Revision 505 - (view) (annotate) - [select for diffs]
Modified Thu Jan 10 13:37:09 2008 UTC (16 years, 9 months ago) by duarte
File length: 3910 byte(s)
Diff to previous 492

Now converting also secondary structure in pairwise alignment graph conversion

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: 3906 byte(s)
Diff to previous 455

Copied the aglappe-jung branch into trunk.

Revision 455 - (view) (annotate) - [select for diffs]
Modified Tue Dec 4 19:01:47 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/SecStrucElement.java
File length: 3906 byte(s)
Diff to previous 419

Minor change : fixed 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/SecStrucElement.java
File length: 3866 byte(s)
Diff to previous 407

Re-branching for JUNG2 development

Revision 407 - (view) (annotate) - [select for diffs]
Modified Tue Nov 20 18:41:56 2007 UTC (16 years, 11 months ago) by filippis
File length: 3866 byte(s)
Diff to previous 383

contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Revision 383 - (view) (annotate) - [select for diffs]
Modified Tue Nov 6 18:35:17 2007 UTC (16 years, 11 months ago) by filippis
File length: 3867 byte(s)
Diff to previous 382

inSameSheet, isOther and getSheetSerial methods added in SecStrucElement

Revision 382 - (view) (annotate) - [select for diffs]
Modified Tue Nov 6 15:42:05 2007 UTC (16 years, 11 months ago) by filippis
File length: 3309 byte(s)
Diff to previous 274

Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred

Revision 274 - (view) (annotate) - [select for diffs]
Modified Tue Aug 14 10:26:32 2007 UTC (17 years, 2 months ago) by stehr
File length: 2458 byte(s)
Diff to previous 259

Added new SecondaryStructure object to Pdb and Graph

Revision 259 - (view) (annotate) - [select for diffs]
Added Fri Aug 10 16:40:44 2007 UTC (17 years, 2 months ago) by stehr
File length: 1279 byte(s)

completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes