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Revision 1642 - Directory Listing
Modified Thu Jun 13 10:57:42 2013 UTC (8 years, 11 months ago) by jmduarteg
Now both taxonomy and uniprot tables are read from same database
Revision 1637 - Directory Listing
Modified Wed Mar 20 09:47:07 2013 UTC (9 years, 1 month ago) by jmduarteg
Minor javadoc improvement
Revision 1635 - Directory Listing
Modified Thu Mar 14 08:45:20 2013 UTC (9 years, 2 months ago) by jmduarteg
Fixed pisa oligomeric prediction behaviour when mixed assembly sizes in same assembly group
Revision 1634 - Directory Listing
Modified Wed Mar 6 11:49:39 2013 UTC (9 years, 2 months ago) by jmduarteg
Introduced a check to see if pisa server returns data or not
Revision 1632 - Directory Listing
Modified Tue Feb 26 13:37:13 2013 UTC (9 years, 2 months ago) by jmduarteg
Now sorting the mappings in the order they happen in the PDB chain
Revision 1629 - Directory Listing
Modified Thu Feb 14 10:38:40 2013 UTC (9 years, 3 months ago) by nikhilbiyani
Removed Warnings from SiftsConnection
Revision 1628 - Directory Listing
Modified Thu Feb 14 10:28:18 2013 UTC (9 years, 3 months ago) by nikhilbiyani
Implementation of new method which returns a unique mapping of uniprot ids for all PDB chains
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 1598 - Directory Listing
Modified Thu Nov 15 10:34:15 2012 UTC (9 years, 6 months ago) by jmduarteg
New classes to parse PiQSi annotation file
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 1595 - Directory Listing
Modified Sun Nov 4 19:36:53 2012 UTC (9 years, 6 months ago) by jmduarteg
Added a main method to output some sifts statistics
Revision 1582 - Directory Listing
Modified Tue Aug 21 13:13:25 2012 UTC (9 years, 8 months ago) by jmduarteg
Important fix to interface calculation: finally total symmetry redundancy elimination is working!
- fixed a bug present since rev 1573: translation vectors of transforms were not stored properly and thus wasn't comparing the right operators
- extracted TransformIdTransform private class to new class CrystalTransform. Rationalise some of the code thanks to that (still more to be done)
- better debug output in interface calculation to show duplicates info

Revision 1559 - Directory Listing
Modified Tue May 15 10:39:24 2012 UTC (10 years ago) by jmduarteg
Method to close the connection
Revision 1557 - Directory Listing
Modified Thu May 10 08:15:52 2012 UTC (10 years ago) by jmduarteg
Fixed bug: for a uniref100 cluster member, was taking the representative's uniprot id/tax id instead of the member's. Database was not correctly modelled -> need also the tax  ids for cluster members (and then to query the tax ids from members and not from representative)
Revision 1542 - Directory Listing
Modified Wed Feb 29 17:37:21 2012 UTC (10 years, 2 months ago) by jmduarteg
Fixed issues with homologs with a uniparc id as reference, now the reference can be either uniprot or uniparc
Revision 1541 - Directory Listing
Modified Tue Feb 28 15:01:00 2012 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug: version 4.0 was using "UniProt ID" attribute tags and "representativeMember" tags. That was a mix of oldest and newer formats, now fixed for all
Revision 1540 - Directory Listing
Modified Tue Feb 28 14:18:48 2012 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug in uniref xml parser: was not taking the right uniprot representative for old style (e.g. ver 1.0) xml files. They also contain several uniprot ids sometimes: first one being the active representative and the remaining being the inactive ones.
Revision 1539 - Directory Listing
Modified Mon Feb 27 13:58:44 2012 UTC (10 years, 2 months ago) by jmduarteg
New code to dump local uniprot db into a fasta file that can be use to formatdb and blast
Revision 1538 - Directory Listing
Modified Sun Feb 26 15:12:05 2012 UTC (10 years, 2 months ago) by jmduarteg
Implemented retrieval of uniprot KB data from local database
Revision 1537 - Directory Listing
Modified Sat Feb 25 17:55:47 2012 UTC (10 years, 2 months ago) by jmduarteg
Changed naming convention of uniprot db/tables
Revision 1536 - Directory Listing
Modified Fri Feb 24 17:23:03 2012 UTC (10 years, 2 months ago) by jmduarteg
New class for extracting information from a local Uniprot KB database. Not tested yet.
Revision 1535 - Directory Listing
Modified Fri Feb 24 13:29:26 2012 UTC (10 years, 2 months ago) by jmduarteg
Restructured how the UniprotConnection is used. Now all uniprot connection stuff done within the class
Revision 1532 - Directory Listing
Modified Thu Feb 23 14:01:55 2012 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug: for members of clusters there's also inactive uniprot ids in rare cases, now only taking the active uniprot id for the member and ignoring the inactives
Revision 1531 - Directory Listing
Modified Thu Feb 23 11:37:40 2012 UTC (10 years, 2 months ago) by jmduarteg
More complete parsing: cluster members and inactive ids
Revision 1530 - Directory Listing
Modified Thu Feb 23 08:43:35 2012 UTC (10 years, 2 months ago) by jmduarteg
Some refactoring
Revision 1529 - Directory Listing
Modified Wed Feb 22 17:07:14 2012 UTC (10 years, 2 months ago) by jmduarteg
A new parser for uniref xml files
Revision 1507 - Directory Listing
Modified Tue Dec 13 14:47:32 2011 UTC (10 years, 5 months ago) by jmduarteg
Now supporting both uniprot and uniparc entries in HomologList
Revision 1482 - Directory Listing
Modified Wed Oct 26 15:36:05 2011 UTC (10 years, 6 months ago) by jmduarteg
Now we consider pisa gray predictions as well
Revision 1479 - Directory Listing
Modified Fri Oct 14 09:26:13 2011 UTC (10 years, 7 months ago) by jmduarteg
Improved pisa assembly parsing and implemented a oligomeric predictor to automatically call the oligomeric assembly type from the PISA output
Revision 1478 - Directory Listing
Modified Thu Oct 13 08:29:22 2011 UTC (10 years, 7 months ago) by jmduarteg
New feature: pisa assembly parsing
Revision 1472 - Directory Listing
Modified Wed Sep 28 15:06:19 2011 UTC (10 years, 7 months ago) by jmduarteg
Fixed a couple of problems with ScopConnection. Added another atom type.
Revision 1462 - Directory Listing
Modified Tue Aug 30 16:20:36 2011 UTC (10 years, 8 months ago) by jmduarteg
Fixed issues with mixed nucleic acid/protein entries and getAllInterfaces and calculation of ASAs in DNA
Revision 1413 - Directory Listing
Modified Tue Jun 7 15:14:35 2011 UTC (10 years, 11 months ago) by jmduarteg
New option to output interfaces serialized file
Revision 1405 - Directory Listing
Modified Thu May 26 15:56:12 2011 UTC (10 years, 11 months ago) by jmduarteg
Now can calculate interfaces also for non-polymer chains, introduced new parameter to do only polymer chains or both poly/non-poly.
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 1386 - Directory Listing
Modified Thu Apr 7 15:09:48 2011 UTC (11 years, 1 month ago) by jmduarteg
Changed constant name after change in kraken api
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 1370 - Directory Listing
Modified Tue Mar 29 18:29:16 2011 UTC (11 years, 1 month ago) by hstehr
Updated some JavaDocs
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 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 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 1312 - Directory Listing
Modified Mon Feb 7 15:00:47 2011 UTC (11 years, 3 months ago) by jmduarteg
Put back the parsing of score p values (was commented out)
Revision 1310 - Directory Listing
Modified Mon Jan 31 16:49:11 2011 UTC (11 years, 3 months ago) by jmduarteg
Fixed bug: was not checking whether the uniprot japi was actually returning all requested records for ids given when using getMultipleEntries. Now checking, logging it and removing the not-found ids from the homolog list.
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 1296 - Directory Listing
Modified Fri Jan 7 11:16:43 2011 UTC (11 years, 4 months ago) by jmduarteg
Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.
Revision 1266 - Directory Listing
Modified Thu Oct 21 15:26:35 2010 UTC (11 years, 6 months ago) by jmduarteg
Now throwing IOException when the server returns an error (happens for example when it is down)
Revision 1265 - Directory Listing
Modified Wed Oct 20 08:01:41 2010 UTC (11 years, 6 months ago) by jmduarteg
Now keeping track of ASA calc method
Revision 1258 - Directory Listing
Modified Fri Oct 8 13:15:13 2010 UTC (11 years, 7 months ago) by jmduarteg
Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators.
Added a test for SpaceGroup to test for proper parsing of algebraic strings
Revision 1234 - Directory Listing
Modified Thu Sep 9 13:36:28 2010 UTC (11 years, 8 months ago) by hstehr
New method to get PDB cross refs for a Uniprot entry
Revision 1233 - Directory Listing
Modified Thu Sep 9 11:36:44 2010 UTC (11 years, 8 months ago) by hstehr
Renaming UniprotPdbRef to UniProtPdbRef to be consistent with UniProtConnection
Revision 1232 - Directory Listing
Modified Thu Sep 9 11:27:45 2010 UTC (11 years, 8 months ago) by hstehr
Merging (yet again) my personal UniProtConnection with owl.core.connections.UniProtConnection; new features: Methods for retrieving cross references for PDB and PhosphoSitePlus
Revision 1231 - Directory Listing
Modified Thu Sep 9 11:26:08 2010 UTC (11 years, 8 months ago) by hstehr
Adding class PhosphoSiteConnection
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (11 years, 8 months ago) by jmduarteg
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
Revision 1226 - Directory Listing
Modified Mon Sep 6 10:15:25 2010 UTC (11 years, 8 months ago) by hstehr
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
Revision 1217 - Directory Listing
Modified Tue Aug 31 17:11:30 2010 UTC (11 years, 8 months ago) by jmduarteg
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.
Revision 1215 - Directory Listing
Modified Fri Aug 27 17:03:45 2010 UTC (11 years, 8 months ago) by jmduarteg
Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side.
Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa.
Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct.
Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
Revision 1172 - Directory Listing
Modified Wed Aug 4 15:26:03 2010 UTC (11 years, 9 months ago) by jmduarteg
Now using apache commons logging
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (11 years, 10 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1108 - Directory Listing
Modified Thu Jun 10 16:27:48 2010 UTC (11 years, 11 months ago) by jmduarteg
Now parsing the symmetry operators.
Revision 1107 - Directory Listing
Modified Thu Jun 10 10:20:35 2010 UTC (11 years, 11 months ago) by jmduarteg
Fixed bug: was nullpointing with empty cache files
Revision 1103 - Directory Listing
Modified Wed Jun 9 16:11:18 2010 UTC (11 years, 11 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1101 - Directory Listing
Modified Wed Jun 9 09:26:27 2010 UTC (11 years, 11 months ago) by jmduarteg
Now serializable (to be able to write them to file)
Revision 1096 - Directory Listing
Modified Fri Jun 4 14:48:12 2010 UTC (11 years, 11 months ago) by jmduarteg
Minor doc fix
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (11 years, 11 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (11 years, 11 months ago) by jmduarteg
Some new methods
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (11 years, 11 months ago) by hstehr
fixed bug in printf statement because pdbResSer has changed from int to String
Revision 1082 - Directory Listing
Modified Fri May 28 15:00:31 2010 UTC (11 years, 11 months ago) by jmduarteg
Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.
Revision 1079 - Directory Listing
Modified Fri May 28 12:52:31 2010 UTC (11 years, 11 months ago) by jmduarteg
Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)
Revision 1078 - Directory Listing
Modified Thu May 27 10:33:41 2010 UTC (11 years, 11 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (11 years, 11 months ago) by jmduarteg
Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes
Revision 1075 - Directory Listing
Modified Fri May 21 17:33:34 2010 UTC (11 years, 11 months ago) by jmduarteg
PISA connection and xml interfaces description parser
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (12 years ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1061 - Directory Listing
Modified Fri May 7 14:13:07 2010 UTC (12 years ago) by hstehr
Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView
Revision 1060 - Directory Listing
Modified Fri May 7 11:53:13 2010 UTC (12 years ago) by hstehr
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
Revision 1054 - Directory Listing
Modified Wed Apr 28 13:37:00 2010 UTC (12 years ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (12 years ago) by hstehr
Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph
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 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (12 years ago) by jmduarteg
New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
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 1040 - Directory Listing
Modified Wed Apr 21 10:44:19 2010 UTC (12 years ago) by jmduarteg
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (12 years, 1 month ago) by jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision 1034 - Directory Listing
Modified Mon Apr 19 12:42:21 2010 UTC (12 years, 1 month ago) by jmduarteg
Extracted Scop parsing code to its own connection class.
Revision 1033 - Directory Listing
Modified Mon Apr 19 12:26:22 2010 UTC (12 years, 1 month ago) by jmduarteg
Extracted the CSA parsing code to its own connection 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 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (12 years, 1 month ago) by hstehr
Copied from: trunk/src/connections revision 1002
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 998 - Directory Listing
Modified Mon Mar 29 10:04:04 2010 UTC (12 years, 1 month ago) by jmduarteg
Original Path: trunk/src/connections
Minor refactoring and comment fixes
Revision 987 - Directory Listing
Modified Thu Mar 18 11:08:58 2010 UTC (12 years, 2 months ago) by jmduarteg
Original Path: trunk/src/connections
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.

Revision 985 - Directory Listing
Added Tue Mar 16 13:47:40 2010 UTC (12 years, 2 months ago) by hstehr
Original Path: trunk/src/connections
Adding new package owl.connections with connector classes to online databases and services. Starting with PhosphoSitePlusConnection for accessing a database of posttranslational modifications and PDomainsConnection for accessing a very useful webservice which calculates structural domains using a variety of methods including Scop, Cath, DomainParser, ProteinDomainParser and others.