ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/core/connections
Sticky Revision:
Sort logs by:
Revision 1347 - Directory Listing
Modified Mon Mar 21 10:38:06 2011 UTC (9 years, 7 months ago) by hstehr
moving project CCCP to this repository
Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (9 years, 7 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 (9 years, 7 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 (9 years, 7 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 (9 years, 8 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 (9 years, 8 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 (9 years, 9 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 (9 years, 9 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 (10 years 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 (10 years ago) by jmduarteg
Now keeping track of ASA calc method
Revision 1258 - Directory Listing
Modified Fri Oct 8 13:15:13 2010 UTC (10 years 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 (10 years, 1 month 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 (10 years, 1 month 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 (10 years, 1 month 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 (10 years, 1 month ago) by hstehr
Adding class PhosphoSiteConnection
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (10 years, 1 month 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 (10 years, 1 month ago) by hstehr
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
Revision 1217 - Directory Listing
Modified Tue Aug 31 17:11:30 2010 UTC (10 years, 1 month 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 (10 years, 2 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 (10 years, 2 months ago) by jmduarteg
Now using apache commons logging
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (10 years, 3 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1108 - Directory Listing
Modified Thu Jun 10 16:27:48 2010 UTC (10 years, 4 months ago) by jmduarteg
Now parsing the symmetry operators.
Revision 1107 - Directory Listing
Modified Thu Jun 10 10:20:35 2010 UTC (10 years, 4 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 (10 years, 4 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1101 - Directory Listing
Modified Wed Jun 9 09:26:27 2010 UTC (10 years, 4 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 (10 years, 4 months ago) by jmduarteg
Minor doc fix
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (10 years, 4 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (10 years, 4 months ago) by jmduarteg
Some new methods
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (10 years, 4 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 (10 years, 5 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 (10 years, 5 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 (10 years, 5 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (10 years, 5 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 (10 years, 5 months ago) by jmduarteg
PISA connection and xml interfaces description parser
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (10 years, 5 months 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 (10 years, 5 months 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 (10 years, 5 months 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 (10 years, 6 months ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 6 months 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 (10 years, 7 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 (10 years, 7 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.