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IndexError in FC #199

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What is the expected output? What do you see instead?

Involves 29 entries:
1ay3 1bfw 1d0w 1evd 1fb9 1fv7 1k09 1kqe 1l1v 1nao 1nts 1pdt 1r2l 1r9v 1rpv 1s4a 
1soc 1uph 1w9n 1xt7 1yl8 1yl9 2cyu 2gbh 2jnd 2jue 2k1q 2k5u 2k9e

grep chemCompDict $dir_link/*/*_merge.log

Model read finished. Duration 1.00199604034
Model validity check skipped
Defined allChemCompDataPath:/Users/jd/ccpn_tmp/data/allChemComps
Read msd.adatah.localConstants.py version Tue Sep  2 14:56:33 CEST 2008
Doing 1ay3...
  Using preset values...
    > This looks like one molecule, connected by 'other' residue...
Traceback (most recent call last):
  File "/Users/jd/workspace34/recoord/python/recoord2/msd/linkNmrStarData.py", line 680, in <module>
    LinkNmrStarData(sys.argv)
  File "/Users/jd/workspace34/recoord/python/msd/adatah/Generic.py", line 87, in __init__
    self.catchError(raiseError,timeFlag)
  File "/Users/jd/workspace34/recoord/python/msd/adatah/Generic.py", line 80, in __init__
    self.runSpecific()
  File "/Users/jd/workspace34/recoord/python/recoord2/msd/linkNmrStarData.py", line 169, in runSpecific
    self.readNmrStarFile(inNmrStarFile, version = self.originalNmrStarVersion, maxNum = self.numModelsToRead)
  File "/Users/jd/workspace34/recoord/python/msd/adatah/NmrStar.py", line 37, in readNmrStarFile
    self.formatObjectDict[formatKey].readProject(nmrStarFile, entry = self.entry, molSystem = self.molSystem, strucGen = self.strucGen, useOriginalChainCode = True, linkAtoms 
= False, version = version, chemCompPath = chemCompArchiveDataDir, 
minimalPrompts = 1, **localKeywds)
  File "/Users/jd/workspace34/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 917, in readProject
    self.getFullProject(fileName,**keywds)
  File "/Users/jd/workspace34/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 549, in getFullProject
    chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
  File "/Users/jd/workspace34/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1030, in readSequence
    (createMoleculeDict,molSystemBonds) = self.checkMolecules()
  File "/Users/jd/workspace34/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 5786, in checkMolecules
    chemCompDict[origMolName][-1] = (newResidueType,chemCompDict[origMolName][-1][1])
IndexError: list index out of range

Original issue reported on code.google.com by jurge...@gmail.com on 24 Mar 2009 at 12:22

GoogleCodeExporter commented 9 years ago 
Made small fix, is now working on my laptop.

Update CCPN SourceForge CVS.

Original comment by wfvran...@gmail.com on 27 Mar 2009 at 9:05

GoogleCodeExporter commented 9 years ago 
Cool, first 2 entries tested fine at nmr.

Chris, can you do all in a batch with the processDOCR.. script now?

After that I'm going to be able to fetch the final numbers for the paper.

Original comment by jurge...@gmail.com on 2 Apr 2009 at 9:53

GoogleCodeExporter commented 9 years ago 
processDOCR.. is having troubles. See issue 205

http://code.google.com/p/nmrrestrntsgrid/issues/detail?id=205

Original comment by schulte....@gmail.com on 2 Apr 2009 at 7:53

GoogleCodeExporter commented 9 years ago 
Results - I'm looking at them now

1ay3
1ay3 Counts   111     0   0.0
1ay3 no completeness report

1bfw
1bfw Counts   120     0   0.0
1bfw no completeness report

1d0w
1d0w Counts   132    89  67.4

1evd
1evd Counts    48     3   6.2

1fb9
1fb9 Distance max violation(s): 2.335
1fb9 Counts   505   466  92.3

1fv7
1fv7 Counts   186   124  66.7

1k09
1k09 Counts   195   143  73.3

1kqe
1kqe Counts  2572     0   0.0
1kqe no completeness report

1l1v
1l1v Counts   214   122  57.0

1nao
1nao Counts   212   188  88.7
1nao no completeness report

1nts
1nts Counts   228   195  85.5

1pdt
1pdt Counts   311   125  40.2

1r2l
1r2l Counts   331   317  95.8

1r9v
1r9v No items counted
1r9v no completeness report

1rpv
1rpv Counts    87    81  93.1

1s4a
1s4a No items counted
1s4a no completeness report

1soc
1soc Counts    14     0   0.0
1soc no completeness report

1uph
1uph Distance max violation(s): 1.850

1w9n
1w9n Counts   321   266  82.9

1xt7
1xt7 Counts    51    22  43.1

1yl8
1yl8 Distance max violation(s): 2.590
1yl8 Counts   154   134  87.0

1yl9
1yl9 Counts   155     0   0.0
1yl9 no completeness report

2cyu

2gbh
2gbh Distance max violation(s): 4.854 8.547
2gbh Counts   523   506  96.7

2jnd
2jnd Counts  1941  1740  89.6

2jue
2jue Distance max violation(s): 6.441
2jue Counts   285    39  13.7

2k1q
2k1q Counts  1833  1794  97.9

2k5u
2k5u Counts  2100  2069  98.5

2k9e
2k9e Distance max violation(s): 6.902 3.809
2k9e Counts   656   625  95.3
Finished processing weekly for DOCR/FRED batch.

Original comment by schulte....@gmail.com on 9 Apr 2009 at 8:15

GoogleCodeExporter commented 9 years ago 
Thanks Chris, clearly not all convert well but most problems are related to 
uncommon residue problems of a 
different issue. Closing this issue. Cheers!

Original comment by jurge...@gmail.com on 14 Apr 2009 at 12:40

GoogleCodeExporter commented 9 years ago 
We have looked at the entries but clearly not all converted well. The entries 
need to be reexamined for there are 
different problems with them. Until we reexamined I'm keeping the problem 
entries linked to this issue id 
although the current title doesn't cover the problem anymore.

Original comment by jurge...@gmail.com on 12 May 2009 at 1:06

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 12 May 2009 at 1:07

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 12 May 2009 at 1:07

GoogleCodeExporter commented 9 years ago 
This information has been transfered to problemEntryList.csv

Original comment by jurge...@gmail.com on 3 Aug 2009 at 8:43