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root/owl/trunk/src/owl/core/structure/contactTypes.dat
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Revision 1302 - (view) (annotate) - [select for diffs]
Modified Fri Jan 14 18:15:38 2011 UTC (8 years, 9 months ago) by hstehr
File length: 3339 byte(s)
Diff to previous 1301
adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
Revision 1301 - (view) (annotate) - [select for diffs]
Modified Fri Jan 14 16:24:16 2011 UTC (8 years, 9 months ago) by hstehr
File length: 2146 byte(s)
Diff to previous 1012
overwriting default contactTypes.dat with the one needed for CMView release versions (only contains standard contact types). The old version with all esoteric contact types is renamed to contactTypes.all.dat
Revision 1012 - (view) (annotate) - [select for diffs]
Modified Thu Apr 1 08:41:01 2010 UTC (9 years, 6 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 (9 years, 6 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 (9 years, 8 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 (10 years, 2 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 (11 years, 9 months 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 (11 years, 10 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 (11 years, 10 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 (12 years, 1 month 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

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