End message of whatif gets intermingled with the values that need to be parsed

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Happens kinda randomly so can't be easily reproduced.

What is the expected output? What do you see instead?
Very rarely it happens that the end-message of whatif gets intermingled with 
the values parsed 
here:
Side chain planarity           : STOP Normal end of WHAT IF.
0.324 (tight)

Workaround for now so CING doesn't crash completely:
Wrapped this parse in a try/except clause.

Needs better parse; from individual files as before perhaps.

Original issue reported on code.google.com by jurge...@gmail.com on 30 Apr 2010 at 5:04

[GoogleCodeExporter]

Happened again for:
jd:nmr/CASD-NMR-CING/ grep INOCHK data/*/*/log_validateEntryForCasd/*.log
data/GR/CGR26AUtrecht2/log_validateEntryForCasd/CGR26AUtrecht2_2010-05-10_17-57-
11.log:ERROR: 
Failed to parse value as a float for check [INOCHK] for line 
[<cing.Libs.AwkLike.AwkLike instance at 
0x646d1c0>] from What If string [STOP]; setting value to a None

Original comment by jurge...@gmail.com on 10 May 2010 at 5:52

• Added labels: Entry-CGR26AUtrecht2

[GoogleCodeExporter]

and again: 
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9 (r770)        
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd              on: nmr.cmbi.umcn.nl (darwin/32bit)               at: Fri 
Apr 30 03:01:27 2010
DEBUG: Using:
DEBUG: inputDir:             
file:///Users/jd/wattosTestingPlatform/pdb/data/structures/divided/pdb/li
DEBUG: outputDir:            /Library/WebServer/Documents/PDB-CING/data/li/1lir
DEBUG: pdbConvention:        .
DEBUG: restraintsConvention: .
DEBUG: archiveType:          BY_CH23
DEBUG: projectType:          PDB
DEBUG: modelCount:           None
copying file: 
//Users/jd/wattosTestingPlatform/pdb/data/structures/divided/pdb/li/pdb1lir.ent.
gz to: pdb1lir.ent.gz
DEBUG: Removing file: pdb1lir.ent.gz
==> Parsing pdbFile "1lir.pdb" ... 
PDB parser: unknown record type: NUMMDL
Non-standard (residues and their) atoms to add:
PCA : C    CA   CB   CD   CG   H    HA   HB2  HB3  HG2  HG3  N    O    OE   [ 1]
DEBUG: Calculating dihedral angles
==> Molecule 1lir: No potential disulfide bridged residues found
Calculating rmsd's (residues: 1-37, models: 0-21)
DEBUG: Removing tmp: 1lir.pdb
-------------------------------------------------------
==> Saving <Project 1lir>
==> Saved <Molecule "1lir" (C:1,R:37,A:815,M:22)> to 
"1lir.cing/Data/Molecules/1lir.molecule"
DEBUG: saveTalosPlus: No talos+ was run
==> Running shiftx
runShiftx: non-protein residues [<Residue 1lir.A.PCA1 (15776)>] will be skipped.
0.........1.........2.
==> calculating Q-factors for chemical shift
==> Calculating secondary structure by DSSP
WARNING: runWhatif: non-standard residue <Residue 1lir.A.PCA1 (15776)> found 
and will be written out for What If
==> Running What If checks on 814 residues for an estimated (7 residues/s): 116 
seconds; please wait
0.........1.........2.
==> Processing the WHATIF results into CING data model
CING started at : Fri Apr 30 03:01:22 2010
CING stopped at : Fri Apr 30 03:07:00 2010
CING took       : 337.654 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 344, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 262, in main
    doWattos=doWattos, doTalos=doTalos):
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 985, in validate
    doWattos = doWattos, doTalos = doTalos)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 127, in validate
    project.runWhatif(parseOnly=parseOnly)
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Whatif.py", line 1086, in runWhatif
    if whatif._processWhatifSummary(pathPdbOut):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Whatif.py", line 393, in _processWhatifSummary
    value = float(valueStringList[0])
ValueError: invalid literal for float(): sh

Original comment by jurge...@gmail.com on 9 Jun 2010 at 12:14

• Added labels: Entry-1lir, Priority-High
• Removed labels: Priority-Medium

[GoogleCodeExporter]

Was already worked around in r772. But needs a different real fix.

Original comment by jurge...@gmail.com on 9 Jun 2010 at 12:27

• Changed state: Started

[GoogleCodeExporter]

Had to put yet another workaround in the r810 for entry 2kqu.

Original comment by jurge...@gmail.com on 21 Jul 2010 at 3:39

[GoogleCodeExporter]

Issue 263 has been merged into this issue.

Original comment by jurge...@gmail.com on 1 Nov 2010 at 8:50

[GoogleCodeExporter]

Original comment by jurge...@gmail.com on 13 Dec 2010 at 9:54

• Removed labels: Entry-CGR26AUtrecht2

[GoogleCodeExporter]

Perhaps inserting a short sleep before exiting syncs the streams better. Hard 
to test so leaving issue open until executing a large batch.

Original comment by jurge...@gmail.com on 3 Jan 2011 at 9:45

[GoogleCodeExporter]

Seems to be fixed by short sleep work around. Not certain though.

Original comment by jurge...@gmail.com on 1 Feb 2011 at 10:09

• Changed state: Fixed