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Revision 1244 - (view) (annotate) - [select for diffs]
Modified Thu Sep 30 09:09:36 2010 UTC (11 years, 10 months ago) by jmduarteg
File length: 212 byte(s)
Diff to previous 1242 , to selected 1241
Finally ASA/BSA comparison to PISA test passes. Have to exclude one case where slight difference interface area values led to different sorting and so comparsion doesn't work. This will still be a problem whenever that happens (whenever different sorting of PISA vs ours)
Revision 1242 - (view) (annotate) - [select for diffs]
Modified Wed Sep 29 15:22:49 2010 UTC (11 years, 10 months ago) by jmduarteg
File length: 69 byte(s)
Diff to previous 1241
Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
Revision 1241 - (view) (annotate) - [selected]
Modified Tue Sep 21 17:08:36 2010 UTC (11 years, 10 months ago) by jmduarteg
File length: 68 byte(s)
Diff to previous 1225
Fixed bug: the bsa values of residues of the different interfaces were being updated on the same references, we have to copy before creating ChainInterface objects in getAllInterfaces.
Implemented interface pdb file outputting in enumerateInterfaces
Still interfaces tests don't pass because of 2 problems: a) order of first/second molecule not necessarily same as PISA (and in case of same chain codes can't catch it with chain codes), b) in many cases there are many minor discrepancies, usually associated to a lot of small negative bsa values.
Revision 1225 - (view) (annotate) - [select for diffs]
Modified Wed Sep 1 15:57:23 2010 UTC (11 years, 11 months ago) by jmduarteg
File length: 66 byte(s)
Diff to previous 1217 , to selected 1241
Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.
Revision 1217 - (view) (annotate) - [select for diffs]
Added Tue Aug 31 17:11:30 2010 UTC (11 years, 11 months ago) by jmduarteg
File length: 39 byte(s)
Diff to selected 1241
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.

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