What steps will reproduce the problem?
1. Reading DOCR file.
What is the expected output? What do you see instead?
Happens for entries: 1aj3 1d0w 1e0a 1f8h 1kft 1mek 1rkl 1w9r 1yyj 2ca7 2exg
2h2m 2j15 2jnc 2jxh 2kcc 2l4g 2xfm
jd:nmr/4a1m/ cat
/Library/WebServer/Documents/NRG-CING/prep/F/aj/1aj3/1aj3_FC_assign.log
Model read finished. Duration 1.10111188889
Model validity check skipped
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r1060)
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd on: nmr.cmbi.umcn.nl (darwin/32bit/8cores/2.6.7) at: (24330)
Mon Aug 22 12:00:28 2011
Going to destination: fcProcessEntry with(out) on entry_code 1aj3 with extra
arguments ['/Library/WebServer/Documents/NRG-CING/recoordSync/1aj3/1aj3.tgz',
'1aj3_assign.tgz', 'swapCheck']
entry_code
1aj3
allowPopups
False
isInteractive
False
minimalPrompts
True
verbose
True
doSwapCheck
True
doSaveProject
True
doExport
True
DEBUG: Looking at 1aj3
Doing command: tar -xzf
/Library/WebServer/Documents/NRG-CING/recoordSync/1aj3/1aj3.tgz
Renaming standard directory linkNmrStarData to entry: 1aj3
Warning: Project file has moved from
"/raid/docr/ccpn_tmp/data/recoord/1aj3/linkNmrStarData"
to
"/Volumes/tria3/NRG-CING/prep/F/aj/1aj3/1aj3"
Backup is being changed from
"/raid/docr/NRG/link/1aj3/1aj3_backup"
to
"/Volumes/tria3/NRG-CING/prep/F/aj/1aj3/1aj3_backup"
refData has been changed from
"/raid/docr/workspace/ccpn/data"
to
"/Users/jd/workspace35/ccpn/data"
generalData has been changed from
"/home/docr/.ccpn/data"
to
"/Users/jd/.ccpn/data"
### Checking stereo swaps and deassignment ###
Checking swap status and cleaning prochiral groups in constraint lists...
Made resAtomDict, resAtomSetDict
Made resAtomSwapDict,prochiralResonancesDict
DEBUG maintaining tripletIdx 1 because criterium not met:
percentageModelFavoured >= swapPercentage: 10.0 75.0
DEBUG maintaining tripletIdx 2 because criterium not met: totalEnergyHighState
> totalEnergyLowState: 0.000 and 0.000
DEBUG swapping tripletIdx 3
ERROR: Traceback (most recent call last):
File "/Users/jd/workspace35/cingStable/python/cing/Scripts/FC/utils.py", line 284, in <module>
if fcProcessEntry( entry_code, ccpnTgzFile, outputCcpnTgzFile, functionToRun ):
File "/Users/jd/workspace35/cingStable/python/cing/Scripts/FC/utils.py", line 196, in fcProcessEntry
swapCheck(nmrConstraintStore, structureEnsemble)
File "/Users/jd/workspace35/cingStable/python/cing/Scripts/FC/utils.py", line 126, in swapCheck
swapCheck.checkSwapsAndClean()
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/process/stereoAssignmentSwap.py", line 1224, in checkSwapsAndClean
(prochiralViolationInfo,allConstraintItems) = self.checkProchiralKeyConstraints(prochiralKey,debug)
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/process/stereoAssignmentSwap.py", line 1872, in checkProchiralKeyConstraints
avgSumContrib = 1.0 / math.pow(getDistanceFromCoordinates(self.atomCoordDict[atom][i],self.atomCoordDict[otherAtom][i]),6)
File "/Users/jd/workspace35/ccpn/python/ccp/general/Geometry.py", line 173, in getDistanceFromCoordinates
return math.sqrt(math.pow(coord1.x-coord2.x,2) + math.pow(coord1.y-coord2.y,2) + math.pow(coord1.z-coord2.z,2))
AttributeError: 'NoneType' object has no attribute 'x'
CING started at : Mon Aug 22 12:00:25 2011
CING stopped at : Mon Aug 22 12:00:52 2011
CING took : 27.472 s
Original issue reported on code.google.com by jurge...@gmail.com on 10 Oct 2011 at 9:07
Original issue reported on code.google.com by
jurge...@gmail.comon 10 Oct 2011 at 9:07