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PiRSquared17 / cing

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validateSaltbridge fails for 1bzb; bad import of uncommon residues #194

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. run NRG-CING for entry

What is the expected output? What do you see instead?
ERROR: DihedralRestraintList.analyze: "dihedral_constraint_list" empty list
==> validateRestraints, output to 1bzb.cing/1bzb/Cing/restraints.txt
Skipping molecule.mergeResonances because there are no resonances
==> checkSaltbridges, output to 1bzb.cing/1bzb/Cing/saltbridges.txt
CING started at : Tue Oct 20 14:00:51 2009
CING stopped at : Tue Oct 20 14:02:41 2009
CING took       : 110.804 s

Traceback (most recent call last):
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 266, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 195, in main
    if project.validate(htmlOnly = htmlOnly, doProcheck = doProcheck, doWhatif = doWhatif):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/validate.py", line 128, in validate
    project.runCingChecks(ranges=ranges)
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/validate.py", line 95, in runCingChecks
    project.checkForSaltbridges(toFile=True)
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/validate.py", line 752, in checkForSaltbridges
    s = validateSaltbridge(res1,res2)
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/validate.py", line 842, in validateSaltbridge
    atm = residue[atmName]
KeyError: 'NH1'

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Original issue reported on code.google.com by jurge...@gmail.com on 20 Oct 2009 at 12:16

GoogleCodeExporter commented 9 years ago 
Should be fixed in r648 by checking for the existence of atom but it's caused 
by the routine being written on 
using the 1 letter abbreviated residue names. That's a bigger bug.

The CING report is not right because it misses several residues NAG and MAN!

I like Geerten's input on this one.

Original comment by jurge...@gmail.com on 20 Oct 2009 at 12:50

GoogleCodeExporter commented 9 years ago 
Geerten confirmed to rewrite code and store info inside db instead of code.

Original comment by jurge...@gmail.com on 2 Nov 2009 at 1:01