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jakesylvestre / cing

Automatically exported from code.google.com/p/cing
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Bad read of CCPN CS #210

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Can't reproduce without project file.

What is the expected output? What do you see instead?
===========================================================
===========================================
| CING: Common Interface for NMR structure Generation version 0.9 (r645)        
AW,JFD,GWV 
2004-2009 |
===========================================================
===========================================
User: root            on: nmr.cmbi.umcn.nl (darwin)                     at: Wed 
Oct 28 17:20:56 2009
==> Importing data from Ccpn project "Qua1"
Non-standard (residues and their) atoms added:
LYS : [ 157]
==> Ccpn molecule 'Qua1' imported
WARNING: Ccpn Shift List has no members; is empty
==> CCPN ShiftList 'ShiftList 1' imported from CCPN Nmr project 'Qua1'
CING started at : Wed Oct 28 17:20:52 2009
CING stopped at : Wed Oct 28 17:21:11 2009
CING took       : 18.884 s

Traceback (most recent call last):
 File "/Users/jd/workspace34/cing/python/cing/main.py", line 761, in <module>
  main()
 File "/Users/jd/workspace34/cing/python/cing/main.py", line 615, in main
  project.initCcpn(ccpnFolder=options.initCcpn)
 File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 2252, in initCcpn
  if not ccpn.importFromCcpn(modelCount = modelCount):
 File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 336, in 
importFromCcpn
  if self.importFromCcpnPeakAndShift():
 File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 910, in 
importFromCcpnPeakAndShift
  doneSetShifts = self._getCcpnShiftList(ccpnMolSystem, ccpnShiftList)
 File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 846, in 
_getCcpnShiftList
  NTmessage("==> CING (pseudo-)atom with resonances updated %s" % atomsTouched.keys())
UnboundLocalError: local variable 'atomsTouched' referenced before assignment

Looks like a simple bug in CING.
Please send project if public so I can check the code when I'm done fixing.

Original issue reported on code.google.com by jurge...@gmail.com on 30 Oct 2009 at 9:17

GoogleCodeExporter commented 8 years ago 
I'm close to releasing the fix. Just need to check it with the data.

Snippet from Helge's message:

...this data is unpublished and ongoing work and has to be kept strictly
confidential! Please let me know if you also need the input data, which
I used for the FormatConverter.

It seems that I have the same problem with all the project files I
generate with the FormatConverter. If it helps, I can generate a project
file (e.g. of ubiquitin) which you then could make public for bug fixing.

Original comment by jurge...@gmail.com on 30 Oct 2009 at 10:45

GoogleCodeExporter commented 8 years ago 
The CS list (ShiftList 1) is empty when I look at Helge's project file Qua1 
with Analysis.
Probably you want that to be fixed with Wim's FormatConverter.

The above bug is fixed in r656 but there are other problems with your project 
now. I'm opening a separate 
issue for it: issue 212. I'll keep this issue blocked on it. Wim, could you 
take a look at it?

I've updated iCing's CING version to r656 so you can test.Look in the CING log 
for the correct revision number.

Original comment by jurge...@gmail.com on 30 Oct 2009 at 11:24

GoogleCodeExporter commented 8 years ago 
I need to keep the list fresh.

Original comment by jurge...@gmail.com on 5 Nov 2009 at 1:10