Additional method for coordinate transversion.

Additional method for coordinate transversion.

New Residuescoringfunctionimplementation

New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.

Rotation and translation procedure transfered into extra class GmbpGeometry

GmbpGeometry class implements rotation and translation invariant framework.

Improved the selection of representative CDS

Some refactoring

Now implementing HasFeatures

New class UniprotEntry. Things make a lot more sense now...

Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.

RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.

Now checking codon length before translating

Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.

Changes in edge-cluster direction!

New feature: code for dna to protein translation

Now getting also gene encoding organelle from uniprot api

Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.

Methods added to Save and Load settings of SphoxelMap_Traces_View.

Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.

Now parsing the symmetry operators.

Fixed bug: was nullpointing with empty cache files

Implemented caching of blast in UniprotHomologList

Our own copy file method! :-)

Now reading uniprot version from reldate.txt and checking against the uniprot api version

Implemented caching for EMBWSDBfetchConnection

Cluster-edge direction evaluated.

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

Implementation of class that performs clustering on the nbhStringNodes.

Some fixes to the help string

Fixed bug: was nullpointing at retrieveUniprotKBData because of a single uniprot id can have multiple blast hits and was using the uni ids as unique identifiers => the lookup map was failing. Now the lookup map is from uniIds to lists of homologs(hits)

Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.

Minor doc fix

Fixed bug: was nullpointing when the letter encountered in counting the column was unknown.

Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.

checking in some of Michael's example files

Contact Map for server prediction directory evaluation added

Class OptimalSingleEnv for scoring of different substrings.

little contact map example done

added a package for example scripts using the library

max number of traces

Improved the getRimAndCore method

Extract maximum number of traces!

Some new methods

renamed  conflicting ContactMap class.

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.

Fixed bug with '-' embl cds identifiers.

Undoing some stuff commited by error in last commit

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

Implemented profile counting and entropy calculation for alignment.

Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()

Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.

Histogram for different sstypes --> number of nodes per trace.

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.

New methods to retrieve uniprot data and embl cds for a single homolog

HandOverThetaPhiRanges

fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()

new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()

fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung

Creating constructor which was apparently lost during some previous refactoring but which was needed by class cccp.testGraphAverager

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.

Fixed java doc

Load from zip-file!

add psi/phi constraints from secondary structure to tinker reconstructions

New example implementation of ResidueContactScoringFunction

Removed code left over from debugging.

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

Minor fix to java docs

Load precalc sphoxel data if possible.

removing @Override annotations which were causing compilation errors for me

New classes UniprotHomolog and UniprotHomologList to contain a set of homologs of a given sequence, including the blast hit data, embl cds coding sequences etc.

SecondaryStructure now implements Iterable after refactoring of getIterator

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 interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.

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.

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.

New class gmbp for handling (saving) angle (theta-phi) ranges for certain contacts (iNum-jNum combinations);

revert. wasn't the best idea.

adding phi/psi constraints to edges

Changed return type of addFeature to boolean to match the java Collection interface

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.

Extracted the calc-vol and calc-surf runner code to its own Runner class.

Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.

Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.

Fixed hard-coded resources paths broken since major restructuring of project.

Faster SQL queries

Fixed some docs and indentation

changes

Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!

FloatPairSet first commit

new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)

adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()

Classes for sphoxel and nbhstraces handling. csv handling

First version of class for sphoxel computation.

removing a warning in owl.embed.contactmaps.Demes

New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.

Added a supresswarnings tag (it's simply unused code)

Fixed import (was a compile error)

cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics

resolving conflicts

bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found

Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 

refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests

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: adapting test packages to match new package structure

refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl

refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker

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

starting refactoring: first creating packages owl and owl.core

latest version of gabriel (embed.contactmaps)

latest version of gabriel

Now DsspRunner is purely static (makes more sense)

Fixed the dsspRunner call (now it's static).

Minor refactoring and comment fixes

Turns the RIGraph into a GMatrix 
public void convert2GMatrix( GMatrix A)

reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.  

Removed the executable property

new method AminoAcid.valuesInOrderOfHydrophobicity()

adding a method RIGraph.getOrderedNeighbors(Node) because the default method getNeighbors(Node) returns the neighbours in non-deterministic order(!) which caused me lots of trouble

Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

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.

fixing a bug where floats in CASP RR files are rendered with comma for those unfortunate people stuck on german computers. 

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.

Commiting an old change of some constant in PolyposeRunner. I forgot what this does but it must be good :)

adding some convenience methods to IntervalSet

Restoring deleted class Pair because it is needed by one of my programs. 

Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.

Better error message for no tinker paths set up

Moving the CASP project into OWL as the casp package.

Now PDB data will be loaded from online PDB's ftp if no PDBASE_DB specified in config file

Now configuration (tinker paths) is read from config file.

Updated make-aglappe script (and renamed to make-owl).
Changed aglappe strings to OWL (following new name of library)

Fixed paths of tests (was missing the src directory since we moved everything under src)

new class for sparse double matrices

some new classes

minor changes, that now fit into the renewed version

Now analyseHistone will output the coordinates of the side chains of ARGs (NH1 atom) and LYSs (NZ atom) instead of the CA atoms.
Some new methods in Pdb

New executable class from my workspace.

Moved IntervalTest class to test.tools package

Moved Interval* and IntPair* classes to tools package

Added some useful tools to the default package from my workspace. More clean up.

Removed some obsolete classes.

Now removed variable and put back code that shouldn't have been commented out

Commented out some unused variables to get rid of warnings

Refactoring of inconsistently named methods in RIGraph

Added some new prediction measures for DecoyScoreSet: rank, delta rmsd, n% enrichment value
Extended the range of the distance bins.

Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.