New functionality: added methods to get node/edge neighbours

made Graph.directed public

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

FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database

FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!

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

Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file

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

FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id
Bugs:
- nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes
- in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types
New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info

Made cutoff and ct public

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

NEW FEATURE: Read and write graphs from file fully implemented.

Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present
New method write_graph_to_file

FIXED BUG: last commit didn't fix bug correctly:
Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet()

Made public accode and chain fields in Graph

FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues

Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented)
In ContactMap constructor different handling when sequence is blank

Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)

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

FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes

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

Implemented basic reading contacts from file

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

2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless

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

ContactMap and EdgeState classes moved here from CMPredict repository

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

MYSQLUSER now taken from unix name with new getUserName method

Added error handling for PdbaseInfo: 2 new exception classes

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