Fixed bug CRK-128: in a non-crystallographic entry with cofactors it was crashing at getCofactors because we weren't checking for non-crystallographic entry there. The crash was a "cannot invert matrix" error, happening because the cell parameters where 0,0,0. Funnily enough this would not happen in my local machine (OpenJDK java 1.6.0_27), but it did happen in merlin (OpenJDK java1.6.0_24)

Fixed bug: was null pointing on pdb files with a TER record positioned just before a HETATM record in the middle of a poly chain, now added more checks for duplicated PDB chain codes assignments which will catch that problem plus possibly others

Fixed 'I 1 2 1' issue: it was actually a bug rather than a "feature", we were parsing everything in symoplib but some space groups happened to have alternative names and 'I 1 2 1' is the alternative name of 'I 2" which we were allowing. Now parsing and storing in lookup map both names.
Fixed also a bug by which the last space group in file was not added to the lookup-by-name map

Several fixes:
- bug fix: was always throwing exception in pdb parser for no secondary structure when not protein
- new reasonable-crystal-cell check when loading PDB entries
- safer pdb file parsing: now all substrings should be checked. For instance now swiss-model output files are parseable

Another small fix related to last commit

Fixed issue: now setting unknown atom type whenever we can't guess the element. If we read from PDB file and there is an unguesseable atom that we then have to write out again the code would fail because in writeAtoms we assume we have atom types for everything.

Added AtomTypes till atomic number 110

Bugfix: Check for nulls while reading QParams.

BugFix: A check for protein chain introduced before initializing secondary structure. This avoids problems with pdb files not containing protein chains and still have HELIX information!!

BugFix: While getting cofactors, do not transform an asymmetric unit if crystal cell is not present! New check introduced!

Minor issue fix: now heavy water (deuterated water) treated as water, i.e. not read. Also extracted the constants to HetResidue

Fixed bug in ASA calculation: was taking in finding neighbours procedure the default vdw element radius rather thatn the one set in setRadius: NOTE this changes slightly the area values we are getting.
Fixed issue in parsing of atoms when no atom type can be guessed: now whenever we can't guess we write a warning, also setRadius will use default radius if element not known (instead of null pointing)

BugFix: Included the possibility of cell parameters being non double values.

Included more possible first lines to guess a PDB file, plus added a better error message to hint that one should add a HEADER record

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

Fixed bug: was null pointing in parsing 2bi6 mmCIF file. It had a multi-line quoted value in a _struct_conf non-loop element. We weren't handling that correctly. 
Also added a new peptide-linked 3-letter code het residue

Fix bug with resolution and rfree parsing: wasn't catching non-question-mark strings

Fixed bug: very strange PDB entries can have no atoms observed in a chain at all (e.g. 1oax) or all atoms of a chain in one alt location only (e.g. 3nji). We throw now exceptions for them as in my opinion they don't follow the data-modelling standards properly.

Complete list of of atoms, their masses, and their vdW radii's.

Bug fix: Checks if the method is Crystallographic before getting the unit cell. The can be errors in mmCIF files, where a cell is defined but the space group is not defined for non-crystallographic methods. Hence the check needed!

Bug fixes for 
- Rsym/RMerge not a number, Previously was handling occurrence of ? but not other characters. 
- Check for missing _pdbx_poly_seq_scheme lines in mmCIF file

New method to write PDB files with pdbChainCodes

Fixed bug: some cif files use double quotes (e.g. 1hhu) and we were not parsing correctly the space group for them

Adding new elements found after a sample of 10000 random pdb entries

Another element

New element added

Now also checking the translation component of the SCALE matrix, and if different from (0,0,0) throwing an exception. Some entries still have a shifted origin (e.g. 1hga, 1hgb, 1hgc). Let's hope they fix this in next remediation.

New feature: now we can take cofactors into account for calculation of ASA in interfaces

Now using a minimum threshold value for considering a residue at surface (instead of 0 before)

Made new CrystalTransform class serializable

Important fix to interface calculation: finally total symmetry redundancy elimination is working!
- fixed a bug present since rev 1573: translation vectors of transforms were not stored properly and thus wasn't comparing the right operators
- extracted TransformIdTransform private class to new class CrystalTransform. Rationalise some of the code thanks to that (still more to be done)
- better debug output in interface calculation to show duplicates info

Even less symmetry redundancy elimination, due to strange counter-example found: 2gqv

Fixes to interface calculation:
- removed redundant overlap check on AUs
- introduced overlap checks at chain level, avoids the grid creation for AICgraph
- better debug output: now we show "." for non-overlap chains, "o" for empty AICgraph calculation, "x" for non-empty AICgraph calculation

Another important optimisation: now the ASA calculation for the list of interfaces is a lot more efficient by only calculating uncomplexed ASAs once per chain code per transform id. 
Not supporting anymore calculation of interfaces areas with NACCESS

Got rid of the ad-hoc fix to translate the sym related objects to "first cell". Now interface calculation works without it since it is done exhaustively and correctly.

Important change in interface calculation:
- another massive gain in run-time and memory usage: we first use the bounding boxes translations to see if it is worth translating the whole unit cells
- thanks to that we now go to 2nd neighbors! (still performance is better than before with only 1st neighbors!). With that we fixed the long-standing bug by which we miss interfaces beyond the 1st neighbor
- included a few examples of 2nd neighbor problem in test
- re-done the symmetry redundancy elimination, it is there but it has a very little effect on overall performance. Now we only don't use an operator when we are very sure its partner was in the right place. In effect we could get rid of it because it wouldn't really affect the performance, we rather keep it as it is good to remember that there is a lot of symmetry redundancy

Another important optimisation: now bounds are translated and not recalculated from scratch after translation. Fixed a bug in bounds copying (wasn't copying the boundsProtOnly boolean)

A small but important fix to make sure the transformations set in the PdbAsymUnit objects are independent from those taken from the SpaceGroup objects

Fixes related to last commit: now checked that cached bounds/centroid are properly reset and copied. They weren't copied at all before and not always reset

IMPORTANT changes and fixes in interface calculation:
- very important bug fix: BoundingBox was not always telling properly whether 2 boxes overlap. This not only fixes the important bug but also boosts the speed of interface calculation
- optimisation of PdbChain.getAICGraph not to return an empty graph whenever no overlap of boxes is found (instead of generating empty distance matrix and checking its emptiness): this alone gives the biggest performance boost to interface calculation, around 5x faster thanks to this alone
- fine optimisation of max/min calculation in BoundingBox
- made sure that bounds caching is done properly
- introduced the right solution for symmetry redundancy elimination: operators multiplication is the identity. Before we had an ad-hoc solution that wasn't comprehensive at all
- in any case the symmetry redundancy elimination is right now almost turned off because we introduced new conditions to re-check equivalent operators to fix cases like 2gsg, 3ka0, 1vzi, 1g3p and 1eaq, where some interfaces are missed due to an equivalent operator making the molecule fall in a cell where there's no contacts
All in all this totally changes the interface calculation: 1) by a massive boost in performance 2) by making it more correct, surely there were cases with missing interfaces, we were just lucky not to find them in testing

Fixed bug in PDB file parser: checking for TER records was done with a trailing space "TER ", that was fine for PDB deposited files but not for others (for instance phenix files). Because of that it was failing to parse properly some multi non-poly chains phenix files. Now removed the trailing space and problem seems to be gone. PDB parsers test passed

Fixed minor issue: phenix PDB files use lower case for double-letter atom symbols, now forcing the upper case

Bug fix: was null pointing when a Deuterium atom was present in a standard amino acid (not clear anyway whether that is standard PDB practice). Now checking for unknown atoms in standard amino acids when getting their radii. Will output error and continue with their standard vdw radius.

Now checking the SCALE1,2,3 PDB records when loading PDB data, in order to detect PDB entries that are not in the standard crystal frame (after remediation of 2011 only 148 non-virus entries are in nonstandard frame, marked with REMARK 285)

Adding another atom type

Fixed another small bug in cif parser: wasn't setting the sequence tags correctly

Fixed bug in cif parser: wasn't setting the parent PdbAsymUnit in the PdbChains

New method to calculate contact order

Fixed bug CRK-64: was crashing in interface calculation with space group P-1. Solve by not doing redundancy elimination for non-enantiomorphic space groups.

Better docs and clean up of core/rim calculation code

Added atom type

Now printing warnings if Hydrogens present when calculating interfaces

Fixed issue: was only considering axes in a, b, c. Now we properly check whether two operators are in same axis, by storing in a HashMap all operator ids per axis. Was affecting some exotic space groups like P 2 3.

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

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

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

New method for getting sequence with MSEs as METs

New method

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

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 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

Some more modified aminoacids

More features for PymolRunner to display fancy pymol interface representations

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.

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.

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

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.

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.

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

Improved javadocs

More debug output

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.

More optimisation on geometric hashing algorithm.

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

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

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

adding some missing documentation

moving project CCCP to this repository

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

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)

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.

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.

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

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

calling readStructureOrNull was exiting rather than returning null

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.

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

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

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 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.

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.

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. 

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.

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.

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 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. 

Fixed bug: was missing one operator in getTransformations

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.

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 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 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

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

HahpMap keytype changed to Pair instead of String

print function

PrintOut method ion RIGGeometry

Getter for Atoms-TreeMap.

Check for consistency in translation rotation framework.

Additional method for coordinate transversion.

New Residuescoringfunctionimplementation

Rotation and translation procedure transfered into extra class GmbpGeometry

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

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

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.

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

renamed  conflicting ContactMap class.

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

add psi/phi constraints from secondary structure to tinker reconstructions

New example implementation of ResidueContactScoringFunction

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

removing @Override annotations which were causing compilation errors for me

SecondaryStructure now implements Iterable after refactoring of getIterator

JPredConnection now returns a SecondaryStructure object; some updated javadocs

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

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.

revert. wasn't the best idea.

adding phi/psi constraints to edges

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.

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()

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.

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

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