AlphaBetaTest / cing

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Add chain ids with all potentially intermolecular information #254

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago
What steps will reproduce the problem?
When you go to the Details(flat) page of a dimer, some of the files don't have 
a chain identification. So it's difficult to find out to which chain the 
residues belong.

What is the expected output? What do you see instead?
These files include:
-restraints.txt
-hBond constraint list
-dihedral constraint
-distance constraint
-salt bridges
(-disulfides, probably, I didn't find an example of it yet)

Original issue reported on code.google.com by k.berntsen@student.science.ru.nl on 21 Sep 2010 at 11:19

GoogleCodeExporter commented 9 years ago
[deleted comment]
GoogleCodeExporter commented 9 years ago
[deleted comment]
GoogleCodeExporter commented 9 years ago
I've to mention that the chain ids are included if you go directly from the 
home page to dehedral constraints, distance constraints and hBond constraints.

Original comment by k.berntsen@student.science.ru.nl on 21 Sep 2010 at 12:46

GoogleCodeExporter commented 9 years ago
E.g. 
http://nmr.cmbi.ru.nl/NRG-CING/data/hg/2hgh/2hgh.cing/2hgh/Cing/restraints.txt
http://nmr.cmbi.ru.nl/Education/Validation/CINGreports/1y4o.cing/1y4o/Cing/saltb
ridges.txt

Since this issue comes up so frequently it might be better to change all 
residue's string representation (by __str__()) to include the chain id.

Fixed in revision 839 by replacing classes.py:
            s = s + sprintf('(%-11s - %11s)   ', p[0]._Cname(1), p[1]._Cname(1))
by:
            s = s + sprintf('(%-13s - %13s)   ', p[0]._Cname(2), p[1]._Cname(2)) # include chain id.

Original comment by jurge...@gmail.com on 22 Sep 2010 at 12:16