Now both taxonomy and uniprot tables are read from same database

Minor javadoc improvement

Fixed pisa oligomeric prediction behaviour when mixed assembly sizes in same assembly group

Introduced a check to see if pisa server returns data or not

Now sorting the mappings in the order they happen in the PDB chain

Removed Warnings from SiftsConnection

Implementation of new method which returns a unique mapping of uniprot ids for all PDB chains

Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering

New classes to parse PiQSi annotation file

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.

Added a main method to output some sifts statistics

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

Method to close the connection

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)

Fixed issues with homologs with a uniparc id as reference, now the reference can be either uniprot or uniparc

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

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.

New code to dump local uniprot db into a fasta file that can be use to formatdb and blast

Implemented retrieval of uniprot KB data from local database

Changed naming convention of uniprot db/tables

New class for extracting information from a local Uniprot KB database. Not tested yet.

Restructured how the UniprotConnection is used. Now all uniprot connection stuff done within the class

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

More complete parsing: cluster members and inactive ids

Some refactoring

A new parser for uniref xml files

Now supporting both uniprot and uniparc entries in HomologList

Now we consider pisa gray predictions as well

Improved pisa assembly parsing and implemented a oligomeric predictor to automatically call the oligomeric assembly type from the PISA output

New feature: pisa assembly parsing

Fixed a couple of problems with ScopConnection. Added another atom type.

Fixed issues with mixed nucleic acid/protein entries and getAllInterfaces and calculation of ASAs in DNA

New option to output interfaces serialized file

Now can calculate interfaces also for non-polymer chains, introduced new parameter to do only polymer chains or both poly/non-poly.

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.

Changed constant name after change in kraken api

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.

Updated some JavaDocs

moving project CCCP to this repository

Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit

Renamed xxxxError classes to xxxxException as they should be.

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

Put back the parsing of score p values (was commented out)

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.

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.

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.

Now throwing IOException when the server returns an error (happens for example when it is down)

Now keeping track of ASA calc method

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

New method to get PDB cross refs for a Uniprot entry

Renaming UniprotPdbRef to UniProtPdbRef to be consistent with UniProtConnection

Merging (yet again) my personal UniProtConnection with owl.core.connections.UniProtConnection; new features: Methods for retrieving cross references for PDB and PhosphoSitePlus

Adding class PhosphoSiteConnection

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.

Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb

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.

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.

Now using apache commons logging

Implemented logging with log4j library

Now parsing the symmetry operators.

Fixed bug: was nullpointing with empty cache files

Implemented caching for EMBWSDBfetchConnection

Now serializable (to be able to write them to file)

Minor doc fix

Improved the getRimAndCore method

Some new methods

fixed bug in printf statement because pdbResSer has changed from int to String

Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.

Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)

Now parsing the seq_num residue number.

Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes

PISA connection and xml interfaces description parser

fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public

Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView

New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.

Minor changes, couple of new methods.

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

JPredConnection now returns a SecondaryStructure object; some updated javadocs

Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.

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)

New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.

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.

Extracted the EC data parsing code to its own connection class.

Extracted Scop parsing code to its own connection class.

Extracted the CSA parsing code to its own connection class.

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

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

Minor refactoring and comment fixes

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.

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.