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Revision 1694 - Directory Listing
Modified Fri Jan 17 11:45:00 2014 UTC (2 years, 4 months ago) by jmduarteg
Tagging for eppic release 2.0.4:
no changes from last owl release.
Revision 1693 - Directory Listing
Modified Wed Nov 27 09:02:57 2013 UTC (2 years, 6 months ago) by jmduarteg
Tagging for eppic release 2.0.3
- more PDB metadata parsing: biounit assembly and release date
- improved rmsd calculation: new OptimalSuperposition class introduced
- improvements in interface calculation: now going to 12th cell
- introduced chain clusters and interface clusters
- some more checks in cif file parsing: now won't crash on phenix files
Revision 1664 - Directory Listing
Modified Thu Aug 22 14:20:01 2013 UTC (2 years, 9 months ago) by jmduarteg
Tagging for eppic release 2.0.2
- bug fix: null pointer in pdb file parsing when no TER records present or misplaced
- many improvements in SpaceGroup and its testing
- operators can now be classified into their types, including calculation of screw directions
- bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1
- bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.
Revision 1662 - Directory Listing
Modified Thu Aug 22 14:10:10 2013 UTC (2 years, 9 months ago) by jmduarteg
Removing tag because another bug was found and we want to put it into the 2.0.2 release
Revision 1661 - Directory Listing
Modified Thu Aug 22 08:41:56 2013 UTC (2 years, 9 months ago) by jmduarteg
Tagging for eppic release 2.0.2
- bug fix: null pointer in pdb file parsing when no TER records present or misplaced
- many improvements in SpaceGroup and its testing
- operators can now be classified into their types, including calculation of screw directions
- bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1
- bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.
Revision 1640 - Directory Listing
Modified Fri Apr 19 10:54:42 2013 UTC (3 years, 1 month ago) by jmduarteg
Tagging for eppic release 2.0.1
- fixed bug: can't read 'I 1 2 1' space group. Now using both main and alternative names for looking up space groups
Revision 1631 - Directory Listing
Modified Fri Feb 15 14:40:13 2013 UTC (3 years, 3 months ago) by jmduarteg
Tagging for eppic release 2.0.0
- many bug fixes, especially in cif and pdb parsers. Now hopefully a lot more robust. Cif parser was tested in whole PDB as of Feb 2013. File guesser will be more flexible with PDB files: it allows now a lot more possible first lines
- all elements added to AtomType
- better dealing with unknown elements when reading from PDB file
- fixed bug in ASA calculation: for finding neighbours we were taking default vdw radius instead of one set in setRadius
- BlastXML parser can now read both raw xml and gzipped xml blast output (autodetecting it)
Revision 1600 - Directory Listing
Modified Tue Nov 27 10:21:02 2012 UTC (3 years, 6 months ago) by jmduarteg
Tagging for eppic release 1.9.6.
- totally redone interface calculation: huge improvements in runtime and memory usage, explores also 2nd neighbours, uses symmetry-redundancy elimination, bugs fixed
- introduced minimum ASA threshold for considering residue at surface
- cofactors can now be used for ASA calculation in interfaces
- blast runner now chooses matrix to use based on sequence length as it is standard use in blast servers
- introduced blast+ support
- introduced clustalo support in HomologsList
- improvements and important fixes in HomologsList alignments
Revision 1571 - Directory Listing
Modified Fri Aug 10 15:47:06 2012 UTC (3 years, 9 months ago) by jmduarteg
Tagging for eppic release 1.9.5.
- better alignment in HomologsList
- better redundancy reduction in HomologList through clustering
- many bug fixes, a few of them in parsers
Revision 1549 - Directory Listing
Modified Wed Mar 21 17:47:24 2012 UTC (4 years, 2 months ago) by jmduarteg
Tagging for crk release 1.9.4
Revision 1528 - Directory Listing
Modified Tue Feb 21 14:05:30 2012 UTC (4 years, 3 months ago) by jmduarteg
Tagging for crk version 1.9.3
Revision 1502 - Directory Listing
Modified Tue Dec 6 11:29:25 2011 UTC (4 years, 5 months ago) by jmduarteg
Tagging version for crk 1.9.2
Revision 1469 - Directory Listing
Modified Thu Sep 8 07:56:48 2011 UTC (4 years, 8 months ago) by jmduarteg
Tagging version for crk 1.9.1
Revision 1440 - Directory Listing
Modified Thu Aug 18 07:03:28 2011 UTC (4 years, 9 months ago) by jmduarteg
Tagging from bug fix branch for bug fixed version of CMView 1.9.4 (released as 1.1.1). Important bug fix of DaliRunner
Revision 1418 - Directory Listing
Modified Fri Jun 10 09:14:26 2011 UTC (4 years, 11 months ago) by jmduarteg
Tagging version 1.9.5. Many bug fixes after introduction of hetatoms, especially with regards to read/write of PDB files. First tag with hetatoms-support.
Revision 1393 - Directory Listing
Modified Thu May 19 14:41:29 2011 UTC (5 years ago) by jmduarteg
Tagging version 1.9.4 before major change: support for HETATMs
Revision 1371 - Directory Listing
Modified Wed Mar 30 07:34:06 2011 UTC (5 years, 2 months ago) by jmduarteg
Tagging owl-1.9.3 before major interface change.
Revision 1369 - Directory Listing
Modified Tue Mar 29 16:20:18 2011 UTC (5 years, 2 months ago) by jmduarteg
tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5
Revision 1368 - Directory Listing
Modified Tue Mar 29 16:12:26 2011 UTC (5 years, 2 months ago) by jmduarteg
Removing tag owl-1.9.2 because it doesn't include some minor fixes.
Revision 1365 - Directory Listing
Modified Mon Mar 28 16:51:55 2011 UTC (5 years, 2 months ago) by hstehr
tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5
Revision 1364 - Directory Listing
Modified Mon Mar 28 16:49:11 2011 UTC (5 years, 2 months ago) by hstehr
removing tag owl-1.9.2 which contained wrong contents (copy of all tags instead of trunk)
Revision 1352 - Directory Listing
Modified Tue Mar 22 18:18:36 2011 UTC (5 years, 2 months ago) by jmduarteg
tagging version 1.9.2 to match CMView-1.9.2-released-as-1.1rc5
Revision 1323 - Directory Listing
Modified Sat Feb 26 11:17:51 2011 UTC (5 years, 3 months ago) by hstehr
tagging version 1.9.1 to match CMView-1.9.1-released-as-1.1rc4
Revision 1303 - Directory Listing
Modified Fri Jan 14 20:21:03 2011 UTC (5 years, 4 months ago) by hstehr
tagging version 1.9.0 matching CMView 1.9.0 released as 1.1rc3
Revision 1003 - Directory Listing
Modified Wed Mar 31 11:54:57 2010 UTC (6 years, 1 month ago) by hstehr
tagging OWL 1.2.0 in sync with CMView 1.2.0 before major refactoring
Revision 949 - Directory Listing
Modified Thu Jan 28 16:11:34 2010 UTC (6 years, 4 months ago) by duarte
Tagging version 1.1.2 before major refactoring.
Revision 881 - Directory Listing
Modified Tue Aug 11 12:49:20 2009 UTC (6 years, 9 months ago) by duarte
Tagging 1.1.1 before major changes
Revision 732 - Directory Listing
Modified Wed Aug 27 13:40:11 2008 UTC (7 years, 9 months ago) by duarte
Tagging ver 0.9.6 for CMView 0.9.6. Now using jung beta1 jars.
Revision 731 - Directory Listing
Modified Wed Aug 27 13:39:11 2008 UTC (7 years, 9 months ago) by duarte
Tagging ver 1.1.0 for CMView 1.1.0. Now using jung beta1 jars.
Revision 692 - Directory Listing
Modified Mon Jun 23 09:53:23 2008 UTC (7 years, 11 months ago) by stehr
tagging version 0.9.5 matching CMView 0.9.5
Revision 676 - Directory Listing
Modified Tue May 27 12:38:07 2008 UTC (8 years ago) by duarte
Tagging ver. 0.9.4 matching CMView 0.9.4
Revision 555 - Directory Listing
Modified Thu Feb 28 14:29:15 2008 UTC (8 years, 3 months ago) by duarte
Tagging 0.9.3 for CMView release 0.9.3
Revision 554 - Directory Listing
Modified Thu Feb 28 14:28:19 2008 UTC (8 years, 3 months ago) by duarte
Deleting tag 1.0-rc1. That was too premature for a RC
Revision 545 - Directory Listing
Modified Tue Feb 19 16:29:50 2008 UTC (8 years, 3 months ago) by duarte
Tagging version 1.0-rc1 for CMView-1.0-rc1
Revision 527 - Directory Listing
Modified Thu Jan 31 09:15:44 2008 UTC (8 years, 3 months ago) by duarte
Tagging ver 0.9.2 for CMView 0.9.2
Revision 510 - Directory Listing
Modified Thu Jan 10 16:30:27 2008 UTC (8 years, 4 months ago) by stehr
tagging version 0.9.1 for CMView 0.9.1
Revision 494 - Directory Listing
Modified Wed Jan 2 14:02:55 2008 UTC (8 years, 4 months ago) by stehr
Tagging version 0.9 to use with CMView 0.9 (same as aglappe-jung 0.1.2 but moved to trunk)
Revision 490 - Directory Listing
Modified Wed Jan 2 11:13:39 2008 UTC (8 years, 4 months ago) by duarte
Tagging version 0.8.7 from trunk: last pre-JUNG before merging the JUNG branch to the trunk
Revision 486 - Directory Listing
Modified Thu Dec 20 11:13:54 2007 UTC (8 years, 5 months ago) by lpetzo
version for CMView-jung-0.1.2
Revision 476 - Directory Listing
Modified Sat Dec 15 09:51:44 2007 UTC (8 years, 5 months ago) by lpetzo
version for CMView-jung-0.1.1
Revision 473 - Directory Listing
Modified Thu Dec 13 10:23:03 2007 UTC (8 years, 5 months ago) by lpetzo
to be used for CMView-jung-0.1
Revision 440 - Directory Listing
Modified Wed Nov 28 16:42:41 2007 UTC (8 years, 6 months ago) by duarte
Tagging ver. 0.8.6. This will be the last pre-JUNG tag
Revision 364 - Directory Listing
Modified Mon Oct 22 08:47:44 2007 UTC (8 years, 7 months ago) by stehr
tagging version 0.8.5 in sync with CMView-0.8.5
Revision 304 - Directory Listing
Modified Mon Aug 27 14:42:40 2007 UTC (8 years, 9 months ago) by stehr
tagging version 0.8.3 corresponding to CMView 0.8.3
Revision 251 - Directory Listing
Modified Mon Aug 6 15:55:26 2007 UTC (8 years, 9 months ago) by stehr
tagging version 0.8.2 to be used with CM2PyMol 0.8.2
Revision 220 - Directory Listing
Modified Wed Jul 4 10:02:52 2007 UTC (8 years, 10 months ago) by stehr
tagging aglappe 0.8.1 to use with cmview 0.8.1
Revision 205 - Directory Listing
Modified Tue Jun 26 16:58:50 2007 UTC (8 years, 11 months ago) by stehr

Revision 201 - Directory Listing
Modified Tue Jun 19 09:27:11 2007 UTC (8 years, 11 months ago) by stehr
tagging version 0.7 matching CM2PyMol 0.7
Revision 197 - Directory Listing
Modified Thu Jun 14 14:44:44 2007 UTC (8 years, 11 months ago) by duarte
Tagging version 0.6 for release of cmview 0.6
Revision 188 - Directory Listing
Modified Mon Jun 11 14:05:50 2007 UTC (8 years, 11 months ago) by duarte
Tagging version 0.5 for release of CM2PyMol version 0.5
Revision 164 - Directory Listing
Modified Thu May 24 10:53:48 2007 UTC (9 years ago) by duarte

Revision 122 - Directory Listing
Modified Thu May 3 08:32:27 2007 UTC (9 years ago) by stehr
tagged version 0.3.4

Revision 111 - Directory Listing
Modified Tue Sep 19 13:10:03 2006 UTC (9 years, 8 months ago) by duarte
Tagging version 0.3.3. at rev110 after adding some renaming getNodes method to getMySQLNodes in DataDistribution and adding some functionality
Revision 105 - Directory Listing
Modified Tue Aug 8 11:52:56 2006 UTC (9 years, 9 months ago) by duarte
Tagging at rev104, slight modifications in DataDistributer. To be used with a slightly improved dumpnload.java
Revision 103 - Directory Listing
Modified Fri Aug 4 14:50:57 2006 UTC (9 years, 9 months ago) by duarte
Tag 0.3.1 at rev 102. Introduced slight modifications in DataDistributer class to use with dumpnload.java

Revision 101 - Directory Listing
Modified Tue Jul 25 10:30:02 2006 UTC (9 years, 10 months ago) by duarte
tools version 0.3 from rev98. To use with jed (includes new TableSorter)
Revision 100 - Directory Listing
Modified Tue Jul 25 10:29:27 2006 UTC (9 years, 10 months ago) by duarte
Sorry that was wrong!!
Revision 99 - Directory Listing
Modified Tue Jul 25 10:28:31 2006 UTC (9 years, 10 months ago) by duarte
tools version 0.3 from rev98. To use with jed (includes new TableSorter)
Revision 91 - Directory Listing
Modified Fri May 5 12:16:35 2006 UTC (10 years ago) by duarte
Creating of tools version 0.2:
Freeze of tools package at rev89.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)
Revision 90 - Directory Listing
Modified Fri May 5 12:15:03 2006 UTC (10 years ago) by duarte
This tag was wrongly created, should have contained a tools directory as a subdir. Deleting it
Revision 88 - Directory Listing
Modified Wed May 3 11:57:23 2006 UTC (10 years ago) by duarte
Creating of tools version 0.2:
Freeze of tools package at rev87.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)
Revision 82 - Directory Listing
Modified Thu Apr 13 10:54:05 2006 UTC (10 years, 1 month ago) by duarte
Creation of tools version 0.1:
Freezing tools rev81 to tag tools-0.1
I am planning to change completely some of the classes: DataDistribution and ClusterConnection. Will continue developing on trunk while we have this freeze so others can use programs as they are now.
Revision 1 - Directory Listing
Added Wed Jan 18 17:48:52 2006 UTC (10 years, 4 months ago) by filippis
Initial import of tools