CING saving project to SML fails

[GoogleCodeExporter]

Geerten, can you look at this one?

What is the expected output? What do you see instead?
Traceback (most recent call last):
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 266, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 194, in main
    project.save()
  File "/Users/jd/workspace34/cingStable/python/cing/core/classes.py", line 604, in save
    self[pl.nameListKey] = pl.save() # Save returns a list of name; store these in project
  File "/Users/jd/workspace34/cingStable/python/cing/core/classes.py", line 963, in save
    if self.classDef.SMLhandler.toFile(l, l.objectPath) == l:
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 339, in toFile
    object.SMLhandler.toSML( object, fp )
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 907, in toSML
    self.list2SML( drl, fp )
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 275, in list2SML
    item.SMLhandler.toSML( item, fp )
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 884, in toSML
    rl.append((r[0].nameTuple(SMLsaveFormat),r[1].nameTuple(SMLsaveFormat)))
  File "/Users/jd/workspace34/cingStable/python/cing/core/molecule.py", line 3434, in nameTuple
    return (self.residue.chain.molecule.name,
AttributeError: 'NoneType' object has no attribute 'molecule'

Original issue reported on code.google.com by jurge...@gmail.com on 22 Oct 2009 at 10:18

[GoogleCodeExporter]

Original comment by jurge...@gmail.com on 2 Nov 2009 at 1:03

• Added labels: Component-NRG-CING
• Removed labels: Component-CING

[GoogleCodeExporter]

Try to fix this at reading time:

===================================================================
===================================
| CING: Common Interface for NMR structure Generation version 0.9 (r657)        
AW,JFD,GWV 2004-2009 |
===================================================================
===================================
User: jd              on: nmr.cmbi.umcn.nl (darwin)                     at: Tue 
Nov  3 00:28:30 2009
Enforcing a redo
Moving CCPN directory from [linkNmrStarData] to [1x5b]
==> Importing data from Ccpn project "1x5b"
Non-standard (residues and their) atoms added:
GLY : HA3  [ 1 163]
==> Molecule 1x5b: Potential disulfide bridges: 1. applying bonds: True
==> Mutating 1x5b.A.CYS79 to CYSS
==> Mutating 1x5b.A.CYS83 to CYSS
==> Ccpn molecule '1x5b' imported
==> Ccpn project imported
-------------------------------------------------------
==> Saving <Project 1x5b>
CING started at : Tue Nov  3 00:28:27 2009
CING stopped at : Tue Nov  3 00:28:57 2009
CING took       : 30.650 s

Traceback (most recent call last):
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 266, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 194, in main
    project.save()
  File "/Users/jd/workspace34/cingStable/python/cing/core/classes.py", line 604, in save
    self[pl.nameListKey] = pl.save() # Save returns a list of name; store these in project
  File "/Users/jd/workspace34/cingStable/python/cing/core/classes.py", line 963, in save
    if self.classDef.SMLhandler.toFile(l, l.objectPath) == l:
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 339, in toFile
    object.SMLhandler.toSML( object, fp )
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 907, in toSML
    self.list2SML( drl, fp )
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 275, in list2SML
    item.SMLhandler.toSML( item, fp )
  File "/Users/jd/workspace34/cingStable/python/cing/core/sml.py", line 884, in toSML
    rl.append((r[0].nameTuple(SMLsaveFormat),r[1].nameTuple(SMLsaveFormat)))
  File "/Users/jd/workspace34/cingStable/python/cing/core/molecule.py", line 3452, in nameTuple
    return (self.residue.chain.molecule.name,
AttributeError: 'NoneType' object has no attribute 'molecule'

Original comment by jurge...@gmail.com on 5 Nov 2009 at 2:35

• Changed state: Started

[GoogleCodeExporter]

Ok now in:
http://nmr.cmbi.ru.nl/NRG-CING/data/x5/1x5b

Original comment by jurge...@gmail.com on 27 Nov 2009 at 1:35

• Changed state: Fixed