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jakesylvestre / cing

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CING fails to process CCPN project dh1 #189

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Read from user molecules: [<Molecule "dh1" (C:1,R:190,A:4335,M:1)>]

ERROR: Molecule.models2list: invalid model number 1 ( >=  modelCount: 1)
ERROR: Failed keepSelectedModels; please check the input string [0-202]

Finally fails to generate html pages. Asking author for reprint permissions now.

Original issue reported on code.google.com by jurge...@gmail.com on 28 Sep 2009 at 1:08

GoogleCodeExporter commented 9 years ago 
 ==> Analyzing <DistanceRestraintList "hbonds_corrected_upl" (keep,138)>, output to 
Kalcya1model.cing/dh1/Cing/hbonds_corrected_upl.txt
^CTraceback (most recent call last):
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/test/test_ccpn.py", line 139, in <module>
    unittest.main()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 768, in 
__init__
    self.runTests()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 805, in 
runTests
    result = self.testRunner.run(self.test)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 705, in 
run
    test(result)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 437, in 
__call__
    return self.run(*args, **kwds)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 433, in 
run
    test(result)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 437, in 
__call__
    return self.run(*args, **kwds)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 433, in 
run
    test(result)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 281, in 
__call__
    return self.run(*args, **kwds)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 260, in 
run
    testMethod()
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/test/test_ccpn.py", line 79, in testInitCcpn
    doWattos=doWattos ))
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/validate.py", line 128, in validate
    project.runCingChecks(ranges=ranges)
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/validate.py", line 101, in runCingChecks
    project.criticize(toFile=True)
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/validate.py", line 366, in criticize
    drl.criticize(project, toFile=toFile)
  File "/Users/jd/workspace34/cing/python/cing/core/classes.py", line 1750, in criticize
    self.rogScore.setMaxColor(dr.rogScore.colorLabel, comment = 'Cascaded from: %s' % dr)
  File "/Users/jd/workspace34/cing/python/cing/core/ROGscore.py", line 129, in setMaxColor
    self.colorCommentList.removeDuplicates()
  File "/Users/jd/workspace34/cing/python/cing/Libs/NTutils.py", line 269, in removeDuplicates
    if self[i] in self[0:i]:
  File "/Users/jd/workspace34/cing/python/cing/Libs/NTutils.py", line 109, in __getslice__
    return NTlist(*list.__getslice__(self, i, j))
  File "/Users/jd/workspace34/cing/python/cing/Libs/NTutils.py", line 91, in __init__
    self.append(a)
  File "/Users/jd/workspace34/cing/python/cing/Libs/NTutils.py", line 160, in append
    list.append(self, item)
KeyboardInterrupt

Original comment by jurge...@gmail.com on 28 Sep 2009 at 1:55

GoogleCodeExporter commented 9 years ago 
Data is treated confidentially.
Problem was not a bug but a very inefficient coding for removing duplicates 
when dealing with larger (n>1000) 
lists.
Fixed in r637.

Original comment by jurge...@gmail.com on 28 Sep 2009 at 6:05