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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
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