FC crashed on existing chem comp

[GoogleCodeExporter]

FC crashed again. The error log said:
Could not create, pre-existing object had same key: 
<ccp.molecule.ChemComp.NonStdChemComp ['DNA', '3dr']>

This does exist in ccpn-chemcomp as:
DNA+3DR+pdbe_ccpnRef_2009-03-12-11-43-04-335_00001.xml

I checked ligand expo against the atom nomenclature, and these seem to have the 
same atoms, so I don't get why it would have crashed. Should I set
self.numModelsToRead, autoCreateChemComps = True) to false?

Traceback (most recent call last):
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 753, in <module>
    LinkNmrStarData(sys.argv)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 89, in __init__
    self.catchError(raiseError,timeFlag)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 82, in __init__
    self.runSpecific()
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 169, in runSpecific
    self.readNmrStarFile(inNmrStarFile, version = self.originalNmrStarVersion, maxNum = self.numModelsToRead, autoCreateChemComps = True)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/NmrStar.py", line 46, in readNmrStarFile
    **localKeywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 951, in readProject
    self.getFullProject(fileName,**keywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 566, in getFullProject
    chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1071, in readSequence
    (createMoleculeDict,molSystemBonds) = self.checkMolecules()
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 6035, in checkMolecules
    self.makeChemComp()
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 14169, in makeChemComp
    chemComp = self.project.newNonStdChemComp(**createDict)     
  File "/raid/docr/workspace/ccpn/python/memops/api/Implementation.py", line 16375, in newNonStdChemComp
    return NonStdChemComp(self, **attrlinks)
  File "/raid/docr/workspace/ccpn/python/ccp/api/molecule/ChemComp.py", line 25641, in __init__
    + ": %s" % (self,)
memops.general.Implementation.ApiError: 
ccp.molecule.ChemComp.NonStdChemComp.__init__:
             Could not create, pre-existing object had same key: <ccp.molecule.ChemComp.NonStdChemComp ['DNA', '3dr']>

Original issue reported on code.google.com by schulte....@gmail.com on 2 Nov 2010 at 3:23

[GoogleCodeExporter]

Tried to rerun 2kid, and a few others, because Dimitri found an incorrect tag. 
2kid was the only one to not go through. It crashed with a similar traceback to 
the one above:

  Using preset values...
    > 
    >   Warning: Did not map CCPN chain codes ['B']
    >   Final mapping: [['A', ' ', 2, 0], ['C', ' ', 1, 148]]
    > 
Traceback (most recent call last):
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 753, in <module>
    LinkNmrStarData(sys.argv)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 89, in __init__
    self.catchError(raiseError,timeFlag)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 82, in __init__
    self.runSpecific()
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 169, in runSpecific
    self.readNmrStarFile(inNmrStarFile, version = self.originalNmrStarVersion, maxNum = self.numModelsToRead, autoCreateChemComps = True)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/NmrStar.py", line 46, in readNmrStarFile
    **localKeywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 951, in readProject
    self.getFullProject(fileName,**keywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 566, in getFullProject
    chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1071, in readSequence
    (createMoleculeDict,molSystemBonds) = self.checkMolecules()
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 6035, in checkMolecules
    self.makeChemComp()
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 14318, in makeChemComp
    raise self.FormatConverterError, "  Error: no link code %s, %s" % (linkCode,descriptor)
ccpnmr.format.converters.DataFormat.FormatConverterError: '  Error: no link 
code prev, neutral'

Original comment by schulte....@gmail.com on 8 Dec 2010 at 3:38

• Added labels: Entry-2kid

[GoogleCodeExporter]

This is related to the automatic creation of chemComps and is now fixed (update 
SF repository python/ccpnmr/format/).  B27 is not a CCPN chemComp, not sure why 
- might have been missed, obsoleted, or too recent?

Original comment by wfvran...@gmail.com on 8 Dec 2010 at 7:05

[GoogleCodeExporter]

Thanks Wim. That fixed 2kid, but 2l2u still crashes.

sorry

Original comment by schulte....@gmail.com on 8 Dec 2010 at 7:47

• Removed labels: Entry-2kid

[GoogleCodeExporter]

Well 2l2u works for me... do you have a presetDict entry for it? Strange that 
you get this error, like you say DNA 3DR exists, in my setup it just uses the 
existing one, no problem.

Original comment by wfvran...@gmail.com on 9 Dec 2010 at 10:20

[GoogleCodeExporter]

I don't have a presetDict entry for it. What settings do I need? I can't get to 
the point where I can analyze it. The log file ends here:

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

  Selecting naming system PDB_REMED.
  Molecule DNA__5__D__CP_AP_GP_CP_GP__3DR_P_GP_TP_AP_TP_AP_AP_GP_C__3__ set to type DNA from sequence file information.
  Molecule DNA__5__D__GP_CP_TP_TP_AP__3DR_P_AP_CP_AP_CP_GP_CP_TP_G__3__ set to type DNA from sequence file information.
Error: Cannot find ChemComp XML file other, 3dr.
    ######################################
    # Warning: autocreating chemComp 3dr #
    ######################################

 in createLinkAndVars
  Made linkEnd prev
  Made linkEnd next
Created 3dr,DNA: neutral,none
Created 3dr,DNA: neutral,middle
Created 3dr,DNA: neutral,end
Created 3dr,DNA: neutral,start
start generating output :  ccp.molecule.ChemComp.NonStdChemComp
Error: Cannot find ChemComp XML file other, 3dr.
    ######################################
    # Warning: autocreating chemComp 3dr #
    ######################################

 in createLinkAndVars

Original comment by schulte....@gmail.com on 9 Dec 2010 at 4:06

[GoogleCodeExporter]

Alright. I set "autoCreateChemComps = False" and got results. I'll work on this 
and let you know.

Original comment by schulte....@gmail.com on 9 Dec 2010 at 4:26

[GoogleCodeExporter]

Yes the problem seems to be that somehow in your setup it doesn't find the 3dr 
chemComp initially, then tries to make it, but fails because it's already 
there. I don't have the issue, it finds the chemComp straight away.

In any case, not sure if you can disable autoCreateChemComps, because other 
projects (recent ones with chemComps missing) might fail.

Original comment by wfvran...@gmail.com on 9 Dec 2010 at 4:31

[GoogleCodeExporter]

Now it's refusing to recognize 3dr - I'm going to reset autoCreateChemComps 
because that does more good than not. What would be different in the setups? 

Created chain 'A', start seqCode 1, end seqCode 13, molecule 
'DNA__5__D__CP_AP_GP_CP_GP__3DR_P_GP_TP_AP_TP_AP_AP_GP_C__3__'...
Created chain 'B', start seqCode 15, end seqCode 27, molecule 
'DNA__5__D__GP_CP_TP_TP_AP__3DR_P_AP_CP_AP_CP_GP_CP_TP_G__3__'...

    Original chain code 'STR1'. Higher scores below are better.

      1    : C (8)
      2    : A (6)
      3    : G (6)
      4    : C (8)
      5    : G (6)
      7    : G (6)
      8    : T (5)
      9    : A (6)
      10   : T (5)
      11   : A (6)
      12   : A (6)
      13   : G (6)
      14   : C (8)

    Original chain code 'STR2'. Higher scores below are better.

      1    : G (6)
      2    : C (8)
      3    : T (5)
      4    : T (5)
      5    : A (6)
      7    : A (6)
      8    : C (8)
      9    : A (6)
      10   : C (8)
      11   : G (6)
      12   : C (8)
      13   : T (5)
      14   : G (6)

Original comment by schulte....@gmail.com on 9 Dec 2010 at 4:41

[GoogleCodeExporter]

I think you guys nailed this issue already. I get data thru to NRG-CING as 
well. Can I close?

Original comment by jurge...@gmail.com on 24 Feb 2012 at 9:42

• Changed state: Fixed

[GoogleCodeExporter]

Yeah, I haven't seen this in a while.

Original comment by schulte....@gmail.com on 24 Feb 2012 at 3:29

[GoogleCodeExporter]

Original comment by schulte....@gmail.com on 24 Feb 2012 at 3:30

• Changed state: Verified