Revision 1012 - (view) (annotate) - [select for diffs]
Modified Thu Apr 1 08:41:01 2010 UTC (10 years, 9 months ago) by hstehr
File length: 3953 byte(s)
Diff to previous 1005

bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found

Revision 1005 - (view) (annotate) - [select for diffs]
Modified Wed Mar 31 12:29:26 2010 UTC (10 years, 9 months ago) by hstehr
File length: 3850 byte(s)
Copied from: trunk/src/proteinstructure/contactTypes.dat revision 1002
Diff to previous 951

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

Revision 951 - (view) (annotate) - [select for diffs]
Modified Fri Jan 29 16:12:34 2010 UTC (10 years, 11 months ago) by duarte
Original Path: trunk/src/proteinstructure/contactTypes.dat
File length: 3850 byte(s)
Diff to previous 885

Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.

Revision 885 - (view) (annotate) - [select for diffs]
Modified Fri Aug 14 10:37:31 2009 UTC (11 years, 5 months ago) by duarte
Original Path: trunk/proteinstructure/contactTypes.dat
File length: 3850 byte(s)
Diff to previous 492

Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.

Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (13 years ago) by duarte
Original Path: trunk/proteinstructure/contactTypes.dat
File length: 2657 byte(s)
Diff to previous 419

Copied the aglappe-jung branch into trunk.

Revision 419 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (13 years, 2 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/contactTypes.dat
File length: 2657 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 (13 years, 2 months ago) by filippis
Original Path: trunk/proteinstructure/contactTypes.dat
File length: 2657 byte(s)
Diff to previous 326

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 326 - (view) (annotate) - [select for diffs]
Added Thu Sep 20 14:49:55 2007 UTC (13 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/contactTypes.dat
File length: 2237 byte(s)

Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly