Author: bugman
Date: Thu Aug 11 11:05:46 2011
New Revision: 14342
URL: http://svn.gna.org/viewcvs/relax?rev=14342&view=rev
Log:
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
................
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()'.
................
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.
................
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.
................
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.
................
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()'.
................
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.
................
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.
................
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.
................
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.
................
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().
................
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.
................
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.
................
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'.
................
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.
................
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'.
................
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.
................
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.
................
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.
................
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.
................
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*').
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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().
................
r13235 | han87 | 2011-06-27 15:16:46 +0200 (Mon, 27 Jun 2011) | 7 lines
Reverted r13234 as it contains several unrelated changes.
The command used was:
svn merge -r 13234:13227 .
This commit contains several unrelated changes in
/generic_fns/structure/main.py and /generic_fns/mol_res_spin.py.
................
r13239 | han87 | 2011-06-27 15:21:31 +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().
................
r13245 | han87 | 2011-06-27 18:51:42 +0200 (Mon, 27 Jun 2011) | 4 lines
Adding code for extracting the vector in the system test
test_read_xyz_internal2()
Code for extracting a vector of two given atoms was added in the system
test test_read_xyz_internal2().
................
r13246 | han87 | 2011-06-27 18:55:51 +0200 (Mon, 27 Jun 2011) | 4 lines
A new function vector_xyz() was generated.
A new function vector_xyz() was generated in '/prompt/structure.py' for
extracting a vector of two given atoms in a xyz file.
................
r13249 | han87 | 2011-06-28 10:25:55 +0200 (Tue, 28 Jun 2011) | 7 lines
Reverted r13246 as different approach will be used.
The command used was:
svn merge -r 13246:13239 .
The new function vectors_xyz() in the /prompt/structure.py is not needed.
The current code will be fixed for xyz file format suggested in
https://mail.gna.org/public/relax-devel/2011-06/msg00244.html.
................
r13414 | han87 | 2011-07-04 14:27:05 +0200 (Mon, 04 Jul 2011) | 4 lines
The system test for loading a single spin from a xyz has been changed.
The function return_spin() from the 'mol_res_spin' has been used to load a
single spin for the system test 'test_read_xyz_internal2'.
................
r13415 | han87 | 2011-07-04 14:30:59 +0200 (Mon, 04 Jul 2011) | 4 lines
Adding a new system test to load a vector.
A system test for loading a vector between two spins has been included in
the 'test_read_xyz_internal2'.
................
r13416 | han87 | 2011-07-04 14:35:25 +0200 (Mon, 04 Jul 2011) | 4 lines
Changing the keyword argument
The argument of the keyword 'unit' in the function 'vectors' in
'prompt/structure.py' has been changed from 'True' to 'False'.
................
r13417 | han87 | 2011-07-04 14:43:10 +0200 (Mon, 04 Jul 2011) | 4 lines
Adding code for extracting a vector of a xyz file.
Code for extracting a vector between specified spins in a xyz file has been
included in the '/generic_fns/structure/internal.py'.
................
r13891 | han87 | 2011-07-26 17:36:01 +0200 (Tue, 26 Jul 2011) | 4 lines
Debugging in the generic_fns/structure/main.py
Debugging in the function load_spin in order to load a spin for xyz file
properly.
................
r13894 | han87 | 2011-07-26 17:38:38 +0200 (Tue, 26 Jul 2011) | 4 lines
Changing the code in the test_read_xyz_internal2
Test to load a spin of the already loaded model of the molecule.
................
r13900 | han87 | 2011-07-26 18:47:49 +0200 (Tue, 26 Jul 2011) | 4 lines
Changing the code in the generic_fns/structure/main.py
For printing out of modified spins, a test to check whether the spin_name
exists or not is added.
................
r13924 | han87 | 2011-07-27 11:17:48 +0200 (Wed, 27 Jul 2011) | 4 lines
Deleting the function 'vector_xyz' in the generic_fns/structure/main.py
The code of the function 'vector_xyz' was removed since it will be not used.
................
r13931 | han87 | 2011-07-27 17:51:49 +0200 (Wed, 27 Jul 2011) | 4 lines
Changing the value of the unit arg in the function 'vectors' in
'prompt/structure.py'
The argument of the keyword 'unit' in the function 'vectors' in
'prompt/structure.py' has been changed back from 'False' to 'True' since it
causes many test failure.
................
r13933 | han87 | 2011-07-27 17:58:05 +0200 (Wed, 27 Jul 2011) | 8 lines
Reverted r as it contains several unrelated changes.
The command used was:
svn merge -r 13931:13924 .
This commit contains several unrelated changes in
/generic_fns/structure/main.py and /prompt/structure.py.
................
r13934 | han87 | 2011-07-27 17:59:07 +0200 (Wed, 27 Jul 2011) | 5 lines
Changing the value of the unit arg in the function 'vectors' in
'prompt/structure.py'
The argument of the keyword 'unit' in the function 'vectors' in
'prompt/structure.py' has been changed back from 'False' to 'True' since it
causes many test failure.
................
r13944 | han87 | 2011-07-28 10:15:38 +0200 (Thu, 28 Jul 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12830" from
svn+ssh://han87@xxxxxxxxxxx/svn/relax/1.3
................
r13947 | bugman | 2011-07-28 11:44:06 +0200 (Thu, 28 Jul 2011) | 622 lines
This should have been the commit message of the previous commit (r13946).
This change actually contains a trivial comment modification in the XYZ
file reading system tests.
Merged revisions
12937-12941,12943-12945,12947-12952,12954-12957,12959-12960,12965-12967,12969-12975,12982-13022,13028-13029,13045-13046,13153,13258,13357-13359,13411,13510-13512,13577,13631-13632,13641,13655,13660,13683,13686,13706,13742-13743,13748-13749,13780,13835-13836,13845-13857,13904-13906,13909,13919,13926-13927,13929,13932
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r12937 | bugman | 2011-06-09 17:52:04 +0200 (Thu, 09 Jun 2011) | 3 lines
Removed a duplicated self.SetSize() call for the main GUI window.
........
r12938 | bugman | 2011-06-09 17:53:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Changed the Frame.SetSize() call to SetMinSize() to prevent the main GUI
window becoming too small.
........
r12939 | bugman | 2011-06-09 17:54:12 +0200 (Thu, 09 Jun 2011) | 5 lines
Both SetSize() and SetMinSize() are now used for the main GUI window.
This allows for a proper layout.
........
r12940 | bugman | 2011-06-09 18:19:37 +0200 (Thu, 09 Jun 2011) | 3 lines
Simplified and localised a variable.
........
r12941 | bugman | 2011-06-09 18:31:46 +0200 (Thu, 09 Jun 2011) | 3 lines
Added a hard coded variable for the size of the graphical part of the
analysis frames.
........
r12943 | bugman | 2011-06-09 19:06:49 +0200 (Thu, 09 Jun 2011) | 3 lines
The text controls are now horizontally expandable.
........
r12944 | bugman | 2011-06-09 19:11:05 +0200 (Thu, 09 Jun 2011) | 3 lines
The model-free, Rx, and NOE frame main box sizers all expand horizontally
now.
........
r12945 | bugman | 2011-06-09 19:33:23 +0200 (Thu, 09 Jun 2011) | 3 lines
A spacer is now used for add_text_sel_element() if no button is present
to fill the button space.
........
r12947 | bugman | 2011-06-09 20:10:45 +0200 (Thu, 09 Jun 2011) | 5 lines
Big simplification by shifting the widths of the text selection GUI
element to hard coded variables.
These hard coded class variables are located in the base class.
........
r12948 | bugman | 2011-06-09 20:16:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Added some horizontal spacing between the elements of the text selection
GUI element.
........
r12949 | bugman | 2011-06-10 09:42:25 +0200 (Fri, 10 Jun 2011) | 5 lines
Created the setup_analysis_element() base method for laying out the main
analysis GUI element.
This currently adds a border of 10 px around each analysis.
........
r12950 | bugman | 2011-06-10 09:43:01 +0200 (Fri, 10 Jun 2011) | 3 lines
The auto model-free analysis frame now uses the base
setup_analysis_element() method.
........
r12951 | bugman | 2011-06-10 10:08:05 +0200 (Fri, 10 Jun 2011) | 7 lines
Split the auto model-free build_main_box() method into two.
[... 594 lines stripped ...]
r14342 - in /1.3: ./ generic_fns/structure/ prompt/ test_suite/shared_data/structures/ test_suite/system_tests/