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Revision 1646 - Directory Listing
Modified Wed Jun 26 09:30:03 2013 UTC (8 years, 10 months ago) by jmduarteg
Now interfaces pngs have transparent background. Also changed another instance of "select resi 0" to "select none"
Revision 1645 - Directory Listing
Modified Mon Jun 24 10:25:00 2013 UTC (8 years, 10 months ago) by jmduarteg
Setting default minimum area for magenta dot displaying to 400 (was 500)
Revision 1644 - Directory Listing
Modified Mon Jun 17 14:24:45 2013 UTC (8 years, 11 months ago) by kumaran
1)Javaversion variable is added in build.xml to change the version easily. 
2)Pymol exited with error status 139 due to very long selection string written in the form of every residue(3+4+5+8+9+10). It is fixed by writing in the form of (3-5+8-10)
Revision 1636 - Directory Listing
Modified Mon Mar 18 14:06:43 2013 UTC (9 years, 2 months ago) by jmduarteg
Now will also write png files when generating chain pses.
Revision 1630 - Directory Listing
Modified Fri Feb 15 11:54:22 2013 UTC (9 years, 3 months ago) by jmduarteg
New feature: now blast xml parser can read either raw xml or gzipped xml files. Also HomologList will use xml.gz files only as cache files
Revision 1616 - Directory Listing
Modified Thu Jan 31 17:45:03 2013 UTC (9 years, 3 months ago) by jmduarteg
Fixed minor issue: we were using residue 0 in order to create an empty selection but since now we use PDB residue numbers residue 0 is valid. We now use the "none" keyword used in pymol to create empty selections
Revision 1614 - Directory Listing
Modified Wed Jan 30 10:50:26 2013 UTC (9 years, 3 months ago) by jmduarteg
Fixed small bug in PymolRunner: negative residue numbers need to be escaped
Revision 1613 - Directory Listing
Modified Wed Jan 30 09:25:07 2013 UTC (9 years, 3 months ago) by jmduarteg
Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
Revision 1599 - Directory Listing
Modified Fri Nov 16 10:02:32 2012 UTC (9 years, 6 months ago) by jmduarteg
Fixed important issues with searching and alignment of homologs: 
- ids and coverage were calculated wrongly, based on all BlastHsps for a hit. Now based on single Hsps
- fixed bug in BlastHsp.getQueryCoverage: was miscalculating the coverage by 1 unit
- the useHspsOnly parameter in alignment didn't make much sense. We need always to use the hsp segments only, extending to the full sequence is dangerous and in any case does not make sense at all if the clustering is done in hsps only
Revision 1597 - Directory Listing
Modified Wed Nov 7 08:58:43 2012 UTC (9 years, 6 months ago) by jmduarteg
Several changes related to blast:
- now supporting blast+ blastp. 
- blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired
- refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+
Also updated uniprot jar.
Revision 1593 - Directory Listing
Modified Wed Oct 31 11:43:11 2012 UTC (9 years, 6 months ago) by jmduarteg
Now supporting clustalo as well as tcoffee for alignment of homologs
Revision 1589 - Directory Listing
Modified Mon Oct 1 14:31:11 2012 UTC (9 years, 7 months ago) by jmduarteg
Now the blastp runner will automatically select a substitution matrix based on length of query, following recommendations from ncbi (http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html). Most blast web servers have this behaviour by default.
Revision 1588 - Directory Listing
Modified Thu Sep 27 13:26:00 2012 UTC (9 years, 7 months ago) by jmduarteg
New feature: now we can take cofactors into account for calculation of ASA in interfaces
Revision 1587 - Directory Listing
Modified Tue Sep 18 09:12:00 2012 UTC (9 years, 8 months ago) by jmduarteg
Now using a minimum threshold value for considering a residue at surface (instead of 0 before)
Revision 1585 - Directory Listing
Modified Tue Aug 28 10:03:19 2012 UTC (9 years, 8 months ago) by jmduarteg
New method to create pse of chain conservation and interfaces marked with dots
Revision 1584 - Directory Listing
Modified Thu Aug 23 10:16:34 2012 UTC (9 years, 8 months ago) by jmduarteg
Now making selections for chains as well
Revision 1556 - Directory Listing
Modified Wed May 9 12:04:21 2012 UTC (10 years ago) by jmduarteg
New feature: now reducing redundancy via clustering with blastclust
Revision 1543 - Directory Listing
Modified Thu Mar 1 18:23:02 2012 UTC (10 years, 2 months ago) by jmduarteg
Now can sort the blast hit list by evalue ascending
Revision 1513 - Directory Listing
Modified Wed Jan 25 11:37:32 2012 UTC (10 years, 3 months ago) by jmduarteg
Implemented some basic symmetry redundancy elimination in interfaces search. Moved interfaces-search to a separate class.
New pymol output file in enumerateInterfaces with all interfaces in a single session
Revision 1511 - Directory Listing
Modified Thu Dec 22 10:07:14 2011 UTC (10 years, 4 months ago) by jmduarteg
Improved pymol interface coloring: no showing sticks for whole interface but different colors only for core residues
Revision 1500 - Directory Listing
Modified Tue Dec 6 08:10:12 2011 UTC (10 years, 5 months ago) by jmduarteg
Switching off surface rendering
Revision 1499 - Directory Listing
Modified Mon Dec 5 15:57:36 2011 UTC (10 years, 5 months ago) by jmduarteg
Fixed bug: slight miscalculation in query coverage (by one unit per hsp), would have affected very short entries
Revision 1498 - Directory Listing
Modified Mon Dec 5 11:31:10 2011 UTC (10 years, 5 months ago) by jmduarteg
Fixed minor bug: now will re-blast only if maxNumSeqs above 500 and more hits requested
Revision 1497 - Directory Listing
Modified Sat Dec 3 16:12:05 2011 UTC (10 years, 5 months ago) by jmduarteg
New feature: now can specify a subinterval in UniprotHomologList
Revision 1491 - Directory Listing
Modified Thu Nov 17 14:56:11 2011 UTC (10 years, 6 months ago) by jmduarteg
Now can pass option -v to blast (max number of hits reported)
Revision 1489 - Directory Listing
Modified Wed Nov 16 14:26:57 2011 UTC (10 years, 6 months ago) by jmduarteg
Fixed logging and error handling of tcoffee: now it will really log errors to log file, temp files won't be deleted when exit!=0, command line is logged
Revision 1484 - Directory Listing
Modified Fri Nov 11 16:06:07 2011 UTC (10 years, 6 months ago) by jmduarteg
Now explicitely specifying number of threads in TcoffeeRunner
Revision 1466 - Directory Listing
Modified Mon Sep 5 16:21:32 2011 UTC (10 years, 8 months ago) by jmduarteg
Some improvements to PymolRunner, including reading color mappings from properties file
Revision 1456 - Directory Listing
Modified Mon Aug 22 14:52:42 2011 UTC (10 years, 8 months ago) by jmduarteg
Tidied up PymolRunner and made a bit faster by merging png and pse/pml creation for interfaces
Revision 1454 - Directory Listing
Modified Mon Aug 22 13:05:34 2011 UTC (10 years, 8 months ago) by jmduarteg
More features for PymolRunner to display fancy pymol interface representations
Revision 1453 - Directory Listing
Modified Fri Aug 19 16:15:51 2011 UTC (10 years, 9 months ago) by jmduarteg
Got rid of -p option when executing pymol
Revision 1452 - Directory Listing
Modified Fri Aug 19 14:46:44 2011 UTC (10 years, 9 months ago) by jmduarteg
Now using grey for symmetry related partners in interface thumbnails 
Revision 1435 - Directory Listing
Modified Tue Aug 16 16:03:09 2011 UTC (10 years, 9 months ago) by jmduarteg
Fixed bugs in DaliRunner
- it wouldn't run from cmview when the two chains had same pdb code and pdb chain code
- it wouldn't work with newer versions of DaliLite as apparently the output file names and formats changed 
Revision 1411 - Directory Listing
Modified Tue Jun 7 12:15:51 2011 UTC (10 years, 11 months ago) by jmduarteg
Fixed bug: was not using full path of the given pymol executable
Revision 1403 - Directory Listing
Modified Wed May 25 09:03:49 2011 UTC (10 years, 11 months ago) by jmduarteg
Fixed a few bugs:
- PdbChain: copy() was missing some important fields, PDB file writing method was printing SEQRES for nonpoly chains too
- naccess BSA calculation had a few problems
- PdbAsymUnit: a few important issues with PDB/CIF chain codes
Revision 1399 - Directory Listing
Modified Tue May 24 09:06:15 2011 UTC (10 years, 11 months ago) by jmduarteg
Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (11 years ago) by jmduarteg
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Revision 1391 - Directory Listing
Modified Fri May 13 17:08:44 2011 UTC (11 years ago) by jmduarteg
Now throwing separate exceptions as before
Revision 1390 - Directory Listing
Modified Fri May 13 17:06:19 2011 UTC (11 years ago) by jmduarteg
Fixed bug: pymol was hanging sometimes when running the script through stdin piping. Now using the -d mode it's more stable.
Revision 1384 - Directory Listing
Modified Wed Apr 6 07:59:43 2011 UTC (11 years, 1 month ago) by stehr
System.out.println(cmdline) is commented out.
Revision 1383 - Directory Listing
Modified Tue Apr 5 14:15:39 2011 UTC (11 years, 1 month ago) by stehr
tmp files will be written to the static disk.
Revision 1380 - Directory Listing
Modified Fri Apr 1 07:53:32 2011 UTC (11 years, 1 month ago) by stehr
Going back to old version of PolyposeRunner because new version was way too slow
Revision 1379 - Directory Listing
Modified Thu Mar 31 14:28:20 2011 UTC (11 years, 1 month ago) by stehr
Fixed another problem with persistent temp files
Revision 1377 - Directory Listing
Modified Thu Mar 31 09:11:08 2011 UTC (11 years, 1 month ago) by stehr
Fix: Now deleting polypose temp files which were polluting /tmp directory
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (11 years, 1 month ago) by jmduarteg
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Revision 1355 - Directory Listing
Modified Fri Mar 25 11:30:15 2011 UTC (11 years, 1 month ago) by hstehr
Fixed some conflicts when running multiple instances of this on the same machine
Revision 1347 - Directory Listing
Modified Mon Mar 21 10:38:06 2011 UTC (11 years, 1 month ago) by hstehr
moving project CCCP to this repository
Revision 1345 - Directory Listing
Modified Thu Mar 17 13:58:32 2011 UTC (11 years, 2 months ago) by jmduarteg
Now the colors of chains of pymol generated images are consistent with the letter codes (given a chain letter code the color will always be the same for it for all images generated)
Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (11 years, 2 months ago) by jmduarteg
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
Revision 1338 - Directory Listing
Modified Fri Mar 11 16:53:33 2011 UTC (11 years, 2 months ago) by jmduarteg
Fixed bug. Pymol was blocking
Revision 1336 - Directory Listing
Modified Wed Mar 9 11:05:05 2011 UTC (11 years, 2 months ago) by jmduarteg
New runner for pymol
Revision 1335 - Directory Listing
Modified Wed Mar 9 08:38:35 2011 UTC (11 years, 2 months ago) by jmduarteg
Now throwing InterruptedException. Refactor BlastErro to BlastException
Revision 1334 - Directory Listing
Modified Wed Mar 9 08:13:04 2011 UTC (11 years, 2 months ago) by jmduarteg
Refactoring xxxError to xxxException
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (11 years, 2 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1324 - Directory Listing
Modified Thu Mar 3 10:55:54 2011 UTC (11 years, 2 months ago) by jmduarteg
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before

Revision 1316 - Directory Listing
Modified Wed Feb 9 15:55:49 2011 UTC (11 years, 3 months ago) by jmduarteg
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
Revision 1314 - Directory Listing
Modified Wed Feb 9 11:36:04 2011 UTC (11 years, 3 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (11 years, 3 months ago) by jmduarteg
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (11 years, 3 months ago) by jmduarteg
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
Revision 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (11 years, 4 months ago) by jmduarteg
Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
Revision 1242 - Directory Listing
Modified Wed Sep 29 15:22:49 2010 UTC (11 years, 7 months ago) by jmduarteg
Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
Revision 1230 - Directory Listing
Modified Wed Sep 8 16:30:40 2010 UTC (11 years, 8 months ago) by jmduarteg
Fixed bug: bsa values were wrongly calculated. 
Now sort of interfaces is always descending.
Some more testing for individual residues asa and bsa values. 
Still an issue: individual bsas are not matching pisa's even though total interface areas are fine.
Revision 1211 - Directory Listing
Modified Thu Aug 26 08:21:24 2010 UTC (11 years, 8 months ago) by jmduarteg
First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point. 
Revision 1199 - Directory Listing
Modified Thu Aug 19 10:14:54 2010 UTC (11 years, 9 months ago) by hstehr
added some debug output (commented out)
Revision 1132 - Directory Listing
Modified Fri Jun 25 13:01:53 2010 UTC (11 years, 10 months ago) by jmduarteg
New SelectonRunner class. More taxonomy information retrieved from uniprot.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (11 years, 10 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (11 years, 11 months ago) by jmduarteg
Implemented caching of blast in UniprotHomologList
Revision 1097 - Directory Listing
Modified Mon Jun 7 10:17:58 2010 UTC (11 years, 11 months ago) by jmduarteg
Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (11 years, 11 months ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (12 years ago) by jmduarteg
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (12 years ago) by matt4077
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (12 years ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (12 years ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1043 - Directory Listing
Modified Thu Apr 22 12:21:37 2010 UTC (12 years ago) by jmduarteg
Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.
Revision 1041 - Directory Listing
Modified Wed Apr 21 13:24:18 2010 UTC (12 years ago) by hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (12 years, 1 month ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (12 years, 1 month ago) by hstehr
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 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (12 years, 1 month ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (12 years, 1 month ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (12 years, 1 month ago) by hstehr
Copied from: trunk/src/runners revision 1002
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (12 years, 1 month ago) by jmduarteg
Original Path: trunk/src/runners
Now DsspRunner is purely static (makes more sense)
Revision 996 - Directory Listing
Modified Thu Mar 25 12:07:41 2010 UTC (12 years, 1 month ago) by matt4077
Original Path: trunk/src/runners
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.  
Revision 988 - Directory Listing
Modified Thu Mar 18 12:02:13 2010 UTC (12 years, 2 months ago) by jmduarteg
Original Path: trunk/src/runners
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

Revision 987 - Directory Listing
Added Thu Mar 18 11:08:58 2010 UTC (12 years, 2 months ago) by jmduarteg
Original Path: trunk/src/runners
New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.