CING fails to import CCPN project from Lalit

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Obtained report from CCPN mailing list thru Wayne.

What is the expected output? What do you see instead?
Hello,

I am not sure whether to post this message here but while using CING through 
Analysis (2.1.3), I 
am getting the following error:
===========================================================
======================
Traceback (most recent call last):
 File "/Users/jd/workspace35/cing/python/cing/main.py", line 812, in <module>
   main()
 File "/Users/jd/workspace35/cing/python/cing/main.py", line 666, in main
   project.initCcpn(ccpnFolder=options.initCcpn)
 File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 2290, in initCcpn
   if not ccpn.importFromCcpn(modelCount = modelCount):
 File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 341, in 
importFromCcpn
   if not self.importFromCcpnMolecule(modelCount = modelCount):
 File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 457, in 
importFromCcpnMolecule
   if not self._match2Cing(modelCount = modelCount):
 File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 581, in _match2Cing
   chain.ccpn = ccpnChain
AttributeError: 'NoneType' object has no attribute 'ccpn'
===========================================================
========================

Thanks in advance,

Regards,
Lalit

Asked Lalit for project so I can debug the problem.

Original issue reported on code.google.com by jurge...@gmail.com on 12 May 2010 at 8:11

[GoogleCodeExporter]

Project (confidential) send in by Lalit has a chain id of ' ' which is mapped 
to 'A' but that chain id was already 
present. This is a duplicate of issue 223.

Original comment by jurge...@gmail.com on 12 May 2010 at 11:46

• Changed state: Duplicate

[GoogleCodeExporter]

Perhaps not because in Analysis it looks like there is a chain A & B only. 
Investigating...

Original comment by jurge...@gmail.com on 12 May 2010 at 12:21

• Changed state: Started

[GoogleCodeExporter]

I get:

jd:Stella/cingTmp/ cing --nosave --ipython --name __Shc_May2010 --initCcpn 
__Shc_May2010.tgz 
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9 (r776)        
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd              on: Stella.local (darwin/32bit)                   at: Wed 
May 12 14:20:21 2010
==> Importing data from Ccpn project "__Shc_May2010"
==> Using run specification "CING:1" from CCPN project
Changed chain id from CCPN [ ] to CING [A]
Changed chain id from CCPN [ ] to CING [A]
WARNING: Molecule.addChain: chain "A" already present
CING started at : Wed May 12 14:20:17 2010
CING stopped at : Wed May 12 14:22:12 2010
CING took       : 114.445 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/main.py", line 812, in <module>
    main()
  File "/Users/jd/workspace35/cing/python/cing/main.py", line 666, in main
    project.initCcpn(ccpnFolder=options.initCcpn)
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 2290, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 341, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 457, in importFromCcpnMolecule
    if not self._match2Cing(modelCount = modelCount):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 581, in _match2Cing
    chain.ccpn = ccpnChain
AttributeError: 'NoneType' object has no attribute 'ccpn'

Original comment by jurge...@gmail.com on 12 May 2010 at 12:23

[GoogleCodeExporter]

Wayne, can I ask you to look at this project? I've forwarded the confidential 
project to you. It looks like the 
project does contain multiple chains with a ' ' chain id although in Analysis 
they don't show up to me.

Anyway the code has been updated in r779 to treat chain ids of ' ' in any input 
as invalid for CING and 
consequently be auto generated.

iCing code base has been updated to r779 and was tested with Lalit's project.

Original comment by jurge...@gmail.com on 12 May 2010 at 1:10

• Changed state: Fixed