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r153
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AA.java 135 (12 years ago) by duarte: 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
Contact.java 123 (12 years ago) by duarte: Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
ContactMap.java 143 (12 years ago) by duarte: 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
EdgeState.java 128 (12 years ago) by duarte: ContactMap and EdgeState classes moved here from CMPredict repository
Graph.java 152 (12 years ago) by duarte: 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
GraphIdNotFoundError.java 135 (12 years ago) by duarte: 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
MsdsdAcCodeNotFoundError.java 130 (12 years ago) by duarte: 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
MsdsdInconsistentResidueNumbersError.java 130 (12 years ago) by duarte: 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
MsdsdInfo.java 136 (12 years ago) by duarte: FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
Pdb.java 153 (12 years ago) by duarte: 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
PdbaseAcCodeNotFoundError.java 124 (12 years ago) by duarte: Added error handling for PdbaseInfo: 2 new exception classes
PdbaseInconsistencyError.java 124 (12 years ago) by duarte: Added error handling for PdbaseInfo: 2 new exception classes
PdbaseInfo.java 135 (12 years ago) by duarte: 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
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