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FC fails to accept long entity name in STAR #295

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Converting STAR:
http://nmr.cmbi.ru.nl/NRG-CING/prep/C/77/177d/177d_C_wattos.str
to CCPN using: cingDirScripts, 'FC', 'convertStar2Ccpn.py'

What is the expected output? What do you see instead?
http://nmr.cmbi.ru.nl/NRG-CING/prep/C/77/177d/177d_star2Ccpn.log

This is again due to a too long name for:
save_DNA__5__D__GP_AP_AP_CP_AP_GP_GP_TP_TP_TP_TP_T_CP_CP_TP_GP_TP_TP_CP_TP_TP_TP
_TP_T_CP_TP_TP_TP_TP_CP_C__3__
    _Entity.Sf_category                  entity

Wim, where should we change this? I can modify it in Wattos but I think it's 
best done in the conversion to CCPN. 

This is independent of the NRG setup. No restraints for this entry.

Original issue reported on code.google.com by jurge...@gmail.com on 13 Apr 2011 at 11:09

GoogleCodeExporter commented 9 years ago 
Ok, I just offered FC short names and the problem persists. It seems to be 
because of another problem:

ERROR: Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/Scripts/FC/convertStar2Ccpn.py", line 118, in importFullStarProjects
    ccpnProject.checkAllValid()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 6014, in checkAllValid
    value.checkAllValid(complete)
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 10162, in checkAllValid
    value.checkAllValid(complete)
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3313, in checkAllValid
    self.checkValid(complete)
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3933, in checkValid
    + ": %s" % (self,)
ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['177d', 'A']>

Perhaps because there are coordinates missing for residues 8-12:

       1 223 1 1  7 DG H21  H  -5.700   9.880 -12.225 1.00 0.0 A A . 14 DG H21  1 1 
       1 224 1 1  7 DG H22  H  -5.882  10.463 -13.868 1.00 0.0 A A . 14 DG H22  1 1 
       1 225 1 1 13 DC O5'  O -10.463   9.705  -5.114 1.00 0.0 A A .  1 DC O5'  1 1 
       1 226 1 1 13 DC C5'  C  -9.303   9.818  -5.936 1.00 0.0 A A .  1 DC C5'  1 1 

Is this a Wattos problem Wim? 

It looks with some debug messages that FC is only getting 26 out of the 31 
residues. Exactly those for which there are no coordinates but that should be 
allowable, right?

ll: length 31 frozenset([<ccp.molecule.MolSystem.Residue ['177d', 'A', 21]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 22]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 16]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 2]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 9]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 10]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 12]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 29]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 4]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 15]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 19]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 31]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 20]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 1]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 6]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 23]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 24]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 11]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 17]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 25]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 26]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 8]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 27]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 14]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 5]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 28]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 13]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 7]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 30]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 3]>, 
<ccp.molecule.MolSystem.Residue ['177d', 'A', 18]>])
aset: length 26 frozenset([(13, ' '), (-1, ' '), (14, ' '), (-4, ' '), (19, ' 
'), (4, ' '), (1, ' '), (12, ' '), (9, ' '), (7, ' '), (17, ' '), (0, ' '), 
(-2, ' '), (8, ' '), (21, ' '), (6, ' '), (3, ' '), (16, ' '), (11, ' '), (20, 
' '), (2, ' '), (15, ' '), (-3, ' '), (10, ' '), (5, ' '), (18, ' ')])
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 3]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 19]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 18]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 20]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 21]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 6]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 22]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 23]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 8]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 24]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 9]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 25]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 10]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 26]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 11]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 27]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 2]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 5]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 12]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 28]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 4]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 13]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 29]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 7]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 14]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 30]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 15]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 31]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 1]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 16]>
lll: <ccp.molecule.MolSystem.Residue ['177d', 'A', 17]>
aset: (-4, ' ')
aset: (-3, ' ')
aset: (-2, ' ')
aset: (-1, ' ')
aset: (0, ' ')
aset: (1, ' ')
aset: (2, ' ')
aset: (3, ' ')
aset: (4, ' ')
aset: (5, ' ')
aset: (6, ' ')
aset: (7, ' ')
aset: (8, ' ')
aset: (9, ' ')
aset: (10, ' ')
aset: (11, ' ')
aset: (12, ' ')
aset: (13, ' ')
aset: (14, ' ')
aset: (15, ' ')
aset: (16, ' ')
aset: (17, ' ')
aset: (18, ' ')
aset: (19, ' ')
aset: (20, ' ')
aset: (21, ' ')
ERROR: Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/Scripts/FC/convertStar2Ccpn.py", line 118, in importFullStarProjects
    ccpnProject.checkAllValid()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 6014, in checkAllValid
    value.checkAllValid(complete)
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 10174, in checkAllValid
    value.checkAllValid(complete)
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3313, in checkAllValid
    self.checkValid(complete)
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3945, in checkValid
    + ": %s" % (self,)
ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['177d', 'A']>

Original comment by jurge...@gmail.com on 13 Apr 2011 at 1:14

GoogleCodeExporter commented 9 years ago 
No think this is the one where the sequence is numbered from high to low, my 
code doesn't handle that so it probably messes everything up...

Original comment by wfvran...@gmail.com on 21 Apr 2011 at 3:10

GoogleCodeExporter commented 9 years ago 
Anyway, this is a problem outside the CING project.

Original comment by jurge...@gmail.com on 21 Apr 2011 at 3:23