structure.py the
example for loading all C atoms was changed from 'relax>
structure.load_spins(spin_id='@C')' to relax>
structure.load_spins(spin_id='@*C*').
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r13169 | han87 | 2011-06-22 17:23:16 +0200 (Wed, 22 Jun 2011) | 4 lines
Debugging the system test 'test_read_xyz_internal1()'.
In the system test 'test_read_xyz_internal1()' the molecule name and the
spin name were changed.
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r13179 | han87 | 2011-06-23 11:26:46 +0200 (Thu, 23 Jun 2011) | 7 lines
Reverted r13165 as this change could break other part of the relax.
The command used was:
svn merge -r 13165:13164
The changing of the user functions "load_spins" and "add_item" could
break other part of relax. This was pointed out by Edward in the email:
https://mail.gna.org/public/relax-devel/2011-06/msg00226.html.
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r13180 | han87 | 2011-06-23 15:19:45 +0200 (Thu, 23 Jun 2011) | 4 lines
Debugging the user function load_spins() and changing the system test
test_read_xyz_internal2().
In the user function load_spins() in generic_fns/structure/main.py a
check whether the residue name exists or not has been included. The code is
similiar to the molecule check. Also see email:
https://mail.gna.org/public/relax-devel/2011-06/msg00226.html. And in the
system test 'test_read_xyz_internal2()' all models were loaded instead of 2
and the line for loading proton was removed.
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r13211 | han87 | 2011-06-24 11:06:46 +0200 (Fri, 24 Jun 2011) | 4 lines
Debugging the user function load_spins()
Debugging the user function load_spins() in generic_fns/structure/main.py
for a proper residue check as suggest in:
https://mail.gna.org/public/relax-devel/2011-06/msg00231.html.
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r13214 | han87 | 2011-06-24 11:50:33 +0200 (Fri, 24 Jun 2011) | 4 lines
Debugging the user function load_xyz() and changing the system
test_read_xyz_internal2().
Debugging the user function load_xyz() in
generic_fns/structure/internal.py and changing the system test
test_read_xyz_internal2() so that loading a desired model can be achieved.
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r13215 | han87 | 2011-06-24 11:55:46 +0200 (Fri, 24 Jun 2011) | 4 lines
Debugging the user function load_spins().
Debugging the user function load_spins() in generic_fns/structure/main.py
by using the residue number instead of the residue name for a proper residue
check as suggest in:
https://mail.gna.org/public/relax-devel/2011-06/msg00235.html.
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r13227 | han87 | 2011-06-27 09:59:35 +0200 (Mon, 27 Jun 2011) | 4 lines
Debugging the user function load_spins().
Changing the name from model_increment to xyz_model_increment in the user
function load_spins() in generic_fns/structure/main.py as suggest in:
https://mail.gna.org/public/relax-devel/2011-06/msg00240.html.
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r13234 | han87 | 2011-06-27 15:10:31 +0200 (Mon, 27 Jun 2011) | 4 lines
Adding code for checking the atomic positions in the system test
test_read_xyz_internal2()
Code for checking the atomic position (x, y and z) of the last spin was
added in the system test test_read_xyz_internal2().
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r13235 | han87 | 2011-06-27 15:16:46 +0200 (Mon, 27 Jun 2011) | 7 lines
[... 967 lines stripped ...]
r14369 - in /branches/cst: ./ auto_analyses/ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ scons/ scripts/ sp...