Author: semor
Date: Thu Aug 25 11:17:46 2011
New Revision: 14426
URL: http://svn.gna.org/viewcvs/relax?rev=14426&view=rev
Log:
Merged revisions
13835-13836,13845-13857,13904-13906,13909,13919,13926-13927,13929,13932,13951,13956,13958,13961,13983-13984,14008-14009,14011,14013,14071,14103,14107-14110,14146,14157,14179,14181,14185,14249,14262,14285,14292,14324,14329,14331,14333,14335-14336,14338,14341-14343,14347-14352,14354-14355,14361-14366,14372,14374,14376,14386-14388,14390-14391,14396,14401,14404,14406,14409,14416,14418-14420,14422-14423,14425
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
*** Had to manually edit file "prompt/relax_fit.py" in order to resolve
conflict... ***
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r13835 | bugman | 2011-07-22 16:30:29 +0200 (Fri, 22 Jul 2011) | 6 lines
Fix for the model-free _determine_model_type() method when the spin
container has no 'local_tm'.
This code was failing in certain rare circumstances (when the setting up of
the diffusion tensor was
forgotten).
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r13836 | bugman | 2011-07-22 16:57:05 +0200 (Fri, 22 Jul 2011) | 3 lines
Created a script for byte compiling the Python source files.
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r13845 | bugman | 2011-07-25 10:07:31 +0200 (Mon, 25 Jul 2011) | 5 lines
Added some old 2004 scripts for creating a uniform vector distribution and
calculating relaxation data.
This will be used in the end to build a quick test for the
dauvergne_protocol auto-analysis.
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r13846 | bugman | 2011-07-25 10:13:27 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the spherical vector distribution script in preparation for Python
3.
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r13847 | bugman | 2011-07-25 10:15:19 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the script to only have 3 incs.
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r13848 | bugman | 2011-07-25 10:15:51 +0200 (Mon, 25 Jul 2011) | 3 lines
Created the PDB representation of the spherical vector distribution for 9
vectors.
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r13849 | bugman | 2011-07-25 10:37:49 +0200 (Mon, 25 Jul 2011) | 3 lines
Converted the relaxation data generation script from relax 1.0 format to
relax 1.3.
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r13850 | bugman | 2011-07-25 12:02:17 +0200 (Mon, 25 Jul 2011) | 9 lines
Added initial support for determining protein connectivities in the
internal structural reader.
This is currently only for intra-residue connectivities in the protein
backbone. A number of new
methods have been added:
_mol_type()
_protein_connect()
_protein_intra_connect()
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r13851 | bugman | 2011-07-25 12:20:43 +0200 (Mon, 25 Jul 2011) | 5 lines
Fixes for the test suite relaxation data creation script.
The code was not fully compatible with the relax 1.3 design.
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r13852 | bugman | 2011-07-25 12:21:13 +0200 (Mon, 25 Jul 2011) | 3 lines
Fixes to the relaxation data generation sample script based on the changes
of r13851.
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r13853 | bugman | 2011-07-25 12:22:22 +0200 (Mon, 25 Jul 2011) | 5 lines
The relaxation data is now for 500 and 900 MHz.
This larger difference should hopefully speed up optimisation in the test
suite.
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r13854 | bugman | 2011-07-25 12:23:36 +0200 (Mon, 25 Jul 2011) | 3 lines
Added the relaxation data.
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r13855 | bugman | 2011-07-25 13:45:04 +0200 (Mon, 25 Jul 2011) | 5 lines
Added the argument 'bc' to the relax_data.write() user function front end.
This currently doesn't do anything.
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r13856 | bugman | 2011-07-25 14:33:28 +0200 (Mon, 25 Jul 2011) | 5 lines
The 'bc' arg is now part of the value.write() user function, and all of the
return_value functions.
The arg is also propagated to the back-end of the relax_data.write() user
function.
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r13857 | bugman | 2011-07-25 14:34:12 +0200 (Mon, 25 Jul 2011) | 3 lines
The back calculated data is now written out to file in the synthetic
relaxation data script.
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r13904 | bugman | 2011-07-26 21:40:15 +0200 (Tue, 26 Jul 2011) | 5 lines
Added the data_type() method to the specific functions API.
This will be used to determine the type that a given parameter from
data_names() should be.
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r13905 | bugman | 2011-07-26 21:52:58 +0200 (Tue, 26 Jul 2011) | 3 lines
Modified the specific functions API method data_type() so that Python type
objects should be returned.
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r13906 | bugman | 2011-07-26 21:55:53 +0200 (Tue, 26 Jul 2011) | 3 lines
Implemented the model-free version of the data_type() API method.
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r13909 | bugman | 2011-07-26 22:18:51 +0200 (Tue, 26 Jul 2011) | 3 lines
The data_type() API method is now exposed.
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r13919 | bugman | 2011-07-27 09:37:48 +0200 (Wed, 27 Jul 2011) | 3 lines
The heteronucleus and proton type parameters can now be specified by their
parameter names aas well.
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r13926 | bugman | 2011-07-27 16:01:22 +0200 (Wed, 27 Jul 2011) | 5 lines
The create_molecule, create_residue, and create_spin functions now returned
the created container.
This should not affect any of the current code using these, as normally
None would be returned.
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r13927 | bugman | 2011-07-27 16:05:49 +0200 (Wed, 27 Jul 2011) | 6 lines
Invisible fix for the test_opendx_theta_phi_da() system test.
The spins are extracted from the structure, so they don't need to be read
from the relaxation data
file as well. This is causing problems in the xyz branch, but is not an
issue in the main line.
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r13929 | bugman | 2011-07-27 16:15:41 +0200 (Wed, 27 Jul 2011) | 3 lines
Modified the create_spin() function to overwrite the first spin if empty.
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r13932 | bugman | 2011-07-27 17:54:24 +0200 (Wed, 27 Jul 2011) | 13 lines
Redesign of the structure.load_spins user function back end.
This redesign is required due to problems encountered by Han in the xyz
branch. See the thread
starting at https://mail.gna.org/public/relax-devel/2011-07/msg00021.html.
This commit consists of a number of changes:
- The combine_models argument has been removed as it is a relic, and
isn't used at all.
- The spins are now created in the standard way via the
generic_fns.mol_res_spin.create_spin()
function, eliminating all of the issues and complications of the old code.
- The atomic positions are now converted to numpy arrays.
- Only the created spins are included in the print out, and not
replicated for each model.
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r13951 | bugman | 2011-07-28 15:14:55 +0200 (Thu, 28 Jul 2011) | 7 lines
Redesign of the main relax module.
The module has been renamed to 'relax.py', and the original file 'relax' is
now a very basic python
script which simply loads the module and runs the new start() function for
launching relax. The MS
Windows BAT file has also been updated to feed the module into python.
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r13956 | bugman | 2011-07-28 16:26:16 +0200 (Thu, 28 Jul 2011) | 3 lines
The relax mode normally specified by the command line can now be overridden.
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r13958 | bugman | 2011-07-28 16:35:58 +0200 (Thu, 28 Jul 2011) | 3 lines
Removed the executable svn property on the info module.
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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
[... 9159 lines stripped ...]
r14426 - in /branches/inversion-recovery: ./ auto_analyses/ data/ docs/ generic_fns/ generic_fns/structure/ graphics/ graphi...