Revision 515 - (view) (annotate) - [select for diffs]
Modified Mon Jan 14 10:02:28 2008 UTC (16 years, 9 months ago) by stehr
File length: 8997 byte(s)
Diff to previous 492

Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors

Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 9 months ago) by duarte
File length: 8323 byte(s)
Diff to previous 454

Copied the aglappe-jung branch into trunk.

Revision 454 - (view) (annotate) - [select for diffs]
Modified Tue Dec 4 18:58:14 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/RIGNbhood.java
File length: 8323 byte(s)
Diff to previous 452

Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors

Revision 452 - (view) (annotate) - [select for diffs]
Modified Tue Dec 4 15:40:17 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/RIGNbhood.java
File length: 8302 byte(s)
Diff to previous 421

New class NbhoodBackgrnd representing a set of neighbourhoods loaded from a set of graphs of a non redundant pdb structures set.
Rewrote RIGNbhood so that the TreeMap now contains also the central residue. Added methods equals() and match().
Adapted RIGraph.getNbhood to the new constructor in RIGNbhood

Revision 421 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 19:42:11 2007 UTC (16 years, 11 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/RIGNbhood.java
File length: 4030 byte(s)
Diff to previous 420

Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff))
Loads of better comments

Revision 420 - (view) (annotate) - [select for diffs]
Added Thu Nov 22 17:27:44 2007 UTC (16 years, 11 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/RIGNbhood.java
File length: 4047 byte(s)

First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)