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Restore bug for non-standard residues #269

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

0. Download http://nmr.cmbi.ru.nl/NRG-CING/data/ps/8psh/8psh.tgz
1. cing -n 8psh --initCcpn=8psh.tgz
2. cing -n 8psh 

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

jd:Stella/~/Downloads/ cing -n 8psh 
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9 (r877)        
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd         on: Stella.local (darwin/64bit/2cores/2.6.6)   at: (15754) Wed 
Nov 17 17:12:03 2010
==> Restoring <Project 8psh> ... 
WARNING: Residue._nameResidue: residue "SC" not defined in database by 
convention [INTERNAL_0]. Adding non-standard one now.
WARNING: Residue._nameResidue: residue "GS" not defined in database by 
convention [INTERNAL_0]. Adding non-standard one now.
WARNING: Residue._nameResidue: residue "PST" not defined in database by 
convention [INTERNAL_0]. Adding non-standard one now.
WARNING: Residue._nameResidue: residue "As" not defined in database by 
convention [INTERNAL_0]. Adding non-standard one now.
ERROR: SMLAtomHandler.handle: line 192, invalid nameTuple ('8psh', 'A', 1, 
"HO5'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 197, invalid nameTuple ('8psh', 'A', 1, 
'HOP2', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 199, invalid nameTuple ('8psh', 'A', 1, 
'HOP3', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 201, invalid nameTuple ('8psh', 'A', 1, 
'OP3', None, None, 'INTERNAL_0'), ==> atom skipped

[truncated]

ERROR: SMLAtomHandler.handle: line 2407, invalid nameTuple ('8psh', 'B', 14, 
'HOP2', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 2587, invalid nameTuple ('8psh', 'B', 15, 
'HOP2', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 2752, invalid nameTuple ('8psh', 'B', 16, 
"HO3'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 2757, invalid nameTuple ('8psh', 'B', 16, 
'HOP2', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H6', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H6', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
"H1'", None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H6', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
"H3'", None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H6', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H5', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H5', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
"H1'", None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H5', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
"H3'", None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error decoding ('8psh', 'A', 2, 
'H5', None, None, 'INTERNAL_0')
ERROR: SMLDihedralRestraintHandler.endHandler: invalid atom(s) [<Atom 
A.GUA1.C3'>, <Atom A.GUA1.O3'>, None, None]
ERROR: SMLDihedralRestraintHandler.endHandler: invalid atom(s) [<Atom 
A.GUA1.O3'>, None, None, None]
ERROR: SMLDihedralRestraintHandler.endHandler: invalid atom(s) [<Atom 
A.GUA1.C4'>, <Atom A.GUA1.C3'>, <Atom A.GUA1.O3'>, None]
ERROR: DihedralRestraint: invalid dihedral definition [<Atom A.GUA1.C3'>, <Atom 
A.GUA1.O3'>, None, None]
ERROR: DihedralRestraint: invalid dihedral definition [<Atom A.GUA1.O3'>, None, 
None, None]
ERROR: DihedralRestraint: invalid dihedral definition [<Atom A.GUA1.C4'>, <Atom 
A.GUA1.C3'>, <Atom A.GUA1.O3'>, None]
CING started at : Wed Nov 17 17:12:00 2010
CING stopped at : Wed Nov 17 17:12:04 2010
CING took       : 3.806 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/main.py", line 866, in <module>
    main()
  File "/Users/jd/workspace35/cing/python/cing/main.py", line 723, in main
    project = Project.open(options.name, status='create')
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 460, in open
    return Project.open(name, 'old', restore = restore)
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 568, in open
    pr.restore()
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 718, in restore
    self.runCingChecks(toFile=False)
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 969, in runCingChecks
    return runCingChecks(self, toFile=toFile, ranges = ranges)
  File "/Users/jd/workspace35/cing/python/cing/core/validate.py", line 66, in runCingChecks
    project.validateDihedrals()
  File "/Users/jd/workspace35/cing/python/cing/core/classes.py", line 940, in validateDihedrals
    return validateDihedrals(self)
  File "/Users/jd/workspace35/cing/python/cing/core/validate.py", line 1387, in validateDihedrals
    restoreDihRestraintInfo(self)
  File "/Users/jd/workspace35/cing/python/cing/core/validate.py", line 1373, in restoreDihRestraintInfo
    dihRestraint.residue = dihRestraint.atoms[2].residue #'Invalid'
AttributeError: 'NoneType' object has no attribute 'residue'

Please use labels and text to provide additional information.

Original issue reported on code.google.com by jurge...@gmail.com on 17 Nov 2010 at 4:21

GoogleCodeExporter commented 9 years ago 
I skipped them above but many atoms in uncommon residues are mishandled like 
these from residue 2 of residue type SC

ERROR: SMLAtomHandler.handle: line 207, invalid nameTuple ('8psh', 'A', 2, 
"C1'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 212, invalid nameTuple ('8psh', 'A', 2, 
'C2', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 217, invalid nameTuple ('8psh', 'A', 2, 
"C2'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 222, invalid nameTuple ('8psh', 'A', 2, 
"C3'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 227, invalid nameTuple ('8psh', 'A', 2, 
'C4', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 232, invalid nameTuple ('8psh', 'A', 2, 
"C4'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 237, invalid nameTuple ('8psh', 'A', 2, 
'C5', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 242, invalid nameTuple ('8psh', 'A', 2, 
"C5'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 247, invalid nameTuple ('8psh', 'A', 2, 
'C6', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 252, invalid nameTuple ('8psh', 'A', 2, 
"H1'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 257, invalid nameTuple ('8psh', 'A', 2, 
"H2'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 262, invalid nameTuple ('8psh', 'A', 2, 
"H2''", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 267, invalid nameTuple ('8psh', 'A', 2, 
"H3'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 272, invalid nameTuple ('8psh', 'A', 2, 
"H4'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 277, invalid nameTuple ('8psh', 'A', 2, 
'H5', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 282, invalid nameTuple ('8psh', 'A', 2, 
"H5'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 287, invalid nameTuple ('8psh', 'A', 2, 
"H5''", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 292, invalid nameTuple ('8psh', 'A', 2, 
'H6', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 297, invalid nameTuple ('8psh', 'A', 2, 
'HN41', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 302, invalid nameTuple ('8psh', 'A', 2, 
'HN42', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 307, invalid nameTuple ('8psh', 'A', 2, 
"HO3'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 309, invalid nameTuple ('8psh', 'A', 2, 
'HOP1', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 311, invalid nameTuple ('8psh', 'A', 2, 
'HOP3', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 313, invalid nameTuple ('8psh', 'A', 2, 
'N1', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 318, invalid nameTuple ('8psh', 'A', 2, 
'N3', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 323, invalid nameTuple ('8psh', 'A', 2, 
'N4', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 328, invalid nameTuple ('8psh', 'A', 2, 
'O2', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 333, invalid nameTuple ('8psh', 'A', 2, 
"O3'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 338, invalid nameTuple ('8psh', 'A', 2, 
"O4'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 343, invalid nameTuple ('8psh', 'A', 2, 
"O5'", None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 348, invalid nameTuple ('8psh', 'A', 2, 
'OP1', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 353, invalid nameTuple ('8psh', 'A', 2, 
'OP3', None, None, 'INTERNAL_0'), ==> atom skipped
ERROR: SMLAtomHandler.handle: line 355, invalid nameTuple ('8psh', 'A', 2, 'P', 
None, None, 'INTERNAL_0'), ==> atom skipped

Original comment by jurge...@gmail.com on 17 Nov 2010 at 4:42

GoogleCodeExporter commented 9 years ago 
I setup a unit check for this in r878. Kinda verbose so let's fix quickly.

Original comment by jurge...@gmail.com on 17 Nov 2010 at 7:27

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 17 Nov 2010 at 7:27

GoogleCodeExporter commented 9 years ago 
Explained problem for Geerten.

Original comment by jurge...@gmail.com on 6 Dec 2010 at 9:08

GoogleCodeExporter commented 9 years ago 
In r900 most problems are solved. Below are the remaining ones:

jd:stella/~/Downloads/ cing -n 8psh --initCcpn=8psh.tgz
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r900)       
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd         on: stella.cmbi.umcn.nl (darwin/64bit/2cores/2.6.6) at:  
(3968) Mon Jan  3 10:22:03 2011
Moving CCPN directory from [linkNmrStarData] to [8psh]
==> Importing data from Ccpn project "8psh"
Non-standard (residues and their) atoms added:
A   : [ 13]
As  : C1'  C2   C2'  C3'  C4   C4'  C5   C5'  C6   C8   H1'  H2'  H2'' H3'  H4' 
 H5'  H5'' H8   HN61 HN62 N1   N3   N6   N7   N9   O3'  O4'  O5'  OP1  P    S2P 
 [ 6]
C   : [ 9 10 14 16]
DG  : [ 1]
G   : [ 12 15]
GS  : C1'  C2   C2'  C3'  C4   C4'  C5   C5'  C6   C8   H1'  H2'  H2'' H3'  H4' 
 H5'  H5'' H8   HN1  HN21 HN22 HSP2 N1   N2   N3   N7   N9   O3'  O4'  O5'  O6  
 OP1  P    S2P  [ 3 7 8]
PST : C1'  C2   C2'  C3'  C4   C4'  C5   C5'  C5M  C6   H1'  H2'  H2'' H3'  H4' 
 H5'  H5'' H6   H71  H72  H73  HN3  HO3  HOP1 N1   N3   O2   O3'  O4   O4'  O5' 
 OP1  OP2  P    SP   [ 4]
SC  : C1'  C2   C2'  C3'  C4   C4'  C5   C5'  C6   H1'  H2'  H2'' H3'  H4'  H5  
 H5'  H5'' H6   HN41 HN42 HOP1 N1   N3   N4   O2   O3'  O4'  O5'  OP1  P    S2P 
 [ 2 5]
U   : [ 11]
==> Ccpn molecule '8psh' imported
<ccp.nmr.NmrConstraint.DistanceConstraint [1, 1, 1]> without atom pairs will be 
skipped
<ccp.nmr.NmrConstraint.DistanceConstraint [1, 1, 2]> without atom pairs will be 
skipped
<ccp.nmr.NmrConstraint.DistanceConstraint [1, 1, 3]> without atom pairs will be 
skipped
<ccp.nmr.NmrConstraint.DistanceConstraint [1, 1, 4]> without atom pairs will be 
skipped
<ccp.nmr.NmrConstraint.DistanceConstraint [1, 1, 5]> without atom pairs will be 
skipped
and so on for a total of 158 messages
  Warning: could not create torsion information for DNA__5__D__DGP__SC_P__GS_P__PST_P__SC_P__AS_P__GS_P__GS___3__.1.EPSI - no linking to next residue.
  Warning: could not create torsion information for DNA__5__D__DGP__SC_P__GS_P__PST_P__SC_P__AS_P__GS_P__GS___3__.6.EPSI - no linking to next residue.
  Warning: could not create torsion information for DNA__5__D__DGP__SC_P__GS_P__PST_P__SC_P__AS_P__GS_P__GS___3__.6.ZETA - no linking to prev residue.
  Warning: could not create torsion information for DNA__5__D__DGP__SC_P__GS_P__PST_P__SC_P__AS_P__GS_P__GS___3__.6.ZETA - no linking to prev residue.
  Warning: could not create torsion information for DNA__5__D__DGP__SC_P__GS_P__PST_P__SC_P__AS_P__GS_P__GS___3__.6.ALPHA - no linking to prev residue.
==> Ccpn project imported
----------- Project: 8psh -----------
created:    Mon Jan  3 10:22:03 2011
molecules:  [<Molecule "8psh" (C:2,R:16,A:575,M:1)>]
peaks:      []
distances:  [<DistanceRestraintList "distance_constraint_list" (keep,48)>]
dihedrals:  [<DihedralRestraintList "dihedral_constraint_list" (keep,62)>]
rdcs:       []
coplanars:  []
-------------------------------------
-------------------------------------------------------
==> Saving <Project 8psh>
CING started at : Mon Jan  3 10:21:58 2011
CING stopped at : Mon Jan  3 10:22:06 2011
CING took       : 7.527 s

jd:stella/~/Downloads/ cing -n 8psh 
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r900)       
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd         on: stella.cmbi.umcn.nl (darwin/64bit/2cores/2.6.6) at:  
(3980) Mon Jan  3 10:22:52 2011
==> Restoring <Project 8psh> ... 
ERROR: SMLDistanceRestraintHandler.endHandler: error p0 decoding ('8psh', 'B', 
11, 'H3', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error p0 decoding ('8psh', 'B', 
12, 'H1', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error p0 decoding ('8psh', 'B', 
11, 'H3', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error p1 decoding ('8psh', 'B', 
12, 'H1', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error p1 decoding ('8psh', 'B', 
13, 'H2', None, None, 'INTERNAL_0')
ERROR: SMLDistanceRestraintHandler.endHandler: error p0 decoding ('8psh', 'B', 
13, 'H2', None, None, 'INTERNAL_0')
==> Found assigned/overall/fraction for spins:    13C 0/153/0.00   15N 
0/62/0.00   1H 0/188/0.00   31P 0/16/0.00
==> Only spins with fraction >= 0.85 will be flagged when missing: {'13C': 
False, '1H': False, '31P': False, '15N': False}
==> Generating Macros
Finished restoring project <Project 8psh>
----------- Project: 8psh -----------
created:    Mon Jan  3 10:22:03 2011
molecules:  [<Molecule "8psh" (C:2,R:16,A:559,M:1)>]
peaks:      []
distances:  [<DistanceRestraintList "distance_constraint_list" (keep,48)>]
dihedrals:  [<DihedralRestraintList "dihedral_constraint_list" (keep,62)>]
rdcs:       []
coplanars:  []
-------------------------------------
-------------------------------------------------------
==> Saving <Project 8psh>
CING started at : Mon Jan  3 10:22:49 2011
CING stopped at : Mon Jan  3 10:22:54 2011
CING took       : 5.529 s

jd:stella/~/Downloads/ cing -n 8psh
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r900)       
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd         on: stella.cmbi.umcn.nl (darwin/64bit/2cores/2.6.6) at:  
(4006) Mon Jan  3 10:26:49 2011
==> Restoring <Project 8psh> ... 
==> Found assigned/overall/fraction for spins:    13C 0/153/0.00   15N 
0/62/0.00   1H 0/188/0.00   31P 0/16/0.00
==> Only spins with fraction >= 0.85 will be flagged when missing: {'13C': 
False, '1H': False, '31P': False, '15N': False}
==> Generating Macros
Finished restoring project <Project 8psh>
----------- Project: 8psh -----------
created:    Mon Jan  3 10:22:03 2011
molecules:  [<Molecule "8psh" (C:2,R:16,A:559,M:1)>]
peaks:      []
distances:  [<DistanceRestraintList "distance_constraint_list" (keep,48)>]
dihedrals:  [<DihedralRestraintList "dihedral_constraint_list" (keep,62)>]
rdcs:       []
coplanars:  []
-------------------------------------
-------------------------------------------------------
==> Saving <Project 8psh>
CING started at : Mon Jan  3 10:26:45 2011
CING stopped at : Mon Jan  3 10:26:50 2011
CING took       : 5.798 s

Original comment by jurge...@gmail.com on 3 Jan 2011 at 9:30

GoogleCodeExporter commented 9 years ago 
Fixed in r901.

Original comment by jurge...@gmail.com on 3 Jan 2011 at 2:18