Revision 1009 - (view) (annotate) - [select for diffs]
Modified Wed Mar 31 15:50:04 2010 UTC (14 years, 5 months ago) by hstehr
File length: 8561 byte(s)
Diff to previous 1006

refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

Revision 1006 - (view) (annotate) - [select for diffs]
Modified Wed Mar 31 13:00:35 2010 UTC (14 years, 5 months ago) by hstehr
File length: 8558 byte(s)
Diff to previous 951

refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker

Revision 951 - (view) (annotate) - [select for diffs]
Modified Fri Jan 29 16:12:34 2010 UTC (14 years, 7 months ago) by duarte
File length: 8506 byte(s)
Copied from: trunk/runMD.java revision 949
Diff to previous 715

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 715 - (view) (annotate) - [select for diffs]
Modified Thu Aug 7 11:13:06 2008 UTC (16 years, 1 month ago) by duarte
Original Path: trunk/runMD.java
File length: 8506 byte(s)
Diff to previous 713

New option -s to do split output. 
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)

Revision 713 - (view) (annotate) - [select for diffs]
Added Wed Aug 6 14:35:49 2008 UTC (16 years, 1 month ago) by duarte
Original Path: trunk/runMD.java
File length: 6108 byte(s)

Initial commit of script and classes to interface with gromacs.