Method added which returns complete result in TreeMap

deleting scoreGeomOfPdbSets which had compilation errors because it was checkid in accidentally

bug removed nullpointer?!

Implementation of class for KendallsTau Correlation Calculation
Implementation of class for Check for Correctness of Casp server model files
Implementation of class for Calculation of geometric scoring

Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.

Now correctly parsing the right short name field

New classes to parse and store crystallographic space groups info.

actual methods 

actual version

Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).

Method to get translated and rotated coordinates.

New method setChainCode

minor modifications to casp benchmarking script

Now using apache commons logging

small update for compatibility with Casp9 data (changing baker group name string)

adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.

some more fixes for doing benchmarking on Casp9 targets

Now catching the case when the best translation contains stop codons. This is usually due to a wrong genetic code, but for the moment it's still very difficult to know the genetic code from encoding organelle+organism taxonomy, so this is the temporary solution.

updated casp benchmarking classes for Casp9, still missing: update group suffix

Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)

HahpMap keytype changed to Pair instead of String

Now returning null for the representative CDS when the gene encoding organelle is not nucleus/plasmid. Before the whole program would stop, which wasn't ideal. Eventually we will need to use the proper genetic code when needed.

Got rid of german text (was causing a warning in compilation), anyway there shouldn't be any german... unless we start i8nsing.

Allowing plasmids as gene encoding organelles without having to treat them especially as they don't have a different genetic code.

slight changes

Updating to latest uniprot 2010_08

Reverting change made in last revision. It intended to fix a bug for a particular test case (don't know anymore which one!) but it actually broke most other cases.

print function

Fixed bug, wasn't computing the nucleotide alignment correctly (was missing the last codon)

More fixes to build script

Implemented a simple skimming strategy. Put back some debug level logging to info level, logging aint' easy!

And all other amiguous codons

Another ambiguous nucleotide letter

Fixed make script for new structure of owl

Fixed bug: was null pointing with null cache file (which is a valid value)

PrintOut method ion RIGGeometry

Changed level of some logging messages

New removeRedundancy method

Implemented logging with log4j library

Now can write sequences with or without query

Now can filter also on query coverage

Changed the order of checks in isReferenceSeqPositionReliable

New methods to check for reliability of positions with respect of the CDS matching

Now nucleotide alignment contains reference sequence as well. Moved entropy and kaks calc methods to UniprotHomologList.

methods by saurabh included

Fixed bug: now nucleotide alignment is in same order as protein alignment

Fixed bug: when retrieving (or reading from cache) embl cds sequences and embl dbfetch doesn't have a certain identifier, then we were adding nulls to the list of emblcds sequences of the UniprotHomologList (resulting in a null pointer down the line)

Getter for Atoms-TreeMap.

Now checking the sequence identity of the representative CDS to be above a minimum value.

New ambiguous nucleotide w.

Check for consistency in translation rotation framework.

Check for consistency in translation rotation framework.

Fixed bug: getNucleotideAlignment was nullpointing when encountering a null return from getRepresentativeCDS() (which happens whenever there is no representative CDS for the particular UniprotEntry). Now checking for nulls before using the homolog in the alignment.

New SelectonRunner class. More taxonomy information retrieved from uniprot.

Changes: use different db for traces!

Rotation and translation procedure version 2 available in class Gmbp_Geom. Will be extended by Saurabh.

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

Replacing uniprot japi jar after new uniprot release 2010_07

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

Now using UK mirror

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()

reverting changes to .project and .classpath which were accidentally committed

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.

New script to maintain a local copy of blastable uniprot sequences db.

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()

Removing the svn:executable properties from jars that didn't need it

Removed unneeded code

Setting the svn:executable property of make-owl.sh so that when it is checked out it will be set to executable.

Now classpath passed with -cp instead of using env variable. Hopefully this is more compatible with other platforms (i.e. maybe it will work on Macs)

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.

Changed project name to owl

Fixed some issues

Moved all reconstruct scripts and config files to reconstruct directory. 
Modified scripts accordingly

Better error message for no tinker paths set up

Renamed script and fixed bug

Moved scripts to scripts directory.
New scripts for packaging the reconstruct executable for distribution.

Adding license files

Moving the CASP project into OWL as the casp package.

Adding back removal of temp files

CLASSPATH not hard-coded any more. Now taking the jars list from svn.

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)

Forgot to really add the libraries in the last commit!

Updated jung jars to version 2.0.1 (finally the release version, not alpha or beta!)

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.

Major refactoring and clean-up.
Most important changes are some methods in Pdb class: get_graph->getRIGraph and dump2pdb->writeToPDBFile
Removed all specific FileFormatError exception classes, now using only the generic FileFormatError.
All tests passed.

New test for rmsd on intervals

New rmsd method to calculate rmsd on residue intervals instead of whole chain.
Fixed bug: checkScop was throwing exception when it was called on a PdbfilePdb that didn't have a PDB code

Now passing db explicitely instead of using the db from the connection.

Added new scoring method: atom distance based scoring (scoring based on multiple distance bins, instead of just on contacts)

Fixed bug (hopefully, didn't test!) introduced in last revision. Wasn't initialising properly the maps

contact map rainbows

Moved up to Scorer initResMap and initAtomMap

delta rank

Delta Rank

Fixed bug with notifier (only used from CMView). Now if null it will be skipped.

fixed bugs in getDescription()

fields changed to private

fields changed to private

all fields to private

some methods modifiers were changed from protected to public, since classes of the sub package rely on those

all classes for evolution, correlation function, neighborhood string converter etc.

full package, with all classes

minor changes

final version, might still contain bugs, but seems consistent so far

the older version still had a bug in the setNbhStringMaps(String,String) method

a class that gets neighborhood Strings and queries them

helper class

merged tinker changes into trunk

DALI alignment correction

Fixed bug: was not handling correctly sequences with 'X' in reconstruction
Fixed bug: Pdb.getPhi/Psi were failing because hasCoordinates(int,String) was NullPointing for unobserved residues. 
Added test case for getAllPhiPsi

bugfix for last checkin (null pointer exception)

New convenience methods in MySQLConnection for simple retrieval of String, Integer and Double arrays from an SQL query. Some documentation clean-up.

fixed an interesting bug where a recursive function call would lead to a stack overflow exception

updated constant LATEST_VERSION to CSA version 2.2.11 (of 7th August 2009)

tolerate unobserved residues in DALI alignments

Added DALI Alignment option

new feature type PhosphoSitePlusFeature (for post-translational modifications)

new method getDoubleFromDb()

New classes for triplet scoring.

Now printing some more rmsd stats (numbers of structs below certain rmsd cutoffs).

Moved all decoy scoring stuff to its own package.
Split CombinedScorer into two classes AtomCombinedScorer and ResCombinedScorer. Made combined scorer more efficient: now loading only once the graphs.

Now writing rmsd ranges to stats files

New CombinedScorer class to combined type+count scoring. Now scoreDecoys doesn't take anymore a minSeqSep, it will be taken instead from the scoring matrices meta data.

Added method to get the scoring type

One more field in DecoyScoreSet: the decoy group to which the decoy set belongs. Writing it to db too.

Fixed bug: parse() was not closing file when throwing an exception. The bug surfaced when parsing a dir with a lot of decoys that were somehow malformed PDB files, sometimes it would throw a FileNotFoundException with message "Too many open files".

Now writing more complete info to score files. New feature: can also write decoy score results to database.

Increased number of neighbor-count bins. For higher cutoffs the number of bins go up dramatically.

New class DecoyScoreSetGroup to represent a set of DecoySets. Now scoreDecoys much clearer.

Got rid of redundant class DecoySetStats, its members were all just properties of DecoyScoreSet. Modified accordingly scoreDecoys.

New classes to score decoys based on contact counts (residue or atom contacts). New superclass for all scorer classes Scorer. 

New executable scoreDecoys to score sets of decoy sets. 

Added isAllAtom to Pdb and getNumHeavyAtoms to Pdb and Residue. Fixed some docs that were still not properly clarifying about hydrogens.
Added complete main methods to AtomTypeScorer and ResTypeScorer with command line options and defaults.

New classes for scoring protein structures based on residue/atom type empirical potentials.

Bug fixes in pdb file parser. Was throwing string out of bounds exception with some pdb files.

New spearman method

New methods for mean and (sample-) standard deviation

rewrote method getPerAtomDistances such that atom serials do not need to match between the two structures (matching corresponding atoms based in resser)

New executable writePerAtomDistancesToBFactor (see doc for details), new method Pdb.getPerAtomDistances(Pdb referencePdb), made Atom.DEFAULT_B_FACTOR public.

Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.

Major commit: 
- change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors
- added many tests and test files for Pdb (and merged some already existing tests from the default package)
- removed obsolete classes related to msd
- bug fix: PdbfilePdb now properly reads files with alt codes
- all tests passed

some cosmetic changes

updated version to 1.2.0 (forgot to change version number in last tag)

deleting obsolete package proteinstructure.features

moving all classes in proteinstructure.features to features

preparing to move package 'proteinstructure.features' to 'features'

Testing package-info.java for adding javadoc comment at the package level

New methods for writing sequence in Fasta format

new method getUniprotTypeName()

updated static convenience methods for loading Pdb objects

adding main method for testing

adding compareTo method to compare two IntervalSets

New and updates feature types (UniprotFeature, PrositeFeature, CsaFeature)

New classes for scanning Prosite Database

HasFeatures.addFeature() now throws OverlappingFeatureException and new InvalidFeatureCooordinatesException

New package proteinstructure.features with basic interfaces and classes for a general feature mechanism which could eventuelly replace classes like Scop, ScopRegion, ECRegion, CatalyticSite, CatalyticSiteSet and the corresponding variables in the Pdb class.

New class Atom. Not doing anything yet. Now only need it so that Residue class can compile.

Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb

Minor changes: added comments, docs, reorganized

Extracted constants. Written a basic test for consurf parsing.

New check in PdbfilePdb parser. New test for pdb file parsing in PdbParsersTest.

Adapted PdbasePdb and CiffilePdb to new mmCIF format (introduced in new remediated release in Feb 2009). Now the atom_sites_alt table is gone so we have to read alt locs from atom_site instead. All tests passed (PdbParsersTest)

Fixed +1 issues

class to estimate the correlation function to a given error function, deals onlz with Population arrays

Fixed docs, now removing some temp files that weren't been removed

new class to deal with arrays of Individuals class, provides methods to generate new arrays of Individuals

major bugs removed and documentation added, couple of method removed to new classes, i.g. Population class and CorrelationFunction class

fixed randomSets method

new class for some evolution

New methods copy() and translate()

distance map and contact map error function

Now aligning x-axis with reference residue ARG G42. Now theta values in [-pi,pi].

Now Polymer can read also DNA. analyseHistone now uses DNA as well: axis calculated with DNA, outputting z/theta stats for phosphates of DNA.

New classes to perform analysis of histone lateral surface.

updated documentation

New class PdbSet providing convenience methods to load sets of PDB objects from list files, directories, ...

new executable for pairwise (global) sequence alignment

Adding a symbol for a stop codon (*, STP)

Move the scoring methods to their own class as statics. Did a bit of refactoring.

New script to mirror a pdb

One more command line argument: contact percent sampling

New method to filter on minWeight

Fixed bug: copy() was throwing NullPointer when the RIGraph had a null SecondaryStructure annotation.

New method getMotifNoGaps

added option to keep pymol script

New class in tools: RegexFileFilter, a convenient FileFilter based on regex, amazingly java doesn't provide this!

Changed the value of the unobserved residue constant from "?" to "X". This is to fix CMView that had a lot of problems with it.

Fixed bug (an old one!): the atomser2coord and atomser2resser maps contained also hydrogen atoms whilst the resset_atom2atomserial map contained only non-H atoms. Now all contain only non-H. The "bug" only surfaced after the rewrite of the Pdb.writeAtoms method: writing the atom lines would give a NullPointer when encountering a Hydrogen (if the read pdb entry contained Hyrdrogens).

Changed scoring: from sum(upi-ui)2 to sum of max(0,upi-ui).
New methods to write subsets to files in table (tab delimited) format.
Now main() writes out all scores/subsets to two files instead of only outputting best, worse and ensemble of bests.
Moved ScoreSet to its own file, new static methods to read subsets from db.

Now using file name as id for reports when reconstructing from cm files.

New method to get an ensemble RIG from a group of best scoring sets.

Changed the scoring so that is an error function: now it is the average sum square upper bounds deviation from the contact map. A perfect fit to the contact maps is err=0.
Cleaned up, refactored and documented.

New experimental class Distiller

now outputting a png image highlighting structure center, catalytic residues and mutated residues

updated to latest CSA version, added toString() methods

New static methods for conveniently loading PDB objects without needing to deal with exceptions (loadStructureOrExit, loadStructureOrNull)

New class GeometryTools for simple geometric operations (currently implemented: torsion angles)

Now printing statistics for both lower and upper violations.

Fixed bug: this time really fixed bug from last revision. Now references of the bounds arrays are properly handled (hopefully!). Tests seem correct: now the output models when metrizing seem not to be correlated anymore

Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization.
In metrize() final sampled matrix is now always reinitialising seed.

Now printing restrains viols and bounds viols.

Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes).
Model pdb files that Reconstructer creates now contain strictly only CA atoms.

New classes Reconstructer and ModelPdb. Reconstructer is a one-stop solution for reconstructing from contact maps (RIGraph) using BoundsSmoother and Embedder. At the moment doesn't support reconstruction of contact maps with non-observed residues.

Removing vecmath package which was not in use.

new command line tools for visualizing surface accessibility and for printing information about a mutated site in a protein structure

added method getTypeDescription to output a string representation of the secondary structure type (currently not distinguishing between different numbers of states)

fixed bug in runAccess : temporary file could not be created when pdb code was not known, now using '1xxx' in this case

New enum class AminoAcid

new executables for pairwise all-against-all sequence alignments (pairwiseSeqId) and for calculating surface accessibilities and writing them to the b-factor column

added methods to set b-factor values; updated writeAtomLines to write b-factors if set (currently b-factors are not being read when creating a pdb object); added method getAtomSersFromResSer(); added writeAtomLines method with simpler interface

Fixed runNaccess to use unique file names and documented it. Wrote also a junit test case for it.

Fixed bug: in check of input of intervals wasn't checking ig intervals was null.

New options -e and -i in reconstruct (for forcing angle constraints)

Two new statics: to get phi/psi constraints for intervals of one given structure.

Introduced some more checks for validity of contact types.

Introduced a delay between runProtein and runXyzpdb in reconstruct to make sure when we run xyzpdb the file is there: we try to find xyzFile a few times with a delay between retries.

Fixed bug: wasn't checking exit value of protein, xyzpdb and pdbxyz. Now throwing exception when exit value not 0.

New method contains().

Added debug option in reconstruct: at the moment just prints some of the stack traces.

Made Bound[][] bounds a member, thus changing the signature of most methods. Refactored getBoundsAllPairs(bounds) to better name computeTriangleInequality: now it uses as input the bounds member variable and updates it as output.

Fisrt full implementation of metrization 

Some big changes: now internally we use the data structure Bound[][] for all steps. We only use graphs for when we need to calculate shortest paths.
Define some static functions for printing info.
Made the scaling method an option passed as an argument to embed()
Extracted to separate file the Bound class.
Drafted an implementation of metrize

Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs

Introduced scaling of the embedded coordinates (first good embedding ever!!)
Make the random generation more consistent. Also introduced for debugging a fixed seed.

Fixed in BoundsSmoother: now the lower bound will be set to the triangle inequality value only if the newly found lower bound is bigger than the hard spheres bound.
Now we also introduce contiguous CA distance constraints (3.8)
In main now checking for violations to the full bounds matrix.
New method in Pdb for getting distance matrix as Jama object

New method in Pdb to set atoms for all coordinates of a given atom. Used in BoundsSmoother and Embedder mains.
Changed slightly how parameters are passed in BoundsSmoother.

Lower bounds bounds-smoothing now also implemented (using Dijkstra's shortest path algorithm and offsetting to avoid negative weights).

First implementation of BoundsSmoother. Does only bounds smoothing through triangle inequality for the upper bounds (for lower bounds just takes a hard-spheres distance value)

Fixed bug (hopefully): was not closing drmaa session after every runParallelDistgeom, only in the shutdown hook. We need to close it always in case there is more than one run within the same instance of the JVM.

Got rid of hard coded mysql server references in scripts.

Cleaned up and updated the testPdb example code.

Cleaned up and updated the mysql connection example

white TO talyn

white TO talyn

white TO talyn

white TO talyn

First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.

Implemented a more robust approach to failure of jobs in parallel distgeom. Now we send 1.1*n jobs and require that only n of them finish successfully. These solves many issues: even if 0.1*n jobs fail the whole thing will be successful, if a jobs hangs forever we will not wait for it to finish.

Fixed bug: now parallel distgeom works even if a relative path  specified in caller script.

Minor change in help string

Got rid of the hardcoded mysql server, user, password. Now read from .my.cnf file

New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.

Implemented shutdown hook. Now all jobs killed upon CTRL-c.
Now submitting directly the distgeom binary without needing writing a shell script. That removes the dependency on java6 (needed for set execution permission on the shell script). 
Introduced (but not in use yet and not fully implemented) the submission of more jobs for failure tolerance.

Some minor fixes and cleanup. Changed timeout to 2hours.

Better error messages

Fixed bug: now correctly capturing exit state. Correctly cleaning up (killing jobs) after a failure. Closing the drmaa session properly.

Added drmaa.jar to make file

Implemented first version of a parallel (using distributed distgeom jobs through sge) reconstruction. Experimental so far, not well tested.

better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner

updated output of pairwiseSeqId

calculate the pairwise identity for a set of sequences

removed output of pairwise overlaps

now taking command line parameters

removing debug output in moveToCenter() methods

added methods and executables to calculate 3d superimpositions using PolyposeRunner

added moveToOrigin() methods

added getGaplessColumns(start, end)

keep on evaluating common cores even if rmsd increased

Minor fix in mirror(): now using getters to access data

adding transform method to rotate/translate the structure

New method in BlastHit to transform the BlastHit local alignment into one that contains the full sequences of subject and query.

Added length sanity check tests

Fixed warnings and error handling in addSecStructAnnotation

Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream

Added printing of pairwise alignment when checkSequnces fail for target sequence

GraphAverager: got rid of redundant code in countVotes. Changed signature of one of the constructors: now requires target sequence.
averageGraph: adapted accordingly
Alignment: new method removeSequence (untested), fixed some docs

now outputing the gapless columns; now assuming that alignment file has axtension .fa (for extracting the name)

New static method in BlastHit to get subjectId from templateId
New member source in TemplateList

New method getAlignmentWithTemplateIDtag

New method geometrizeContactMap

Fixed bug: PDB/graph/scop data loading issues were not correctly implemented. 

BlastHitList: new method getHit(subjectId), a new lookup HastMap member added for that.
TemplateList: new method get(i)
Sequence: new convenience method writeToFastaFile

Now cleaning up correctly paul temp files
Now closing tcoffee's log properly

Now we can run blast with multi threads option

set javaversion to 1.5 for compatibility with cluster

Initial commit, tcoffee runner for sequence to profile alignment

Initial commit of StructAligner interface and implementation PaulStructAligner.
New reader in Alignment: now we can read CLUSTAL alignment files, not extensively tested. Also Alignment now only throws generic FileFormatErrors instead of specific file format errors.

Now outputting info that omega restraints are used.

Now BlastHit printing works correctly for query identifier strings of any length

Using the new XML parser in TemplateSelection.
New method getQueryCoverage in BlastHit

New tests package (should be a folder and under it packages, but for now we can't do that until we move all source code to a src folder).
Moved all existing tests to appropiate tests packages.
New test PdbParsersTest: does cif against pdbase at the moment.
Adde equals method to SecStrucElement
Added some getters to Pdb

New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.

Created getters for missing fields in BlastHit. 
New method removeAll in TemplateList.

Invert behaviour of -F/-O options. Now default is use phi/psi and omega constraints. If -F/-O specified then they won't be used.
New option -I to specify the angle interval for the phi/psi constraints (what used to be -F)

Fixed xmlrpc library dependencies (was still pointing to old ones)

Made active -m option. Method string not hard-coded anymore

Committing empty class HashGrid for later implementation

Committing class MachineTest as an example for a JUnit test case

New package litNet with classes to process our article database

New class AlignmentEvaluator to compare multiple structure alignments in terms of conserved core size and RMSD

Updated version to 1.1.0

Better implementation of getViolatedEdges

Added static method to report violations.

Given a serialVersionUID to class to get rid of warning

Removing test commit

Test commit

committed by stehr: New methods getGaplessColumns and getLongestNonGappedRegion; fixed severe bug in old getGaplessColumns

Now -p accepts also pdb files as input for reconstruction.

can now superimpose subsets of residues + removed canExecute() call which was incompatble with Java 5

Now reconstruction from contact map files also possible. Improvements to help text and error checks.

First version of PolyposeRunner (does an optiomal RMSD superimposition of multiple protein structures)

adding StreamGobbler to aglappe.tools

Improved help text and rationalised options.

New option -s to do split output. 
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)

added comment

Initial commit of script and classes to interface with gromacs.

Switching to JUNG2-beta1:
- got rid of our custom fix to removeEdge
- now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map. 

added static method to print a ruler with sequence numbers

added missing javadoc comment

added methods to return the residue mappings for this alignment

added a comment line

minor update of Usage message

added option to genGraph to output graph in SADP format

New class RIGraphMinSpanningTree for getting the Minimum Spanning Tree of a RIGraph. This is simply a wrapper around JUNG's PrimMinimumSpanningTree.
New method setSerials2NodesMap in RIGraph.

Got rid to direct references to serials2nodes Map in write graph methods, now using the getSerials() and getNodeFromSerial() methods instead.

Fixed bug: was not initialising the type variable in BlastHit and GTGHit constructors

Same fix as in last commit but in another part of the code (when writing CASP RR file)

The change in last commit introduced a problem: we were exiting because when writing CASP TS file we try to parse out the CASP target number from the target tag. Now solved by using a regex for parsing the casp target number.

Now not exiting when -c specified and target tag not in CASP format, instead we simply print a warning.

Fixed bug: now Sequence class considers '.' to be part of the fasta headers (in agreement with what we do in Alignment class). The 2 FASTAHEADER_REGEXes should be always kept in sync.

Fixed bug: now PhiPsiAverager behaves like GraphAverager:  consensus is on templates agreeing out of potential templates (non-gaps) instead of out of total number of templates.

Made voteThreshold and angleInterval global.
Improved comments

Minor change. Fixed some error output

Now averageGraph can use PDB/CASP TS files as templates.
TemplateList/Template classes now can read PDB data either from pdbase database or from files.

Now considering also '.' (dots) part of the  FASTA header tags.

updated version number to 0.9.5

Changed the type used for the set of template graphs/pdbs from arrays to TemplateList. Now the loading of pdb data and getting the graphs is done by TemplateList.

-OligomericState class added

-Pdb
a.checkOligomeric and getOligomericState methods added
b.calcVolume, calcSurface and calcCompactnessCoefficient methods added

Fixed bugs in averageGraph:
- output of benchmark statistics and pairwise comparison was overlapping
- benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes)

Improved:
- better handling of modes through mode variable that takes 1 of 3 states
- better input check
- in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph
- changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph
- now allowing alignments that contain other sequences than the target and the templates
- new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match

Improved dump scripts:
- new feature: dumps first chain if one not specified
- current dir now default
- better help text
Fixed bug in dumppdb: was trying to close Output stream after exception.

Pdb:
-pdbCode and chainCode info added in the error messages in runDssp

getNumScopRes method added in Scop class

Pdb
-restrictToScopDomains methods added to restrict to multiple scop domains
-restrictToIntervalSet is public now

Fixed bug: PhiPsiAverager was not working at all for single template case. 
Fixed bug: in ConsensusInterval changed MARGIN value to 2, for cases where max=min to make sure we pass an Interval bigger than 0 to tinker.

now handling special cases that used to give NaN values

added option to load only first models; added new constructor taking a map of names to protein objects

New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond.
New method in Pdb: getOmega

Relocated Michaels Stuff to MichaSandBox

Changed default force constants to tinker's defaults ones (100.0 for distances and 1.0 for torsions). Reconstruction from averaged graphs was not working well sometimes, with really bad clashes. We think the distance force constant=10 was causing this.

added boolean parameter 'showSequence' to Alignment.writeSecStructMatching()

New option -R for keeping all tinker output in outdir. Option -m now takes a file, still disabled anyway

Added printing of alignment positions in writeSecStructMatching

Important change: now final interval taken for restraints is not anymore of size angleInterval, but simply goes from min to max.

chechScop now looks also for chain A in scop.cla when pdbChainCode is NULL

Introduced some more useful debugging output in the main method: phi/psi of target (if one is avalable from a reconstruction) is also printed.

Fixed bug: can't assign phi/psi torsion angle restraint to first and last residues.

Hard coded the CASP method string

Fixed small bug: was outputting a message about phi/psi when didnd't apply

Fixed (hopefuly) the issue of wrapping angles (at -180,180). Tested minimally and seems fine.

Added new option -m for casp method string

Now casp method string can be several lines.

Now can specify an angle interval with -F

Added phi/psi angle constraints to the reconstruction pipeline. New option -F in averageGraph for using phi/psi angle constraints

Fixed bug: algorithm to find consensus was not working correctly. We weren't taking in account the 2-dimensionality of the problem. Changed the approach completely, new algorithm.
Made the ConsensusInterval class a separate class and added new class ConsensusSquare to represent a phi/psi angle consensus region.

Now enforcing that atom serials have to be in ascending order

Put another test: finding edges is independent of order of indices given for UNDIRECTED.

Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates

Changed return type of sortMapByValue from Map to LinkedHashMap

Method sortByValue now called sortMapByValue and takes an additional argument for the sorting order (ascening/descending)

Dummy commit (forgot comment for previous one): added field caspParents with getter and setter to Pdb. This field is filled when reading from and used when writing to from Casp TS files, therefore interface of writeToCaspTS file has changed slightly (parents now has to be set in Pdb object instead of passed to method as parameter)

added new mode of averaging without consensus threshold but specifiying the number of contacts to be predicted and picking starting from highest consensus down

IntervalCandidate not Comparable anymore, finding max is now done with a specific Comparator. Additionally it now extends Interval so we can use the Interval type for the final public output.

Fixed bug: recenterInterval was not working: was not taking min/max correctly.
New method to get the consensus mapped onto a target sequence.

New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.

Casp 3D predictions now written with NULL chain code

Now phi/psi angle methods using a more general getTorsionAngle. New method to get all phi/psi in a TreeMap

Added methods to calculate phi/psi angles

-writeAtomLines and writePdbFileHeaders have become public
-writeAtomLines and write[CaspTS|Pdbfile]Headers take now PrintStream argument instead of PrintWriter.

dumppdb added

New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.

Fixed bug: command line option c was missing the ':'!!

Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.

added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence

Fixed problem: now -c reading AUTHOR string with underscores and converting them to hyphens (hyphens are problematic for command line parsing)

Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class. 
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.

added automatic conversion of matrix file to ps visualization (using script plot_simmatrix.sh)

Now skipping lines with <PRE> tags.

added 'title' member to Pdb and Template objects, currently only set when loading from Pdbase

Changed default gravity value and default IDENTITY_SCORE for similarity graph

Fixed bug in BlastUtils.writeClusterGraph: was not working at all. Wrong curly brackets, was still using a GDT cutoff instead of rmsd and was never getting Pdb correctly out of the Template.
Two new members in Template: GTGHit and BlastHit, so we can reference back to the hit if needed (like if we want to get the evalue/score). Got rid on MySQLConnection as a member, not very nice design, now a parameter for the specific methods that need to query for PDB data.

put test code for writeClusterGraph in main method of BlastUtils

Got rid of the refined/unrefined field when writing CASP TS files. Now we should be complying correctly with the CASP 8 format.

Now writing the PDB ids for the PARENT fields of CASP TS files correctly (with underscore between pdb code and chain code)

Now author can be passed with the -c option so CASP TS files will be written with the AUTHOR field too.

Now also copying caspMethodStr and caspAuthorStr in AIGraph.
Updated java docs

Now writeClusterGraph uses rmsd for similarity measure instead of GDT (maxcluster was failing almost always with GDT)

Yet another format check

Added one more file format check.

Fixed bug: wasn't catching wrong format in GTG output

Fixed bug: now try/catch of getPdbInfo moved down to getPdb and getScopSccsString (getScopSccsString was throwing NullPointer when pdb load failed)

Fixed bug: now catching when the mapping of observed residue sequence serials to internal residue serials is out of range, which happens in some extremely rare cases (because GTG uses pre-remediation data)

Added code to be able to filter out template ids (pdb codes) by maximum release date.
Some improvements in Hit classes.

Added members and method to ProtStructGraph and Pdb to write AUTHOR and METHOD fields to Casp files. Added missing reconstructFast methods to TinkerRunner.

Added a few more methods to the Template classes: Template now behaves differently in that it doesn't load the PDB data on construction but on demand (when calling getPdb() or getScop())

Added methods to be able to print "graphical" output for GTGHits, all equivalent to the methods in BlastHit
Added compare() and writeIdsToFile() in TemplateList.

Initial commit of GTG parsing classes.
Added method in PdbasePdb to map observed residue sequence serials to internal (cif) residue serials

New method getObservedSequence

Fixed error output of PdbCodeNotFoundException

new class tools.Statistics with currently only one method pearson(x,y) to compute the pearson correlation coefficient of two double[] vectors

PdbfilePdb: catching previously unhandled NumberFormatException, added method setSequence() to override sequence read from file (needed for Casp prediction where 'real' sequence is known but residues may be missing in prediction)
RIGEnsemble: many changes

Changed behaviour of graphAverager: Now evaluating consensus threshold based only on edges that could really exist (i.e. both ends map to non-gaps) rather than simple count of templates. The old behaviour can be restored (for comparison) by setting legacyMode=true in getAverageGraph() and getConsensusGraph().

Now checking wheter read sequence contains spaces and throwing FastaFileFormatError

Added some more error output

Fixed bug: was opening different MySQLConnections for every PdbasePdb object created. Now opening just 1 global connection.

Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

Introduced a new load method, so that is possible to specify cif chain codes (asym_ids) as input. Default is as before: input is pdbChainCode. NOT TESTED.

Moved readTemplatesFile method to TemplateList class (as a static)

Improved javadocs and comments

changed regexp for Casp header to allow target tag with lower case 't'

Added option -c to output final reconstructed model also in CASP TS format

Added method writeToCaspTSFile. Outsourced writing the headers for PDB files and CASP TS files to other methods.
Refactored dumpseq to writeSeqToFile.
Improved a lot the java docs.

Moved method to writeSeqs to Sequence class.
Tidied up the help text in averageGraph

Added -N option for no FASTA header, now -s by default will have fasta headers

Not reporting time anymore in genGraph
Fixed again the help text

New switch -P to write file in paul format instead of aglappe format

Now FASTA header in format pdbCode+pdbChainCode (no underscore) to be consistent with what we do elsewhere
Fixed the help text.

Fixed the fasta header regex to take only first token of header as sequence name (same behaviour as in Alignment class)

RIGraph:
-getCommonEdgesCount added

changed type definitions (Class<?> and Iterator<?> instead of Class and Iterator)

removed import which caused a warning

merged in some changes (now writing similarity matrix in blast utils)

fixed one null pointer bug and some spelling mistakes

Added some missing packages to compilation

Added code to run psipred.
Fixed a few minor bugs.

New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class

write_graph_to_motiffile:
-node serials are assigned now only to non-orphan nodes

fixed bug in writing to gdl file (gravity 1 -> 1.0)

changed some parameters for writing GDL files

added method calculateSequenceIndependentMatrix()

added BlastUtils.writeClusterGraph(String[] templateIds, outFile)

New methods to get the template ids and write them to file

RIGraph:
-bugs in write_graph_to_db methods concerning the node_id field have been fixed.

Made printing hits with graphical overview the default using print() method. Print() takes no parameters, but BlastHitList.setQueryLength() has to be called once to set the length of the query. Introduced new printSome() function to output only the first n hits.

createGraphDb:
-the node_id in the single_model_node table changed to AUTO_INCREMENT

doClassifySingleModels:
-the interSS for CR added

RIGraph:
-write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT
-write_graph_to_motiffile method added

added class Sequence, added ascii-art output of blast hits to BlastHitList

Added a main method for testing

New package sequence. Initial commit of classes to run blast and parse its output.

RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.

DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db.

doClassifySingleModels.sh has been added. You can create your own table with ids for the single models wherever you want.

createGraphDs.sh: mode to drop tables has been added.

reconstruct:
-rmsd to mirrored pdb has been added in the report file

Pdb:
-comment for outputing missing atoms added

PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added

Introduced another check in runMinimize: now we check for CHKXYZ warnings, that happened when the xyz file is somehow not well formatted. In some cases that leads to strange output in minimize.

Fixed script: was exiting after computing native energy!

New feature in TinkerRunner: now it can run "analyze" and "minimize" programs from the tinker package
Fixed some bugs and improved TinkerRunner: 
- flushing instead of closing the log PrintWriter when throwing TinkerError exception. Before it would close and nothing more would get logged after the first error.
- now writing command line to log
- now flusing at the end of each runXXX() method
New script computeEnergies for calculating energies of a set of decoys using tinker.

Fixed bug: the check for contact type validity was not correctly done

Added comments and better javadoc for the get_graph methods

Change command line parameters: eliminated -c and -C. Now pdb codes and chain codes are read together as a xxxxA string that we then split to get pdb/chain codes. The list of templates is now read from file.

Correction in javadoc

Now takes targetDb also from command line. Some clean up

Minor fix: was printing headers in non-benchmark mode

New feature: now can specify more than 1 ct/cutoff. Reconstruction will be done with all of them
Fixed bug with seqFile variable. Was being used for totally different files.
Wrapped muscle call in separate method runMuscle
Changed output style: less verbose and much cleaner (table with statistics)

Better comments, better handling of files, now always using the File object

Added new convenience method printSummary

RIGEnsemble doesn't extend ArrayList anymore, now the ensemble ArrayList is a member, so we now must use the RIGEnsemble interface exclusively

Added reconstruction option (not tested). Improved help text

Initial commit of averageGraph script.

Fixed bug: was printing the value of accuracy for the coverage field.

Changed dumpseq: now complies with FASTA format (80 characters per line) and tag is now pdbCode+pdbChainCode (with no underscore)

New method writeToPaulFile

Added mirror() method in Pdb class
Added getComplement() method in RIGraph class

Changed version in Manifest to 0.9.3

Now throwing exception in checkLengths().
Now fast checking of FASTA/PIR format (we check if first non-empty line starts with ">")

Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db

changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility

deleted testGraphAverager from aglappe/default, now in project CaspConsensusContactPrediction

Fixed bug: write_graph_to_file now writes blank instead of "null" when pdbCode, pdbChainCode or chainCode are null.

Added constant NO_SEQ_SEP_VAL

New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble

Updated version to 1.0-rc1

Now forcing i<j in CASP RR files (as specified by the CASP RR format)

Using Ca/Cg for testing as Ca/Cb is now allowed

Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.

Fixed mega-nasty bug: after introducing the PRMType enum, there was still one instance of the "type" variable being compared to a String in getCorrectedPdbAtomName method

some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)

New option in reconstruct: -f force constant. New constructor in TinkerRunner that takes the force constant, previous constructor will work as before with the default constant.

Fixed another bug in GraphAverager. Was still not working correctly: was putting edges twice in the final graph. 
Also now handling correctly graph averaging for directed or undirected graphs.

Fixed GraphAverager: wasn't working since we introduced JUNG. 
Also added some better output in checkSequences() when sequence don't match between alignment/graphs. Now we take the 2 sequences calculate a pairwise alignment (using jaligner) and output it. This is useful for picking up unobserves and similars.

Added option to output to standard output

Now compiling also scripts in default package

New constructor to read from simple graph files, i.e. list of contacts without any headers

Fixed bug: addEdgeIJ was not checking for presence of contacts

Added convenience methods: containsVertexI, addEdgeIJ

New methods getFisrt/Last residue serial

Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1

Fixed bug in compare(), was not checking correctly for sequence matching

updated version in Manifest to 0.9.2

new package ppi with classes for protein interaction networks

Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()

Added new package vecmath with classes Tuple3d, Point3d, Vector3d, Point3i to replace javax.vecmath while maintaining the same interface. The idea is that our package can be used by simply changing the import statement to remove the dependency on java3d.

Minor change of some error message

Fixed bug! actually it was not an abbot bug but our own, now calling AAinfo.class correctly (instead of System.getRunTime()....). With this abbot runs fine without any dirty fixes

Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.

updated classpath in makefile, changed permissions to execute by all

checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code 

Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this. 
NOTE: graph averaging hasn't been tested after the change

Removed PairwiseAlignmentGraphConverter, not needed anymore by CMView + was very buggy
Improved some comments/java docs

Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors

Latest scop and csa versions updated.

Fixing the fixed bug!
-if graph read is chain graph, then fullLength is set to the maximum observed residue serial
-else if graph is scop graph, then fullLength is set to the number of observed residues
NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.

Added getCommanSeparatedResSerials to RIGCommonNbhood

Added -f command line parameter

added some comments

Fixed bug in DSSP secondary structure assignment, first element was starting at index 0

changed version to 0.9.1

New method to convert secondary structure

Now converting also secondary structure in pairwise alignment graph conversion

Fixed three compiler warnings for unused imports (DbRIGraph, Pdb) and an untyped iterator (CatalSiteSet)

createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned

!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added

!!!!AIGraph:
-getResidueSerial method added

RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field

DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.

testDbRIGraph added:
It reads one graph from a source db based either 
-on pdbcode, chaincode and graph properties or 
-on scop id and graph properties or 
-on a graph id 
and it writes the graph to a destination db.

Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence

CatalSiteSet:
- removeCatalSiteRes(int resser) method added

CatalyticSite:
-remRes(int resser) method added

Scop:
-remove(ScopRegion e) method added

genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.

EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning

Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same

New functionality: now we can get sequences and reset tags based on the order the sequences appear on the file.

Got rid of check for equality of tags

Now also copying the CASP RR identifier fields in RIGraph.copy() and in PairwiseAlignmentGraphConverter.converGraph().

Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF

Rescued the make-aglappe.sh script from the old trunk

added main function and loading from Multi-model PDB files

Changed version number to 0.9

Copied the aglappe-jung branch into trunk.

Deleting everything in trunk to later replace with JUNG branch

Updated version to 0.8.7 in Manifest

don't touch br!!!

MAJOR CHANGES:
- merge the changes from the jung-branch: *Pdb loading scheme together with new methods getChains(), getModels()
- different exceptions

moved GraphAverager and testGraphAverager to repository CaspConsensusContactPrediction

Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()

Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance

Updated version in Manifest for tagging

-expBB is treated correctly now as int field in db in DBGraph and Graph classes
-null secondary structure case fixed in write_graph_to_db in Graph class

Initial commit: script to make aglappe project into one compiled jar

DbGraph-fix bug

Fixed bug in Graph constructor from sadp's ContactMap

abstract class implementing the Runnable interface

- changed the identation mode
- added some comments

Minor changes. Got rid of some warnings

createGraphDb.sh
-pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code
-index for pdb_residue_info table added

Changes in Pdb
-checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores

-writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file.
-another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false
-dump2pdbfile has also been changed in similar way
-runDssp and runNaccess now call the above methods with true pdbCompatible

Changes in genDbGraph
-1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ...
-DSSP is run with 3state

minor changes

minor change

createGraphDb.sh added

minor change

contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Reverting to last revision, changes made in 405 were wrong

Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet

Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!

OXT is taken into account now also for BB contact type

Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!

Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!

-pdb_seq_num is used instead of auth_seq_num in get_ressers_mappings. Now resser2pdbresser contains all residues even the unobserved ones. This has been changed in PdbasePdb and CiffilePdb classes.

-pdb_strand_id not needed in the query in read_seq in PdbasePdb class. Asym_id and pdb_strand_id have 1-1 mapping in case sensitive mode.

-comments have been added about the entity_id-asym_id-pdb_strand_id 1-1-1 mapping and some filters in queries that are no longer necessary.

added class PairwiseSequenceAlignment

Minor changes

Pdb code forced to lowercase in CiffilePdb

Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)

Initial commit. Provisional script to use the genDbGraph program when iterating through loads of structures, because of the "memory leak" problem is not possible to use directly genDbGraph to iterate over many structures (~1000)

New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)

Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker

new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)

started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)

Not creating anymore the score table

implemented tinker reconstruction of consensus graphs created with GraphAverager

New method setSequence

deleted the print part in the checkCSA method in pdb class

MODIFICATIONS
-------------

class SADP:
- added exception handling stuff for exceptions thrown by class Alignment

NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError

hasCSA and getCSA methods added in Pdb.java

inSameSheet, isOther and getSheetSerial methods added in SecStrucElement

Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred

a generic pair class

added a new version of getDiffDistMap(...) that take a sequence alignment as an input to allow for residue mappings between two pdb-models of different size

redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

finally implemented the setCutoff method ;)

fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)

added method setCutoff() and some javadocs

Cleaned up. More command line parameters

Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters

Fixed (yet again) the report output, now also outputting size (number of residues) of protein

Class ContactMap:
- Exception ContactMapConstructionError is thrown if the construction of a contact map from a Graph object fails.
- changed method to determine the number of nodes of a graph object.
- changed method to iterate through the set of edges of the graph (though the previous version seemed to be much more efficient ...)

Class SADP:
- added some new members controlling to input order of the contact maps (preservedInputOrder)
- the progress status of the run() method is send to a Retriever object
- added getters and setter for all data member.
- implemented methods to compute the sequence alignment and the node matching
- a couple of changes in method main

to be thrown if the construction of a contact map from a proteinstructure.Graph instance fails

This package provides a set of very basic abstract classes serving as interfaces to very basic tasks such as:

1. condition checkings (class Checker),
2. data retrieval (class Retriever) and 
3. pure workers that perform any kind of actions that do not depend on any kind of input data (class Doer).

Each of these classes is a subclass of class Action which only purpose is to store the object affected by the subclasses action method.

Now parsing tinker's error function value, changed report file format (again!!)

Changed name of native output pdb file

Now throwing all exceptions

New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object

Method writeUndirUnweightGraphToNetworkFiles added in Graph class

renamed precision to accuracy (in accordance with Casp)

Now weights are kept in the Edge objects rather than separately in a member variable in Graph

Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files

Now can do multiple contact types/cutoffs per pdb structure

Now closing db connection. Better help string.

Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)

Fixed bug: wasn't tokenising well when first field in line was quoted

FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor

Fixed bug: was outputing an empty column before the 'total' column

Changed constructor with all parameters to protected, now shouldn't be used at all outside of package

Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.

added some test programs to default package

Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions

Now writing also original pdb file
Fixed output of rmsd: now only few decimal figures output

Now tinker.log has also baseName in file name

Writing report to file instead of standard output
Catching unknown errors in runDistgeom (all other non-zero exit values)

Doing more input error checks
In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used

Fixed documentation

cathing InterruptedException from TinkerRunner

fixed bug when running distgeom, now waiting for process to exit before checking exit status

added error handling for killed tinker process with error code 139 (presumably out of memory)

Now capturing exit status 137 (2 instances of tinker running in same machine)
Now outputting progress per model

Fixed the output

Now much faster thanks to hashing on pairs (separate script create the hash tables)

Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason!
Throwing less exceptions in ConstraintsMaker

Added two new constructors for Graph (sequence only and no parameters), changed interface of GraphAverager (pass target sequence instead of target graph), extracted constant DEFAULT_WEIGHT in Edge.

extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph

Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"

New class NodesAndEdges (simple graph class), some added javadocs

Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring

added constructor for trivial alignment, renamed getSequence to getAlignedSequence

Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference

added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)

Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs

First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo

fixed missing references to constants in class AA

Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly

added parsing of residue selection strings

2 new methods: getAllAtomSerials, getAtomCoord

Moved tinker stuff to its own package

Initial commit of TinkerRunner and exception class to go with it TinkerError

added test program for difference distance maps, updated Manifest to v0.8.5

added calculation of difference distance map

added constructors for loading from online pdb

added some javadoc comments

Fixed some comments

initial version of sadp

Now parsing each element in different methods (re-opening the file). Parsing first pdbx_poly_seq_scheme so we get the chainCode that we can use for reading the rest
Now taking care of cases where struct_sheet_range is not a loop element
In tokeniseFields now also unquoting double-quoted strings
Tested on a set of 12000 entries

Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception

short form to compress nbstrings = condense multiple occurence of a symbol in the nbhstring to 1. Still a bitz buggy. sometimes 2 symbols are left in ? 

Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case

Bug with '?' in auth_seq_num was not really fixed. Now should be fine: behaviour is the same as PdbasePdb

Fixed bug: needed to read alt locs in advance in another scan of the file because the order of the elements in the cif file is not guaranteed. As read of atom_site needs of alt locs, we need to do first the parsing of atom_sites_alt

Fixed bugs:
- was reading HETATM lines as well as ATOM in atom_site
- auth_seq_num with '?' not taken now when populating the pdbresser2resser map (same behaviour as in PdbasePdb)
- now using chainCodeStr and auth_asym_id to identify chains in pdbx_poly_seq_scheme, struct_conf and struct_sheet_range. atom_site is not guaranteed to appear in file before all the others so we can't rely on having read a chainCode (asym_id) when parsing the other elements

Now taking indices for fields from parsed field names. Still only minimal testing

First implementation of mmCIF file parser. Tested minimally.

Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)

added writeResultsToFile()

changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells

changed constant for unknown pdb code from "Unknown" to XXXX

Faster version that writes to stdoutput, minor changes 

only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell

only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell 

Faster version that writes to stdoutput

Lame version that directly updates a table ...
have to change to stdoutput 

Cleaned up and debugged version (sc/bb were xchanged)   

2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other)

1st version for the pdb_reps25_graph_4_2

2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other) 

1st version scoring with pdb_reps_graph_4_2 and full nbhood string

1st version scoring with pdb_reps_graph_4_2 and full nbhood string

1st version scoring with pdb_reps_graph_4_2 and full nbhood string 

Better checks for sequence equality in compare

Now also filling chain_pdb_code in write_graph_to_db

Fixed bug in  compare, wasn't assigning new weights

Fixed a few bugs in reading of list file
Better output and error messages

Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)

Wasn't deep copying secondary structure when passing it to Graph

Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore

fixed little bug in NodeNbh

changed internal implementation of runDssp method (not using getFullLength anymore)

Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)

Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength

New script genGraph (generates graph to files)
Better error messages in both

Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure

Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph

Added new SecondaryStructure object to Pdb and Graph

final version 
incl. pessimistic tie-break

Initial commit of genDbGraph script

Fixed potential bug in regex for ATOM lines

Was still not fixed!, forgot to insert X for non standard aa

Fixed reading of SEQRES, was putting nulls for non-standard aas

Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings

completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes

Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size

fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)

Added getNumAtoms

PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')

Also writing graph to file

Initial commit. Script to benchmark the graph generation algorithm 

Made constructor public

added application to count grid density, suppressed warning for secondary structure reassignment

New methods containsContact and resetContacts

Added method hasTag

Made regex a constant and added | and \\-

Doing now everythin with maps (using seqTags) rather than arrays. Cleaned up, refactored, using more consistent naming

Added reverse map (from sequences serials to alignment serials) and did a bit of refactoring

Initial commit of Alignmnent, a class representing a multiple sequence alignment

Added correction by matrix size (yields avgdeltaRank)
plus correction jcnsize-1 for direct nbs 
and pessimistic tie-break 

Got rid of doneRes ArrayList in getRanks, was redundant

Now dealing correctly with ties.
Implemented getResiduesSortedByRank
Changed dist to be a TreeMap

Fixed bug in delEdge. Wasn't taking care of if contact was given as i>j in undirected case. Also recount of contacts and set of modified to true was wrong

Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i

Optimised slightly the compareTo method in Edge

Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them

Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case

Implemented rmsd calculation (based on Jama matrix package)
rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)

Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge

Added method getCopy

Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes

production - stable

added class NodeSet

Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases

Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)

single residue target Evaluation in target* tables 
added verbosity level VL to shrink output 

First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct

Only cosmetic changes to polish the output 

Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster

Added cross contacts to isValidCT

New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval

minor bugfix in reportResults( cnsize*deltarank) call

Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)

now casting pdb codes to lower and pdb chain codes to upper in all constructors

Fixed bug: ATOM lines printing was locale dependant, thus was printing ',' for decimal separators in some locales

some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead

debugged version of the iteration/validation of nbhoodstrings 
with added temp_table hashing for speedup (factor ca. 10x) 
needs additional (empty) database <nbhashtables> for storage
 

Buggy version : 2nd to n2th row have same values 
as the first row - ? temp_nbhood stays the same?  

Fixed bug in regex introduced in last revision