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

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

2 new methods: getAllAtomSerials, getAtomCoord

added calculation of difference distance map

added some javadoc comments

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

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

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

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

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

Added new SecondaryStructure object to Pdb and Graph

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

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

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

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

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)

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

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

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

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

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

FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError

Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs

Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up

MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException

New isValidCT methods in AA
New method get_resser_from_atomser in Pdb

NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact

Moved ContactMap and EdgeState out of this repository. 
Extra functionality of ContactMap now in Graph:
- new member variables fullLength, obsLength, numContacts. New method getIntMatrix
- removed getCM method

Now passing also chaincode from Pdb object to Graph object in get_graph

Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality

NEW FUNCTIONALITY: Reading from pdb file given chain code or model serial fully implemented
Changed the chain that is dumped in dump2pdbfile directly to the Pdb.chain field i.e. internal chain identifier
Loads of new comments, including java doc for all constructors

Made some fields public: sequence, accode, chaincode, model

Made Pdb.acccode public

Changed default accode and chaincode to "Unknown" when reading from pdb file

FIXED BUG: wasn't setting the chain field when reading from msdsd

Made chain field in PDB class public

NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError

New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!

NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines

NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap

Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

Added error handling for PdbaseInfo: 2 new exception classes

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures