More improvements and another exclude list

Improved the symmetry redundancy elimination test and added exclude list for a special case

A couple of fixes to the new test 

New test for interface finder with/without redundancy elimination

Implemented some more symmetry redundancy elimination: now also removing redundancy in some of the 3,4,6-fold axes. We still need a more general rule, but this is better than nothing

Implemented some more symmetry redundancy elimination: now also removing redundancy in 2-fold axes

Implemented some basic symmetry redundancy elimination in interfaces search. Moved interfaces-search to a separate class.
New pymol output file in enumerateInterfaces with all interfaces in a single session

Fixed bug: was not setting the transl member of ChainInterface

Improved pymol interface coloring: no showing sticks for whole interface but different colors only for core residues

Fixed bug: was crashing with some NMR entries containing cell constants in cif file but with a "?" value (e.g. 1fmm)

Now producing space group algebraic strings with fractions

Adding flag to use uniparc or not

Now supporting both uniprot and uniparc entries in HomologList

New methods for filtering by domain of life

Now UniprotHomologList contains a full list and a filtered list, making it more flexible

Now catching OutOfMemory errors and continuing in redundancy removal procedure

New method to produce statistics of the sequence entropies variability

Fixed minor issue: now specifying what we print in tabular info

Switching off surface rendering

Fixed bug: slight miscalculation in query coverage (by one unit per hsp), would have affected very short entries

Fixed minor bug: now will re-blast only if maxNumSeqs above 500 and more hits requested

New feature: now can specify a subinterval in UniprotHomologList

New method for getting sequence with MSEs as METs

Fixed issue with uniparc and uniprot isoform ids

New method

Modified the uniref regex to also capture uniprot isoforms identifiers

Improved the blast cache checking

Now can pass option -v to blast (max number of hits reported)

Fixed logging and error handling of tcoffee: now it will really log errors to log file, temp files won't be deleted when exit!=0, command line is logged

Fixed minor issue: wasn't logging an error through logger

More logging

Now blasting against uniref also supported in UniprotHomologList

Now explicitely specifying number of threads in TcoffeeRunner

Fixed bug CRK-29: wasn't calculating interfaces for electron crystallography or neutron diffraction entries

Now we consider pisa gray predictions as well

Minor fix

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

New feature: pisa assembly parsing

Fixed bug: isSecondProtein() was not calling the right molecule

Introduced alternative parsing mode for PDB files: if no SEQRES present now two modes of parsing possible, one where the sequence is padded with Xs based on numbering and one where sequence is taken as is in ATOM lines whatever the numbering

Fixed bug: interface calculation for NMR structures was not done correctly. NMR structures do have a dummy CRYST1 record, so we have to force avoid using it when exp method is not X-RAY.

Fixed minor space group issue: some very weird PDB entries (racemic mixtures) are in space group P -1, unusually PDB use for it the non-standard name P 1-

A few more atom types

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

Introduced some more experimental code for enumeration of assemblies. BEWARE many things are UNFINISHED, namely in InterfaceGraph class the code to find induced and symmetry related interfaces is just a draft. There are many fundamental issues not solved yet. Be careful especially with implementations of equals and hashCode methods in InterfaceGraph, SubunitId, InterfaceGraphEdge etc. They alter "quietly" the behaviour of everything.

Removing some fields to do with zooming and refactoring

Fixed bug: was not getting correctly the chain if it happened to appear only as the second member of the interface

New method for getting URL of uniprot entry

Some improvements to PymolRunner, including reading color mappings from properties file

New method to find all residues in surface that belong to no interface

New methods for transforming vectors to orthonormal or to crystal basis

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

Now really fixed the bug with DNA/RNA ASA calculations (there were a few other issues with atom nomenclature)

Fixed bug: was nullpointing when calculating ASA of DNA/RNA. Atom codes have a '*' in the naccess vdw.radii file, now converting them to proper PDB format

New method to get the chain2repchain map

Adapted to changes in PymolRunner

Some more modified aminoacids

Tidied up PymolRunner and made a bit faster by merging png and pse/pml creation for interfaces

Committing test case file that was missing since a few revisions

More features for PymolRunner to display fancy pymol interface representations

Got rid of -p option when executing pymol

Now using grey for symmetry related partners in interface thumbnails 

Methods for asa and bsa of rim/core

Another peptide-linked HET residue

New method getBSA

Fixed bug in PDB file parsing: wasn't parsing correctly PDB files with no TER records and non-poly HETATMs. They were both merged together into one chain.

Removing duplicate entry

Another removed entry, this time  a mismatch of titles PDB vs CIF

Removed another strange entry (after july 2011 remediation) from test list

Removed a strange entry (after july 2011 remediation) from test list

Converted table names to capitals and extracted constants. Original pdbase has capitals, it worked at mpi mg because we were using mysql in case insensitive mode.

Fixed bugs in DaliRunner
- it wouldn't run from cmview when the two chains had same pdb code and pdb chain code
- it wouldn't work with newer versions of DaliLite as apparently the output file names and formats changed 

New element

Changed behaviour of getId() in ChainInterfaceList, now uses the same ids as the interfaces, i.e. starts counting from 1 and not from 0.
New graph classes for storing interface topology

Fixed bug: title was parsing line until char 80, but sometimes (non PDB deposited) files are trimmed of spaces

Introduced calculation of relative ASAs. 
A few new methods to calculate rim/core of interfaces using alternative definitions.

Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation

Fixed bug in pdb file parsing. Wasn't checking properly for atom serials in ascending order (was checking across chains and needs to be within chains only)

Two more atom types

Another atom type

Minor fix: to avoid nullpointers when calculating radii and atom unknown

Another atom type

New atom type

Fixed bug: was not checking that atom type actually exists

Adding element

Improvements mainly to ChainInterface and associated classes: now can detect a lot more specific interactions in interface: disulfides, hydrogen bonds, any other kind of close interactions

Some improvements and fixes to enumerateInterfaces

Fixed bug: was nullpointing when trying to get radius of unknown atom in het aminoacid

Better doc

Minor fix: now writing the serialized file only once per interface list

New option to output interfaces serialized file

Now outputs core sizes as well

Fixed bug: was not using full path of the given pymol executable

Fixed bug: was not setting the actually used bsaToAsa cutoff when zooming

Fixed minor bug: was outputting duplicate TER records when writing ChainInterface PDB files.

New methods and script to calculate mass of a protein/chain.

Some new methods for disulfide detection and other minor things

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

Introduced some more checks in PDB file parser, now should be even more robust with badly formatted files.
Added some more atom types.

Fixed a few bugs:
- PdbChain: copy() was missing some important fields, PDB file writing method was printing SEQRES for nonpoly chains too
- naccess BSA calculation had a few problems
- PdbAsymUnit: a few important issues with PDB/CIF chain codes

Fixed minor bug: seq identical group string was wrong when only one member in group.

Minor fix to writing of pdb files from ChainInterface

Fixed some issues with writing of pdb files and wrote a test for write/read pdb files.

Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)

Minor fix: was not printing het residues in ChainInterface print methods.

Now using hetatoms for testing interfaces against pisa

New method to produce strings with chain codes of sequence identical chains

Now can calculate interfaces (only of AU) in cases when no crystal info is available

Removed obsolete classes to analyse histone. Moved some useful methods for inertia moment calculation to GeometryTools

MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.

Now throwing separate exceptions as before

Fixed bug: pymol was hanging sometimes when running the script through stdin piping. Now using the -d mode it's more stable.

Added many atoms + corrected masses. Now the mass is the standard mass rather than before (wrongly) the mass of the lightest isotope.

Unzip method

adding package-info for owl.mutanom

Changed constant name after change in kraken api

System.out.println(cmdline) is commented out.

tmp files will be written to the static disk.

Documented the -t option 

Improved javadocs

Going back to old version of PolyposeRunner because new version was way too slow

Fixed another problem with persistent temp files

More debug output

Fix: Now deleting polypose temp files which were polluting /tmp directory

Another test

Fixed bug in finding unique and rep chains.

Adding Serializable interface to some classes

Now PdbChain also implements Iterable

MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.

Updated some JavaDocs

Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')

New class BoundingBox for bounds. Added bounds caching also to PdbAsymUnit. Fixed some issues with it in Pdb. Everything looks a lot cleaner thanks to new class.

Fixed bug: wasn't resetting bounds whenever the coordinates were transformed.

Fixed bug: now caching bounds properly.

Minor fix: now forcing lower case in pdb code so that we can grab the cif file if input is upper case.

New option -d

More optimisation on geometric hashing algorithm.

Some more optimisation, not sure if this really improves run time.

More optimisation and simplification of geometric hashing algorithm. Runs very slightly faster.

Fixed some conflicts when running multiple instances of this on the same machine

Another (very minor) optimisation in geometric hashing algorithm

Optimised and simplified the geometric hashing algorithm implementation, now runs slightly faster.

unnecessary codes removed

add -O to dump observed sequences

moving info about reduced alphabets from main() to printReducedAlphabetInfo()

adding some missing documentation

moving project CCCP to this repository

Now detecting type of sequence: protein/nucleotide

Now the colors of chains of pymol generated images are consistent with the letter codes (given a chain letter code the color will always be the same for it for all images generated)

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

Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta

new script to convert clustalW to fasta format

Fixed bug. Pymol was blocking

Changing file names of contact map test files, windows didn't like the ':' in the file names

New runner for pymol

Now throwing InterruptedException. Refactor BlastErro to BlastException

Refactoring xxxError to xxxException

Important change: for maximum compatibility in no-SEQRES case we are now back to using the existing numbering if there's nothing wrong with it (no negatives or ins codes). If there's something wrong with numbering then we set the SEQRES to be the observed sequence and renumber. 
Now behaviour is as it was before revision 1329. With the difference that a lot more PDB files can be read. 

Another fix to PdbfilePdb parser. Now it is more robust with bad formatting, tested on a whole tar ball of CASP predictions. Added the CASP predictions test set to tests.

Another improvement to PdbfilePdb parsing: now we can also detect some ambiguous cases in alignments by checking the contiguity of the 3D chain. This fixes 2 cases from our test data set: 1dki and 2ofz. Now only 2 warnings for the whole dataset (both because of ambiguous assignment in HIS tags, safe to ignore. Could even be that CIF got them wrong)

Now the re-numbering of residue serials in PDB files has been improved. Instead of aligning the sequences whenever the serials don't match SEQRES, we first try to see if there is a shift in the serials with respect to SEQRES (happens in many cases). Only if we can't find a shift that fully matches SEQRES we proceed to re-aligning. We also treat properly now the ins codes. Mapping is as close to CIF as possible. The parsers test passes for the whole cullpdb20. For some entries like 2ofz the mapping does not coincide 100% with CIF as there are ambiguities in the alignment.

Important change: now the PDB file reader will try to read and fix the numbering of PDB files. Whenever the alignment is wrong it will realign and renumber using the jaligner package. The result of reading original PDB files now will be the same as that of reading CIF files, including proper mapping of classical PDB numbers to SEQRES residue serials (as in CIF). 
There is one change of behaviour in comparison to before: when no SEQRES present the sequence is taken to be that of ATOM lines instead of padding it with Xs.
Still in this version the re-alignment is not perfect as there are some times when ambiguities occur and they are not solved (e.g. in 2nwr where alignment in an unobserved loop can be at two possible places for a GLY). That is anyway a rather minor problem (coordinates are still fine, just the chain is not ordered correctly at 1 or 2 points) and rare (~1% of files)

Removed two exception classes that were only used privately, didn't make much sense. Now using PdbLoadException

Some more atoms seen in pdb files

Renamed xxxxError classes to xxxxException as they should be.

Now pdb file type guessing will guess correctly also with files starting with CRYST1 or SEQRES.
PdbAsymUnit now works with pdb files like those 2 and also with ATOM line only ones

A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before

New method hasChain(String): boolean

New enum for nucleotides

Added atom types that appear in HET residues and details to docs

Removed the serialize/deserialize methods (now in Goodies)

Methods to serialize/deserialize from file

Catching if the server returns non-requested records and throwin IOException for it.

Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.

Removed a now unused method

Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.

Now taking paths from owl_test_paths.dat file

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

Now can do all chains of a given pdb codes instead of only the first one

Fixed bug: was not checking whether the uniprot japi was actually returning all requested records for ids given when using getMultipleEntries. Now checking, logging it and removing the not-found ids from the homolog list.

Fixed important bug that broke the reconstruction programs. Tinker output files don't contain occupancy/bfactors. Thus we have to make their parsing optional. Added a test case for this.

Methods to serialize/deserialize from file ChainInterface

Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.

Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.

Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).

adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException

overwriting default contactTypes.dat with the one needed for CMView release versions (only contains standard contact types). The old version with all esoteric contact types is renamed to contactTypes.all.dat

Better docs

Now storing the query coverage cutoff.

New methods to get sequence identical chains

Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.

Now using Rsym whenever Rmerge and Rsym disagree

Fixed bug: now copying the new fields (exp method, resolution, R free, Rsym) in the copy method

Now parsing experimental method, resolution, R free and R sym.

Control database access! for CGAP

Control database access! for CGAP

add setParametersDB

calling readStructureOrNull was exiting rather than returning null

Now throwing MatchNotFound exception instead of catching it.

Overrides removed

New getName method.

Fixed formatting of the exception message

Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.

Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.

Now asa calc done with our own implementation (was still using naccess)

Fixed the rim/core zooming which wasn't working after redesign of things

Forgot to fix 2 problems in last commit.

More methods to report on interfaces clashes. Extracted clash distance constant.

Fixed bug: was writing out PDB files of interfaces with mixed PDB/cif chain codes. Now they are always PDB chain codes. Got rid of ugly method setChainCode in Pdb

Fixed buf: EMBL DB fetch returns sequences now in upper case, we were not converting properly to lower case in one place, now should be fixed.

New method to get number of interfaces above a certain area

New method to check clashes

Fixed bug: was still not converting well algebraic transformations to matrix: was failing for transformations with terms like "X-Y+1/3"

Fixed bug in SpaceGroupTest. Now it works and test passes.
Introduced checking for clashes in interfaces. Added it to the PdbAsymUnitTest

Fixed some bugs with parsing symop.lib and conversion of transformations. Properly testing SpaceGroups and parsing now. Still one test (transpose equal inverse) does not work for trigonal and hexagonal groups.

Now possible to not retrieve any CDS data

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

Now keeping track of ASA calc method

Added printing of rim and core residues methods.

Some restructuring of code to improve the crk application

Fixed bug: some PDB files (like those output by phenix) don't write the Z number at the end of the CRYST1 record, thus not having enough trailing spaces, we have to take care of this.

Using the new UniprotVerMismatchException instead of IOException

New exception for mismatching uniprot versions

Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators.
Added a test for SpaceGroup to test for proper parsing of algebraic strings

Now reporting on percent burial too

Minor changes to the test.

Made conf file path a resource path so that it is readable from jar file too.

Some minor updates

Implemented some parallelisation in ASA calculation. It doesn't scale very well (could measure x2 speed-up with 4 CPUs in a Core2 Quad) but at least we have it, now this is starting to be better than NACCESS!

Some more complete tests.

Putting back number of sphere points parameter to Bosco's default, the other one was too inaccurate

Some optimisation of the asa code, run time improved substantially.

Now using our own ASA calculation instead of NACCESS for the interface areas calculation. We are slower than NACCESS but at least don't depend on it anymore, old NACCESS methods can still be used.

Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!

Some minor improvements: now populating ids of ChainInterfaces, now interface area is half to match pisa's. 
Fixed bug in getAllInterfaces tester, wasn't comparing properly in small values. 

does most of the job SparseMatrix did before

Finally ASA/BSA comparison to PISA test passes. Have to exclude one case where slight difference interface area values led to different sorting and so comparsion doesn't work. This will still be a problem whenever that happens (whenever different sorting of PISA vs ours)

some methods removed and added to a new class, other simplified

Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).

Fixed bug: the bsa values of residues of the different interfaces were being updated on the same references, we have to copy before creating ChainInterface objects in getAllInterfaces.
Implemented interface pdb file outputting in enumerateInterfaces
Still interfaces tests don't pass because of 2 problems: a) order of first/second molecule not necessarily same as PISA (and in case of same chain codes can't catch it with chain codes), b) in many cases there are many minor discrepancies, usually associated to a lot of small negative bsa values.

suppressing two warnings

sparse matrix exception

Fixed minor bug in test, was not comparing properly the interface count of pisa vs ours.

commit latest version

variable 2D csv-files loadable

Color scale class moved from gmbp to owl

New method to get PDB cross refs for a Uniprot entry

Renaming UniprotPdbRef to UniProtPdbRef to be consistent with UniProtConnection

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

Adding class PhosphoSiteConnection

Fixed bug: bsa values were wrongly calculated. 
Now sort of interfaces is always descending.
Some more testing for individual residues asa and bsa values. 
Still an issue: individual bsas are not matching pisa's even though total interface areas are fine.

New method for finding identical sequences (entities)

Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.

new methods added
-method, takes care of row and column index maps (refreshMatrix())
-methods, adding or removing entries, without refreshing index mapping
-norm methods(norm1(), norm2(), normInf()) as well as a special innerProduct() method

Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb

Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.

added methods

updated classes for evaluating our CASP predictions

please don't check in Mac specific constants

updating annotations to get rid of warnings

deleting two classes which were making problems

added some javadoc

Fixed bug: was null pointing in parsing NMR cif files because they don't have crystal parameter fields. Now skipping that properly. Added NMR test entry to test cases.

First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.

Committing a version that 1st) properly places the symoped generated units of the first unit cell in the first unit cell (and not elsewhere like before) 2nd) does not miss any interfaces because of just doing half of the neighbours (e.g. in 7odc it wouldn't work). Now no interfaces are missing but lots of duplicates are found. So not a fully working version yet.

Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side.
Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa.
Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct.
Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.

Faster BSA calculation by avoiding redundant runs of NACCESS.

Changed default cutoff to coincide with PISA, entry 1pmm was a good clue (one interface has a 1 atom contact with 6 cutoff). 
Now going to the negative side (instead of positive) when translating the unit cell to coincide with PISA operators.

First fully working implementation of interface enumeration!! WAn exact copy of PISA's interface enumeration! (only tested with very few examples so far)

First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point. 

Changes to select certain Secondary Structure Type for Traces extraction!

Fixed bug: was missing one operator in getTransformations

Scoring:KendallsTau-method added to  Statistics

Scoring:KendallsTau-method added to  Statistics

Moved getTransformations method to Pdb and PdbAsymUnit where it really belongs.

Now all crystal transformations work properly: doing the crystal to orthonormal basis conversion properly.

Implemented some methods to do translations properly along crystal axes.

renamed class benchmarkAll to createResultWebPages

suppress "method not used" warning

deleting KendallsTau class (even if it already deleted on the server)

removed some bad characters

added some debug output (commented out)

classes moved

Adding some javadoc

new class for scoring all casp7/casp8/casp9 server models in terms of GDT_TS and Acc/Cov of the contact map

classes moved

classes moved

Created a stub method for KendalsTau in owl.core.util.Statistics

Committing test class for AICGraph

Considerable clean up of Pdb. Now the algorithm for calculating atom contacts is all under new class Grid (also refactored Box to GridCell). Tests for graph calculations passed.

Fixed bug: now properly also including OXTs in inter-chain atom interaction graph calculation.

Implemented inter-chain contact calculation (using same hashing algorithm as in intra-chain).

New class PdbAsymUnit (which should be called Pdb, but we can't for obvious reasons). 
Fixed bug in Pdb.copy(), wasn't copying the new fields crystalCell and spaceGroup

Implementation of class for Check for Correctness of Casp server model files

max Cluster Path two possibilities (Mac Unix)

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

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)

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 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

Now getting also gene encoding organelle from uniprot api

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

Methods added to Save and Load settings of SphoxelMap_Traces_View.

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

Now parsing the symmetry operators.

Fixed bug: was nullpointing with empty cache files

Implemented caching of blast in UniprotHomologList

Our own copy file method! :-)

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

Implemented caching for EMBWSDBfetchConnection

Cluster-edge direction evaluated.

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

Implementation of class that performs clustering on the nbhStringNodes.

Some fixes to the help string

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

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

Minor doc fix

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

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

checking in some of Michael's example files

Contact Map for server prediction directory evaluation added

Class OptimalSingleEnv for scoring of different substrings.

little contact map example done

added a package for example scripts using the library

max number of traces

Improved the getRimAndCore method

Extract maximum number of traces!

Some new methods

renamed  conflicting ContactMap class.

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

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

Fixed bug with '-' embl cds identifiers.

Undoing some stuff commited by error in last commit

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

Now parsing the seq_num residue number.

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

PISA connection and xml interfaces description parser

Implemented profile counting and entropy calculation for alignment.

Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()

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

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

Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.

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

HandOverThetaPhiRanges

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

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

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

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

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

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

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

Fixed java doc

Load from zip-file!

add psi/phi constraints from secondary structure to tinker reconstructions

New example implementation of ResidueContactScoringFunction

Removed code left over from debugging.

Minor changes, couple of new methods.

Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph

Minor fix to java docs

Load precalc sphoxel data if possible.

removing @Override annotations which were causing compilation errors for me

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

SecondaryStructure now implements Iterable after refactoring of getIterator

JPredConnection now returns a SecondaryStructure object; some updated javadocs

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

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

Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.

New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)

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

New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.

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

revert. wasn't the best idea.

adding phi/psi constraints to edges

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

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

Extracted Scop parsing code to its own connection class.

Extracted the CSA parsing code to its own connection class.

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

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

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

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

Faster SQL queries

Fixed some docs and indentation

changes

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

FloatPairSet first commit

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

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

Classes for sphoxel and nbhstraces handling. csv handling

First version of class for sphoxel computation.

removing a warning in owl.embed.contactmaps.Demes

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

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

Fixed import (was a compile error)

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

resolving conflicts

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

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

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

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

refactoring: adapting test packages to match new package structure

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

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

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

starting refactoring: first creating packages owl and owl.core

latest version of gabriel (embed.contactmaps)

latest version of gabriel

Now DsspRunner is purely static (makes more sense)

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

Minor refactoring and comment fixes

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

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

Removed the executable property

new method AminoAcid.valuesInOrderOfHydrophobicity()

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

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

New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.

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

Adding new package owl.connections with connector classes to online databases and services. Starting with PhosphoSitePlusConnection for accessing a database of posttranslational modifications and PDomainsConnection for accessing a very useful webservice which calculates structural domains using a variety of methods including Scop, Cath, DomainParser, ProteinDomainParser and others.

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

adding some convenience methods to IntervalSet

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

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

Better error message for no tinker paths set up

Moving the CASP project into OWL as the casp package.

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

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

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

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

new class for sparse double matrices

some new classes

minor changes, that now fit into the renewed version

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

New executable class from my workspace.

Moved IntervalTest class to test.tools package

Moved Interval* and IntPair* classes to tools package

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

Removed some obsolete classes.

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

Commented out some unused variables to get rid of warnings

Refactoring of inconsistently named methods in RIGraph

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

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