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: 2643 byte(s)
Diff to previous 438

Copied the aglappe-jung branch into trunk.

Revision 438 - (view) (annotate) - [select for diffs]
Modified Wed Nov 28 15:44:57 2007 UTC (16 years, 10 months ago) by filippis
Original Path: branches/aglappe-jung/proteinstructure/Box.java
File length: 2643 byte(s)
Diff to previous 433

AAInfo
-isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+"
-isOverlapping method has been added

AIGEdge
-copy method added

AIGNode
-equals and copy methods has been added

AIGraph
-getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed
-distances are now set for RIGNodes in getRIGraph
-for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph
-we set now the secondaryStructure object of RIGraph in getRIGraph
-addGraph has been added

Box
-we throw away wrong check in getDistancesWithinBox - read the comment

DbRIGraph
-constructors now take argument directed and directionality doesn't depend anymore on isCrossed
-distances are read also from db and set for RIGEdges

Pdb
-get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed
-there is check for forbidden cts in get_graph
-cts with + are taken into account in get_graph

RIGEdge
-setAtomWeight and setDistance methods have been added

RIGNode
-equals method has been added

RIGraph
-getObsLength has been deleted
-we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast

genDbGraph
-argument for directionality is now added

Revision 433 - (view) (annotate) - [select for diffs]
Modified Tue Nov 27 17:58:26 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/Box.java
File length: 2476 byte(s)
Diff to previous 421

Added more comments

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/Box.java
File length: 2261 byte(s)
Diff to previous 419

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 419 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (16 years, 11 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/Box.java
File length: 2112 byte(s)
Diff to previous 282

Re-branching for JUNG2 development

Revision 282 - (view) (annotate) - [select for diffs]
Modified Tue Aug 14 16:15:59 2007 UTC (17 years, 2 months ago) by duarte
File length: 2112 byte(s)
Diff to previous 250

Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore

Revision 250 - (view) (annotate) - [select for diffs]
Modified Mon Aug 6 14:48:37 2007 UTC (17 years, 2 months ago) by stehr
File length: 2085 byte(s)
Diff to previous 228

added application to count grid density, suppressed warning for secondary structure reassignment

Revision 228 - (view) (annotate) - [select for diffs]
Modified Mon Jul 9 14:32:47 2007 UTC (17 years, 3 months ago) by duarte
File length: 1983 byte(s)
Diff to previous 226

Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)

Revision 226 - (view) (annotate) - [select for diffs]
Added Fri Jul 6 13:43:30 2007 UTC (17 years, 3 months ago) by duarte
File length: 1420 byte(s)

First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct