jurgenfd / wattos Goto Github PK

What steps will reproduce the problem?
1. Read mmCIF of 1qch

What is the expected output? What do you see instead?

From: http://nmr.cmbi.ru.nl/NRG-CING/prep/C/qc/1qch/1qch_star2Ccpn.log

Model read finished. Duration 1.8169491291 
Model validity check skipped
Reading NmrStar project from file 
/Library/WebServer/Documents/NRG-CING/prep/C/qc/1qch/1qch_C_wattos.str
Python nmrStar reader courtesy of Jurgen Doreleijers (BMRB) - with 
modifications added.
Parsing STAR file: 
/Library/WebServer/Documents/NRG-CING/prep/C/qc/1qch/1qch_C_wattos.str
Done [0] subs with comment at beginning of line
Done [6740] subs with comment not at beginning of line
##### 100000 chars processed ######
##### 100000 chars processed ######
##### 100000 chars processed ######
##### 100000 chars processed ######
##### 100000 chars processed ######
##### 100000 chars processed ######
Parsed: [11] datanodes (top level count only)

###########################################
# FormatConverter: executing readSequence #
###########################################


  Selecting naming system PDB_REMED.
  Molecule 5__D__AP_TP_GP_CP_AP_T__3_ set to type DNA from sequence file information.
Error: Cannot find ChemComp XML file other, Ngm.
  Warning: no other chemComp 3 letter code NGM selected. Will be ignored.
Created molecule 5__D__AP_TP_GP_CP_AP_T__3_ (molType DNA, 6 chemComps)
Created molecule SODIUM_ION (molType other, 1 chemComps)
Created molecule water (molType other, 1 chemComps)
Created chain 'A', start seqCode 1, end seqCode 6, molecule 
'5__D__AP_TP_GP_CP_AP_T__3_'...
Created chain 'B', start seqCode 7, end seqCode 12, molecule 
'5__D__AP_TP_GP_CP_AP_T__3_'...
Created chain 'C', start seqCode 15, end seqCode 15, molecule 'SODIUM_ION'...
Created chain 'D', start seqCode 16, end seqCode 16, molecule 'SODIUM_ION'...
Created chain 'E', start seqCode 17, end seqCode 17, molecule 'SODIUM_ION'...
Created chain 'F', start seqCode 18, end seqCode 18, molecule 'SODIUM_ION'...
Created chain 'G', start seqCode 19, end seqCode 19, molecule 'SODIUM_ION'...
Created chain 'H', start seqCode 20, end seqCode 20, molecule 'SODIUM_ION'...
Created chain 'I', start seqCode 21, end seqCode 21, molecule 'SODIUM_ION'...
Created chain 'J', start seqCode 22, end seqCode 22, molecule 'SODIUM_ION'...
Created chain 'K', start seqCode 23, end seqCode 23, molecule 'SODIUM_ION'...
Created chain 'L', start seqCode 24, end seqCode 24, molecule 'water'...
Created chain 'M', start seqCode 26, end seqCode 26, molecule 'water'...
Created chain 'N', start seqCode 27, end seqCode 27, molecule 'water'...

Created chain '98', start seqCode 2087, end seqCode 2087, molecule 'water'...
Created chain '99', start seqCode 2088, end seqCode 2088, molecule 'water'...
ERROR: Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/Scripts/FC/convertStar2Ccpn.py", line 177, in <module>
    status = not importFullStarProjects(starFileName, projectName, inputDir)
  File "/Users/jd/workspace35/cing/python/cing/Scripts/FC/convertStar2Ccpn.py", line 103, in importFullStarProjects
    formatNmrStarFormat.getFullProject( starFileNameFull, title = entryTitle, details = entryDetails, **keywds)
  File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 566, in getFullProject
    chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
  File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1084, in readSequence
    self.checkChains(createMoleculeDict,molSystemBonds)
  File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 7047, in checkChains
    pdbOneLetterCode = self.getPdbOneLetterCode(chainCode)
  File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 8433, in getPdbOneLetterCode
    if len(currentChainCode) > 1:
TypeError: object of type 'NoneType' has no len()

ERROR: Failed to importFullStarProjects

What steps will reproduce the problem?
1. Read 2ezs for NRG-CING.

complete list potentially affected:
1crq 1crr 1ezc 1ezd 1kld 1l0r 1qch 1r4e 1sah 1saj 1vve 2axx 2ezq 2ezr 2ezs

What is the expected output? What do you see instead?

================================================================================
======================
| Wattos: Programs for Structural Biology & NMR        version 20101011 (r134) 
JFD,GWV,ELU 1999-2010 |
================================================================================
======================
User: jd on: stella.cmbi.umcn.nl (MacOSX/x86_64/2cores/1.6.0_22) at: (20730) 
Thu Nov 11 15:06:57 2010

DEBUG: Wattos in interactive mode
DEBUG: Wattos in debugging mode
DEBUG: Executing: InitAll
Doing InitAll
DEBUG: Executing: SetProp
Doing SetProp with arguments: [interactiveSession, false]
Doing SetProp with arguments: [verbosity, 9]
Doing SetProp with arguments: [writeSessionOnExit, false]
Doing SetProp with arguments: [stopOnError, true]
DEBUG: getInputChar read: false
Doing ReadEntryMMCIF with arguments: 
[file:/Users/jd/wattosTestingPlatform/pdb/data/structures/divided/mmCIF/ez/2ezs.
cif.gz, false]
ERROR: The models need to be numbered starting at 1 but found:31
ERROR: entry.readmmCIFFormattedFile was unsuccessful. Failed to read nmrstar 
formatted file
ERROR: In getEntryId; Expected 1 and only 1 selected entry but found: 0
ERROR: In getAtomsInMasterModel; Failed to find just one selected entry.
ERROR: Failed to getAtomsInMasterModel
WARNING: Command could not be executed: ReadEntryMmCIF
WARNING: Parameter set for stopping on any error: stopOnError

Wattos started at: November 11, 2010 3:06:57 PM CET
Wattos stopped at: November 11, 2010 3:07:02 PM CET
Wattos took (#ms): 5005

Residue insertion code which caused Wattos FastFileReader?.myReader2 to
fail.

for now I'll leave this as I'm not using the PDB file reader for anything
raw from PDB but rather prefiltered by What If.

What steps will reproduce the problem?
1. Read mmCIF of 1r4e

================================================================================
======================
| Wattos: Programs for Structural Biology & NMR        version 20101011 (r141) 
JFD,GWV,ELU 1999-2010 |
================================================================================
======================
User: jd on: Stella.local (MacOSX/x86_64/2cores/1.6.0_22) at: (37359) Fri Nov 
12 14:17:28 2010

DEBUG: Wattos in interactive mode
DEBUG: Wattos in debugging mode
DEBUG: Executing: InitAll
Doing InitAll
DEBUG: Executing: SetProp
Doing SetProp with arguments: [interactiveSession, false]
Doing SetProp with arguments: [verbosity, 9]
Doing SetProp with arguments: [writeSessionOnExit, false]
Doing SetProp with arguments: [stopOnError, true]
DEBUG: getInputChar read: false
Doing ReadEntryMMCIF with arguments: 
[file:/Users/jd/wattosTestingPlatform/pdb/data/structures/divided/mmCIF/r4/1r4e.
cif.gz, false]
WARNING: Failed to find any atom in first model for entity: 3
WARNING: This was found in for instance entry 1j6t for the PO3 group and was 
reported in NRG issue 157
DEBUG: atomSetNotInFirstModel grew to size: 1
DEBUG: atomSetNotInFirstModel grew to size: 2
...
DEBUG: atomSetNotInFirstModel grew to size: 892
DEBUG: atomSetNotInFirstModel grew to size: 893
DEBUG: atomSetBad size: 893
DEBUG: atomsSetOk size: 8930
DEBUG: atomsSetOk size (after non-Oks zapped): 8037
DEBUG: Disabled syncing over models.
DEBUG: This might lead to inconsistencies in Wattos internal data model.
DEBUG: Needs testing for sure.
DEBUG: The code will definitely not work when reading in restraints on top of 
partily missing atoms.
ERROR: Error invoking reflected command: ReadEntryMMCIF
ERROR: 
java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at Wattos.CloneWars.CommandHub.invoke(CommandHub.java:120)
    at Wattos.CloneWars.UserInterface.doNonGuiMain(UserInterface.java:485)
    at Wattos.CloneWars.UserInterface.main(UserInterface.java:644)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 2147483646
    at Wattos.Soup.Entry.postProcessAfterReading(Entry.java:301)
    at Wattos.Soup.Entry.readmmCIFFormattedFile(Entry.java:620)
    at Wattos.CloneWars.CommandHub.ReadEntryMMCIF(CommandHub.java:617)
    ... 7 more

ERROR: Found throwable error above
WARNING: Command could not be executed: ReadEntryMmCIF
WARNING: Parameter set for stopping on any error: stopOnError

Wattos started at: November 12, 2010 2:17:28 PM CET
Wattos stopped at: November 12, 2010 2:17:30 PM CET
Wattos took (#ms): 2153