bugrelax - Bugs: bug #20335, The rdc.delete and pcs.delete user...

 
 
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bug #20335: The rdc.delete and pcs.delete user functions are non-functional.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Fri 30 Nov 2012 11:54:08 AM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 3 - LowSeverity: 2 - Minor
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.1.2Operating System: All systems

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(Jump to the original submission Jump to the original submission)

Fri 30 Nov 2012 12:02:39 PM UTC, SVN revision 18052:

Merged revisions 18043-18048 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18043 | bugman | 2012-11-30 10:54:48 +0100 (Fri, 30 Nov 2012) | 5 lines

Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure.

This is a test of the long range, absolute RDCs for menthol.
........
r18044 | bugman | 2012-11-30 10:58:01 +0100 (Fri, 30 Nov 2012) | 7 lines

Bug fix for the use of pseudo-atoms for RDCs in the N-state model analysis.

If the second atom of the pair in the intermolecular data container holding the RDC data was a
pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second
atoms being pseudo-atoms is supported.
........
r18045 | bugman | 2012-11-30 11:03:20 +0100 (Fri, 30 Nov 2012) | 3 lines

Fixes for the N_state_model.test_absolute_rdc_menthol system test checks to match the data.
........
r18046 | bugman | 2012-11-30 11:17:02 +0100 (Fri, 30 Nov 2012) | 3 lines

Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
........
r18047 | bugman | 2012-11-30 12:57:10 +0100 (Fri, 30 Nov 2012) | 6 lines

Modified the N_state_model.test_populations system test to catch bug #20335.

This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and
PCS data.
........
r18048 | bugman | 2012-11-30 13:00:20 +0100 (Fri, 30 Nov 2012) | 5 lines

Fix for bug #20335 (https://gna.org/bugs/?20335).

The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
........

(Browse SVN revision 18052)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 30 Nov 2012 12:02:37 PM UTC, SVN revision 18051:

Merged revisions 18043-18048 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18043 | bugman | 2012-11-30 10:54:48 +0100 (Fri, 30 Nov 2012) | 5 lines

Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure.

This is a test of the long range, absolute RDCs for menthol.
........
r18044 | bugman | 2012-11-30 10:58:01 +0100 (Fri, 30 Nov 2012) | 7 lines

Bug fix for the use of pseudo-atoms for RDCs in the N-state model analysis.

If the second atom of the pair in the intermolecular data container holding the RDC data was a
pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second
atoms being pseudo-atoms is supported.
........
r18045 | bugman | 2012-11-30 11:03:20 +0100 (Fri, 30 Nov 2012) | 3 lines

Fixes for the N_state_model.test_absolute_rdc_menthol system test checks to match the data.
........
r18046 | bugman | 2012-11-30 11:17:02 +0100 (Fri, 30 Nov 2012) | 3 lines

Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
........
r18047 | bugman | 2012-11-30 12:57:10 +0100 (Fri, 30 Nov 2012) | 6 lines

Modified the N_state_model.test_populations system test to catch bug #20335.

This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and
PCS data.
........
r18048 | bugman | 2012-11-30 13:00:20 +0100 (Fri, 30 Nov 2012) | 5 lines

Fix for bug #20335 (https://gna.org/bugs/?20335).

The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
........

(Browse SVN revision 18051)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 30 Nov 2012 12:01:41 PM UTC, SVN revision 18050:

Merged revisions 18043-18048 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18043 | bugman | 2012-11-30 10:54:48 +0100 (Fri, 30 Nov 2012) | 5 lines

Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure.

This is a test of the long range, absolute RDCs for menthol.
........
r18044 | bugman | 2012-11-30 10:58:01 +0100 (Fri, 30 Nov 2012) | 7 lines

Bug fix for the use of pseudo-atoms for RDCs in the N-state model analysis.

If the second atom of the pair in the intermolecular data container holding the RDC data was a
pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second
atoms being pseudo-atoms is supported.
........
r18045 | bugman | 2012-11-30 11:03:20 +0100 (Fri, 30 Nov 2012) | 3 lines

Fixes for the N_state_model.test_absolute_rdc_menthol system test checks to match the data.
........
r18046 | bugman | 2012-11-30 11:17:02 +0100 (Fri, 30 Nov 2012) | 3 lines

Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
........
r18047 | bugman | 2012-11-30 12:57:10 +0100 (Fri, 30 Nov 2012) | 6 lines

Modified the N_state_model.test_populations system test to catch bug #20335.

This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and
PCS data.
........
r18048 | bugman | 2012-11-30 13:00:20 +0100 (Fri, 30 Nov 2012) | 5 lines

Fix for bug #20335 (https://gna.org/bugs/?20335).

The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
........

(Browse SVN revision 18050)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 30 Nov 2012 12:01:39 PM UTC, SVN revision 18049:

Merged revisions 18043-18048 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18043 | bugman | 2012-11-30 10:54:48 +0100 (Fri, 30 Nov 2012) | 5 lines

Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure.

This is a test of the long range, absolute RDCs for menthol.
........
r18044 | bugman | 2012-11-30 10:58:01 +0100 (Fri, 30 Nov 2012) | 7 lines

Bug fix for the use of pseudo-atoms for RDCs in the N-state model analysis.

If the second atom of the pair in the intermolecular data container holding the RDC data was a
pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second
atoms being pseudo-atoms is supported.
........
r18045 | bugman | 2012-11-30 11:03:20 +0100 (Fri, 30 Nov 2012) | 3 lines

Fixes for the N_state_model.test_absolute_rdc_menthol system test checks to match the data.
........
r18046 | bugman | 2012-11-30 11:17:02 +0100 (Fri, 30 Nov 2012) | 3 lines

Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
........
r18047 | bugman | 2012-11-30 12:57:10 +0100 (Fri, 30 Nov 2012) | 6 lines

Modified the N_state_model.test_populations system test to catch bug #20335.

This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and
PCS data.
........
r18048 | bugman | 2012-11-30 13:00:20 +0100 (Fri, 30 Nov 2012) | 5 lines

Fix for bug #20335 (https://gna.org/bugs/?20335).

The global alignment ID data structure now has the RDC or PCS ID string correctly removed.
........

(Browse SVN revision 18049)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 30 Nov 2012 12:00:20 PM UTC, SVN revision 18048:

Fix for bug #20335 (https://gna.org/bugs/?20335).

The global alignment ID data structure now has the RDC or PCS ID string correctly removed.

(Browse SVN revision 18048)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 30 Nov 2012 11:57:10 AM UTC, SVN revision 18047:

Modified the N_state_model.test_populations system test to catch bug #20335.

This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and
PCS data.

(Browse SVN revision 18047)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 30 Nov 2012 11:54:08 AM UTC, original submission:

These user functions are not tested in the test suite, so have suffered bit-rot! Attempting to execute these user functions produces an error such as:

relax> rdc.delete(align_id=None)
Traceback (most recent call last):
File "/data/edau/relax/relax-trunk/multi/processor.py", line 479, in run
self.callback.init_master(self)
File "/data/edau/relax/relax-trunk/multi/__init__.py", line 318, in default_init_master
self.master.run()
File "/data/edau/relax/relax-trunk/relax.py", line 184, in run
self.interpreter.run(self.script_file)
File "/data/edau/relax/relax-trunk/prompt/interpreter.py", line 278, in run
return run_script(intro=self.__intro_string, local=locals(), script_file=script_file, quit=self.__quit_flag, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/data/edau/relax/relax-trunk/prompt/interpreter.py", line 585, in run_script
return console.interact(intro, local, script_file, quit, show_script=show_script, raise_relax_error=raise_relax_error)
File "/data/edau/relax/relax-trunk/prompt/interpreter.py", line 468, in interact_script
exec_script(script_file, local)
File "/data/edau/relax/relax-trunk/prompt/interpreter.py", line 341, in exec_script
runpy.run_module(module, globals)
File "/usr/lib64/python2.6/runpy.py", line 140, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.6/runpy.py", line 34, in _run_code
exec code in run_globals
File "/data/edau/long_range_rdcs/cross_predict/predict_long_range.py", line 62, in <module>
rdc.delete()
File "/data/edau/relax/relax-trunk/prompt/uf_objects.py", line 219, in _call_
self._backend(*new_args, **uf_kargs)
File "/data/edau/relax/relax-trunk/generic_fns/rdc.py", line 374, in delete
cdp.align_ids.pop(id)
TypeError: an integer is required

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.

 

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    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Fri 30 Nov 2012 12:00:31 PM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
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