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