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jakesylvestre / cing

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SML restore fails when restoring large shiftx list #317

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Look at stack trace below. SML restore of molecule crashes on this entry 
with 640 models

================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r1117)      
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: i          on: cvca (linux/32bit/8cores/2.7.1+)           at:  (1349) Fri 
Nov 25 01:49:56 2011
DEBUG: Starting doStoreCING2db using:
DEBUG: entry_code:           2kox
DEBUG: archive_id:           ARCHIVE_NRG
DEBUG: user_name:            pdbj
DEBUG: db_name:              pdbmlplus
DEBUG: schema:               nrgcing
DEBUG: doReadProject:        True
==> Restoring <Project 2kox> ... 
CING started at : Fri Nov 25 01:49:54 2011
CING stopped at : Fri Nov 25 01:49:57 2011
CING took       : 3.394 s

Traceback (most recent call last):
  File "/home/i/workspace/cingStable/python/cing/NRG/storeCING2db.py", line 1028, in <module>
    status = doStoreCING2db(*sys.argv[1:])
  File "/home/i/workspace/cingStable/python/cing/NRG/storeCING2db.py", line 105, in doStoreCING2db
    project = Project.open(entry_code, status='old')
  File "/home/i/workspace/cingStable/python/cing/core/classes.py", line 596, in open
    pr.restore()
  File "/home/i/workspace/cingStable/python/cing/core/classes.py", line 729, in restore
    mol = Molecule.open(pathName)
  File "/home/i/workspace/cingStable/python/cing/core/molecule.py", line 1595, in open
    mol = Molecule.SMLhandler.fromFile(fpath) # pylint: disable=E1101
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 282, in fromFile
    newObj  = handler.handle( line, fp, obj, **kwds )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 185, in handle
    newObj  = handler.handle( line, fp, obj )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 467, in handle
    mol[key] = SMLstarthandlers[line[3]].handle( [' '.join(line[3:])] + line[3:], fp, mol )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 331, in handle
    return self.listHandler(listObj, fp, obj)
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 111, in listHandler
    listObj.append( SMLstarthandlers[line[1]].handle( line, fp, obj ) )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 554, in handle
    return self.dictHandler(chain, fp, molecule)
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 141, in dictHandler
    dictObj[line[1]] = SMLstarthandlers[line[3]].handle( [' '.join(line[3:])] + line[3:], fp, obj )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 331, in handle
    return self.listHandler(listObj, fp, obj)
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 111, in listHandler
    listObj.append( SMLstarthandlers[line[1]].handle( line, fp, obj ) )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 603, in handle
    return self.dictHandler(res, fp, molecule)
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 141, in dictHandler
    dictObj[line[1]] = SMLstarthandlers[line[3]].handle( [' '.join(line[3:])] + line[3:], fp, obj )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 331, in handle
    return self.listHandler(listObj, fp, obj)
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 111, in listHandler
    listObj.append( SMLstarthandlers[line[1]].handle( line, fp, obj ) )
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 677, in handle
    return self.dictHandler(atm, fp, molecule)
  File "/home/i/workspace/cingStable/python/cing/core/sml.py", line 147, in dictHandler
    dictObj[line[1]] = eval(' '.join(line[3:]))
  File "<string>", line 1
SyntaxError: more than 255 arguments

I think it's going into the wrong routine but that's for Geerten to figure out. 
I will implement a work around that will skip over the per atom shiftx data.

Original issue reported on code.google.com by jurge...@gmail.com on 30 Nov 2011 at 2:08

GoogleCodeExporter commented 8 years ago 
Work around committed to r1121.

Original comment by jurge...@gmail.com on 30 Nov 2011 at 2:40