bugrelax - Bugs: bug #21499, The rdc.write user function fails...

 
 
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bug #21499: The rdc.write user function fails for back-calculated RDC data.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Fri 17 Jan 2014 10:56:16 AM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 3.1.3Operating System: All systems

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Fri 17 Jan 2014 11:23:16 AM UTC, SVN revision 22028:

Merged revisions 21980,21983-22012,22016,22024-22027 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r21980 | bugman | 2014-01-15 10:40:53 +0100 (Wed, 15 Jan 2014) | 3 lines

Fix for the parameters listed for the IT99 dispersion model in the manual.
........
r21983 | bugman | 2014-01-15 15:55:32 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.cr72 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html.
........
r21984 | bugman | 2014-01-15 15:57:31 +0100 (Wed, 15 Jan 2014) | 3 lines

Spacing fix for the lib.dispersion.cr72 module docstring.
........
r21985 | bugman | 2014-01-15 16:00:51 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.dpl94 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html.
........
r21986 | bugman | 2014-01-15 16:05:26 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.it99 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html.
........
r21987 | bugman | 2014-01-15 16:10:19 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.lm63_3site API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html.
........
r21988 | bugman | 2014-01-15 16:15:23 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.lm63 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html.
........
r21989 | bugman | 2014-01-15 16:20:07 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.m61b API documentation.

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html.

[...]........

[...] r21990 | bugman | 2014-01-15 16:26:03 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.m61 API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html.

[...]........

[...] r21991 | bugman | 2014-01-15 16:31:41 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.mmq_cr72 API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html.

[...]........

[...] r21992 | bugman | 2014-01-15 16:42:33 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.mp05 API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html.

[...]........

[...] r21993 | bugman | 2014-01-15 16:50:56 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_3d API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html.

[...]........

[...] r21994 | bugman | 2014-01-15 16:55:01 +0100 (Wed, 15 Jan 2014) | 3 lines

[...]

[...] Epydoc URL simplifications.

[...]........

[...] r21995 | bugman | 2014-01-15 16:59:09 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_expanded API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html.

[...]........

[...] r21996 | bugman | 2014-01-15 17:14:49 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_star API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html.

[...]........

[...] r21997 | bugman | 2014-01-15 17:16:45 +0100 (Wed, 15 Jan 2014) | 3 lines

[...]

[...] Added the 'NS CPMG 2-site 3D full' model to the lib.dispersion.ns_cpmg_2site_3d module docstring.

[...]........

[...] r21998 | bugman | 2014-01-15 17:33:31 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_mmq_2site API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html.

[...]........

[...] r21999 | bugman | 2014-01-15 17:46:40 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_mmq_3site API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html.

[...]........

[...] r22000 | bugman | 2014-01-15 17:53:00 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_r1rho_2site API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html.

[...]........

[...] r22001 | bugman | 2014-01-15 17:58:09 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.ns_r1rho_3site API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html.

[...]........

[...] r22002 | bugman | 2014-01-15 17:59:22 +0100 (Wed, 15 Jan 2014) | 3 lines

[...]

[...] Small docstring edit for the lib.dispersion.mp05 module.

[...]........

[...] r22003 | bugman | 2014-01-15 18:03:09 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.tap03 API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html.

[...]........

[...] r22004 | bugman | 2014-01-15 18:20:18 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.tp02 API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html.

[...]........

[...] r22005 | bugman | 2014-01-15 18:20:37 +0100 (Wed, 15 Jan 2014) | 3 lines

[...]

[...] Epydoc URL simplifications in the lib.dispersion.mp05 module.

[...]........

[...] r22006 | bugman | 2014-01-15 18:24:35 +0100 (Wed, 15 Jan 2014) | 3 lines

[...]

[...] Epydoc docstring edit in the lib.dispersion.mmq_cr72 module.

[...]........

[...] r22007 | bugman | 2014-01-15 18:30:44 +0100 (Wed, 15 Jan 2014) | 6 lines

[...]

[...] Improvements and addition of many links to the lib.dispersion.tsmfk01 API documentation.

[...]

[...] This is for the API documentation at:

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.tsmfk01-module.html.

[...]........

[...] r22008 | bugman | 2014-01-15 18:32:16 +0100 (Wed, 15 Jan 2014) | 3 lines

[...]

[...] Copyright notice updates for the lib.dispersion modules changed today.

[...]........

[...] r22009 | bugman | 2014-01-16 15:36:04 +0100 (Thu, 16 Jan 2014) | 85 lines

[...]

[...] Added links to the relax wiki, API documentation, and relax website to all dispersion models in the manual.

[...]

[...] This is to make it easier to find additional information about each of the models.

[...]

[...] For reference, the relax wiki links are:

[...] http://wiki.nmr-relax.com/R2eff

[...] http://wiki.nmr-relax.com/No_Rex

[...] http://wiki.nmr-relax.com/LM63

[...] http://wiki.nmr-relax.com/LM63_3-site

[...] http://wiki.nmr-relax.com/CR72_full

[...] http://wiki.nmr-relax.com/CR72

[...] http://wiki.nmr-relax.com/IT99

[...] http://wiki.nmr-relax.com/TSMFK01

[...] http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded

[...] http://wiki.nmr-relax.com/NS_CPMG_2-site_3D_full

[...] http://wiki.nmr-relax.com/NS_CPMG_2-site_3D

[...] http://wiki.nmr-relax.com/NS_CPMG_2-site_star_full

[...] http://wiki.nmr-relax.com/NS_CPMG_2-site_star

[...] http://wiki.nmr-relax.com/MMQ_CR72

[...] http://wiki.nmr-relax.com/NS_MMQ_2-site

[...] http://wiki.nmr-relax.com/NS_MMQ_3-site_linear

[...] http://wiki.nmr-relax.com/NS_MMQ_3-site

[...] http://wiki.nmr-relax.com/M61

[...] http://wiki.nmr-relax.com/M61_skew

[...] http://wiki.nmr-relax.com/DPL94

[...] http://wiki.nmr-relax.com/TP02

[...] http://wiki.nmr-relax.com/TAP03

[...] http://wiki.nmr-relax.com/MP05

[...] http://wiki.nmr-relax.com/NS_R1rho_2-site

[...] http://wiki.nmr-relax.com/NS_R1rho_3-site

[...] http://wiki.nmr-relax.com/NS_R1rho_3-site_linear

[...]

[...] The API documentation links are:

[...] http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.optimisation-module.html#back_calc_r2eff

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.two_point-module.html#calc_two_point_r2eff

[...] http://www.nmr-relax.com/api/3.1/target_functions.relax_disp.Dispersion-class.html#func_NOREX

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.tsmfk01-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html

[...] http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html

[...]

[...] The relax website links are:

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#R2eff

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#No_Rex

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#LM63

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#LM63_3-site

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72_full

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#IT99

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TSMFK01

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_expanded

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_3D_full

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_3D

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_star_full

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_star

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#MMQ_CR72

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_2-site

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_3-site_linear

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_3-site

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61_skew

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#DPL94

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TP02

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TAP03

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#MP05

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_2-site

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_3-site

[...] http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_3-site_linear

[...]........

[...] r22010 | bugman | 2014-01-16 16:06:40 +0100 (Thu, 16 Jan 2014) | 3 lines

[...]

[...] Updated the author list for the submitted paper for the relaxation dispersion analysis.

[...]........

[...] r22011 | bugman | 2014-01-16 16:07:41 +0100 (Thu, 16 Jan 2014) | 5 lines

[...]

[...] Added the primary reference for relaxation dispersion in relax to the dispersion chapter of the manual.

[...]

[...] This is the paper which is not published yet.

[...]........

[...] r22012 | bugman | 2014-01-16 16:09:49 +0100 (Thu, 16 Jan 2014) | 5 lines

[...]

[...] Removed the single quantum R1rho-type data reference in the introduction of the dispersion chapter of the manual.

[...]

[...] This is redundant as R1rho data is always single quantum.

[...]........

[...] r22016 | bugman | 2014-01-16 16:19:10 +0100 (Thu, 16 Jan 2014) | 6 lines

[...]

[...] Backported the relax 3.1.3 CHANGES file addition to trunk.

[...]

[...] The command used was:

[...] svn merge -r22014:22015 svn+ssh://bugman@svn.gna.org/svn/relax/tags/3.1.3 .

[...]........

[...] r22024 | bugman | 2014-01-17 11:51:16 +0100 (Fri, 17 Jan 2014) | 12 lines

[...]

[...] Created the Frame_order.test_generate_rotor2_distribution system test.

[...]

[...] This is to test the Frame Order distribution generating base script, used for creating the synthetic

[...] Frame Order test data, and to demonstrate a failure in handling back-calculated RDC data.

[...]

[...] To implement this, the test_suite/shared_data/frame_order/cam/ path has been converted into a Python

[...] package (with the addition of the _init_.py files). The base data generation script

[...] test_suite/shared_data/frame_order/cam/generate_base.py has also been modified to use the absolute

[...] path for the data files and its run() method now accepts the save_path argument to allow the files

[...] to be saved into a temporary directory.

[...]........

[...] r22025 | bugman | 2014-01-17 11:57:50 +0100 (Fri, 17 Jan 2014) | 6 lines

[...]

[...] Fix for bug #21499 (https://gna.org/bugs/?21499), the failure of the rdc.write user function.

[...]

[...] The rdc.write user function fails for back-calculated RDC data. The fix was to handle the missing

[...] interatom.rdc_data_types variable.

[...]........

[...] r22026 | bugman | 2014-01-17 12:00:43 +0100 (Fri, 17 Jan 2014) | 7 lines

[...]

[...] Fixes for the Frame_order.test_generate_rotor2_distribution system test.

[...]

[...] The test_suite/shared_data/frame_order/cam/generate_base.py script now saves the program state files

[...] into the self.save_path directory, preventing the system test from attempting to save files into the

[...] relax test suite directories.

[...]........

[...] r22027 | bugman | 2014-01-17 12:02:58 +0100 (Fri, 17 Jan 2014) | 7 lines

[...]

[...] Another fix for the Frame_order.test_generate_rotor2_distribution system test.

[...]

[...] The test_suite/shared_data/frame_order/cam/generate_base.py script no longer prints its progress

[...] indicator to sys.__stderr__ but to sys.stderr instead. This avoids the progress text from appearing

[...] during the relax test suite execution.

[...]........

[...]

[...]

(Browse SVN revision 22028)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 17 Jan 2014 10:57:50 AM UTC, SVN revision 22025:

Fix for bug #21499 (https://gna.org/bugs/?21499), the failure of the rdc.write user function.

The rdc.write user function fails for back-calculated RDC data. The fix was to handle the missing
interatom.rdc_data_types variable.

(Browse SVN revision 22025)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 17 Jan 2014 10:56:16 AM UTC, original submission:

The rdc.write user function fails for back-calculated RDC data with the error message:

relax> rdc.write(align_id='dy', file='rdc_dy.txt', dir='/tmp/tmpAmjpAC', bc=True, force=True)
Opening the file '/tmp/tmpAmjpAC/rdc_dy.txt' for writing.
Traceback (most recent call last):
File "/data/relax/relax-trunk/test_suite/system_tests/frame_order.py", line 645, in test_generate_rotor2_distribution
self.interpreter.run(script_file=self.cam_path+'generate_rotor2_distribution.py')
File "/data/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/relax/relax-trunk/prompt/interpreter.py", line 576, in run_script
return console.interact(intro, local, script_file, quit, show_script=show_script, raise_relax_error=raise_relax_error)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 468, in interact_script
exec_script(script_file, local)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 341, in exec_script
runpy.run_module(module, globals)
File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/data/relax/relax-trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py", line 44, in <module>
generate.run(save_path=ds.tmpdir)
File "/data/relax/relax-trunk/test_suite/shared_data/frame_order/cam/generate_base.py", line 77, in run
self._back_calc()
File "/data/relax/relax-trunk/test_suite/shared_data/frame_order/cam/generate_base.py", line 123, in _back_calc
self.interpreter.rdc.write(align_id=tag, file='rdc_%s.txt'%tensors[i], dir=self.save_path, bc=True, force=True)
File "/data/relax/relax-trunk/prompt/uf_objects.py", line 221, in _call_
self._backend(*new_args, **uf_kargs)
File "/data/relax/relax-trunk/pipe_control/rdc.py", line 1275, in write
data[-1].append(repr(convert(interatom.rdc_bc[align_id], interatom.rdc_data_types[align_id], align_id)))
AttributeError: 'InteratomContainer' object has no attribute 'rdc_data_types'

This message comes from the Frame_order.test_generate_rotor2_distribution system test.

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

 

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    Date Changed By Updated Field Previous Value => Replaced By
    Fri 17 Jan 2014 10:57:59 AM UTCbugmanStatusNone=>Fixed
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