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bug #20674: UnboundLocalError in consistency_tests.py - failure due to missing protons in the PDB file.

Submitted by:  None
Submitted on:  Thu 28 Mar 2013 03:37:52 PM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Originator Email: -unavailable-
Open/Closed: ClosedRelease: 2.2.5
Operating System: All systems

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

Tue 02 Apr 2013 09:08:46 AM UTC, SVN revision 19290:

Merged revisions 19289 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r19289 | bugman | 2013-04-02 11:08:27 +0200 (Tue, 02 Apr 2013) | 21 lines

Manually ported r19283 from the 2.2 development line to trunk.

The command used was:
svn merge -r19283:19284 svn+ssh://bugman@svn.gna.org/svn/relax/branches/2.2 .

.....
r19284 | bugman | 2013-04-02 11:02:34 +0200 (Tue, 02 Apr 2013) | 10 lines
Changed paths:
M /branches/2.2/specific_analyses/consistency_tests.py

Fix for bug #20674 (https://gna.org/bugs/?20674) - the failure of the consistency testing analysis.

This was reported by Mengjun Xue .

The problem was that the first residue did not have a single proton 'H' in the PDB file, and
therefore the dipolar relaxation interaction was not set up. The overfit_deselect() method of the
consistency testing specific API was not checking for this. The method is now much more like that
of the model-free specific analysis.
.....
........

(Browse SVN revision 19290)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 02 Apr 2013 09:08:27 AM UTC, SVN revision 19289:

Manually ported r19283 from the 2.2 development line to trunk.

The command used was:
svn merge -r19283:19284 svn+ssh://bugman@svn.gna.org/svn/relax/branches/2.2 .

.....
r19284 | bugman | 2013-04-02 11:02:34 +0200 (Tue, 02 Apr 2013) | 10 lines
Changed paths:
M /branches/2.2/specific_analyses/consistency_tests.py

Fix for bug #20674 (https://gna.org/bugs/?20674) - the failure of the consistency testing analysis.

This was reported by Mengjun Xue .

The problem was that the first residue did not have a single proton 'H' in the PDB file, and
therefore the dipolar relaxation interaction was not set up. The overfit_deselect() method of the
consistency testing specific API was not checking for this. The method is now much more like that
of the model-free specific analysis.
.....

(Browse SVN revision 19289)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 02 Apr 2013 09:06:39 AM UTC, SVN revision 19287:

Merged revisions 19285 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r19285 | bugman | 2013-04-02 11:05:27 +0200 (Tue, 02 Apr 2013) | 24 lines

Manually merged r19282 from the 2.2 development line to trunk.

The command used was:
svn merge -r19281:19282 svn+ssh://bugman@svn.gna.org/svn/relax/branches/2.2 .

.....
r19282 | bugman | 2013-04-02 10:47:26 +0200 (Tue, 02 Apr 2013) | 6 lines
Changed paths:
A /branches/2.2/test_suite/shared_data/consistency_testing
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/2QFK_MONOMERHabc5.pdb
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/NOE dhp 700.txt
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/T1 dhp 700.txt
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/T2 dhp 700.txt
M /branches/2.2/test_suite/system_tests/consistency_tests.py
A /branches/2.2/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py

Created the Ct.test_bug_20674_ct_analysis_failure system test for catching bug #20674.

This was reported by Mengjun Xue at
https://gna.org/bugs/?20674.
.....
........

(Browse SVN revision 19287)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 02 Apr 2013 09:05:27 AM UTC, SVN revision 19285:

Manually merged r19282 from the 2.2 development line to trunk.

The command used was:
svn merge -r19281:19282 svn+ssh://bugman@svn.gna.org/svn/relax/branches/2.2 .

.....
r19282 | bugman | 2013-04-02 10:47:26 +0200 (Tue, 02 Apr 2013) | 6 lines
Changed paths:
A /branches/2.2/test_suite/shared_data/consistency_testing
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/2QFK_MONOMERHabc5.pdb
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/NOE dhp 700.txt
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/T1 dhp 700.txt
A /branches/2.2/test_suite/shared_data/consistency_testing/bug_20674_ct_analysis_failure/T2 dhp 700.txt
M /branches/2.2/test_suite/system_tests/consistency_tests.py
A /branches/2.2/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py

Created the Ct.test_bug_20674_ct_analysis_failure system test for catching bug #20674.

This was reported by Mengjun Xue at
https://gna.org/bugs/?20674.
.....

(Browse SVN revision 19285)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 02 Apr 2013 09:02:35 AM UTC, SVN revision 19284:

Fix for bug #20674 (https://gna.org/bugs/?20674) - the failure of the consistency testing analysis.

This was reported by Mengjun Xue .

The problem was that the first residue did not have a single proton 'H' in the PDB file, and
therefore the dipolar relaxation interaction was not set up. The overfit_deselect() method of the
consistency testing specific API was not checking for this. The method is now much more like that
of the model-free specific analysis.

(Browse SVN revision 19284)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 02 Apr 2013 08:47:26 AM UTC, SVN revision 19282:

Created the Ct.test_bug_20674_ct_analysis_failure system test for catching bug #20674.

This was reported by Mengjun Xue at
https://gna.org/bugs/?20674.

(Browse SVN revision 19282)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 28 Mar 2013 03:37:52 PM UTC, original submission:

Hi Edward,

UnboundLocalError came up, when I run consistency_tests.py Could you tell me what is the problem? Thanks.

Please find the attached nmr data set.

Regards,

Mengjun

Anonymous

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

Attached Files
file #17584:  2QFK_MONOMERHabc5.pdb added by None (283kB - chemical/x-pdb)
file #17579:  T1 dhp 700.txt added by None (75kB - text/plain)
file #17580:  T2 dhp 500.txt added by None (68kB - text/plain)
file #17581:  T2 dhp 700.txt added by None (68kB - text/plain)
file #17582:  logconsistency added by None (372kB - application/octet-stream)
file #17575:  consistency_tests.py added by None (6kB - text/plain)
file #17576:  NOE dhp 500.txt added by None (25kB - text/plain)
file #17577:  NOE dhp 700.txt added by None (25kB - text/plain)
file #17578:  T1 dhp 500.txt added by None (62kB - text/plain)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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  • -unavailable- added by bugman (Updated the item)
  • -unavailable- added by None (Submitted the item)
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    Follow 16 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 02 Apr 2013 09:09:30 AM UTCbugmanCategoryrelax sample scripts=>relax's source code
      StatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
      SummaryUnboundLocalError in consistency_tests.py=>UnboundLocalError in consistency_tests.py - failure due to missing protons in the PDB file.
    Thu 28 Mar 2013 08:05:16 PM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
      Operating SystemMicrosoft Windows=>All systems
    Thu 28 Mar 2013 07:57:27 PM UTCNoneAttached File-=>Added 2QFK_MONOMERHabc5.pdb, #17584
    Thu 28 Mar 2013 03:39:21 PM UTCNoneAttached File-=>Added T1 dhp 700.txt, #17579
      Attached File-=>Added T2 dhp 500.txt, #17580
      Attached File-=>Added T2 dhp 700.txt, #17581
      Attached File-=>Added logconsistency, #17582
    Thu 28 Mar 2013 03:37:52 PM UTCNoneAttached File-=>Added consistency_tests.py, #17575
      Attached File-=>Added NOE dhp 500.txt, #17576
      Attached File-=>Added NOE dhp 700.txt, #17577
      Attached File-=>Added T1 dhp 500.txt, #17578
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